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2ADY.cif
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2ADY.cif
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data_2ADY
#
_entry.id 2ADY
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 4.007
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
PDB 2ADY
NDB PD0694
RCSB RCSB033779
#
loop_
_database_PDB_rev.num
_database_PDB_rev.date
_database_PDB_rev.date_original
_database_PDB_rev.mod_type
_database_PDB_rev.replaces
_database_PDB_rev.status
1 2006-07-11 2005-07-21 0 2ADY ?
2 2009-02-24 ? 1 2ADY ?
#
_database_PDB_rev_record.rev_num 2
_database_PDB_rev_record.type VERSN
_database_PDB_rev_record.details ?
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.db_id
_pdbx_database_related.details
_pdbx_database_related.content_type
PDB 2AC0 'Tumor suppressor protein p53/DNA Complex (I)' unspecified
PDB 2AHI 'Tumor suppressor protein p53/DNA Complex (III)' unspecified
PDB 2ATA 'Tumor suppressor protein p53/DNA Complex (II)' unspecified
#
_pdbx_database_status.entry_id 2ADY
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site PDBJ
_pdbx_database_status.status_code REL
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.SG_entry ?
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Kitayner, M.' 1
'Rozenberg, H.' 2
'Kessler, N.' 3
'Rabinovich, D.' 4
'Shakked, Z.' 5
#
_citation.id primary
_citation.title 'Structural Basis of DNA Recognition by p53 Tetramers'
_citation.journal_abbrev Mol.Cell
_citation.journal_volume 22
_citation.page_first 741
_citation.page_last 753
_citation.year 2006
_citation.journal_id_ASTM MOCEFL
_citation.country US
_citation.journal_id_ISSN 1097-2765
_citation.journal_id_CSD 2168
_citation.book_publisher ?
_citation.pdbx_database_id_PubMed 16793544
_citation.pdbx_database_id_DOI 10.1016/j.molcel.2006.05.015
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
primary 'Kitayner, M.' 1
primary 'Rozenberg, H.' 2
primary 'Kessler, N.' 3
primary 'Rabinovich, D.' 4
primary 'Shaulov, L.' 5
primary 'Haran, T.E.' 6
primary 'Shakked, Z.' 7
#
_cell.length_a 91.997
_cell.length_b 67.903
_cell.length_c 74.989
_cell.angle_alpha 90.00
_cell.angle_beta 92.97
_cell.angle_gamma 90.00
_cell.entry_id 2ADY
_cell.pdbx_unique_axis ?
_cell.Z_PDB 8
_cell.length_a_esd ?
_cell.length_b_esd ?
_cell.length_c_esd ?
_cell.angle_alpha_esd ?
_cell.angle_beta_esd ?
_cell.angle_gamma_esd ?
#
_symmetry.space_group_name_H-M 'C 1 2 1'
_symmetry.entry_id 2ADY
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.Int_Tables_number ?
_symmetry.cell_setting ?
_symmetry.space_group_name_Hall ?
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.details
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.pdbx_ec
1 polymer syn "5'-D(*CP*GP*GP*AP*CP*AP*TP*GP*TP*CP*CP*G)-3'" 3663.422 2 ? ? ? ?
2 polymer man 'Cellular tumor antigen p53' 22505.711 2 ? ? 'residues 94-293' ?
3 non-polymer syn 'ZINC ION' 65.380 2 ? ? ? ?
4 water nat water 18.015 213 ? ? ? ?
#
loop_
_entity_keywords.entity_id
_entity_keywords.text
1 ?
2 ?
3 ?
4 ?
#
loop_
_entity_name_com.entity_id
_entity_name_com.name
1 'Tumor suppressor p53, Phosphoprotein p53, Antigen NY-CO-13'
2 ?
3 ?
4 ?
#
loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.nstd_linkage
_entity_poly.nstd_monomer
_entity_poly.pdbx_seq_one_letter_code
_entity_poly.pdbx_seq_one_letter_code_can
_entity_poly.pdbx_strand_id
1 polydeoxyribonucleotide no no '(DC)(DG)(DG)(DA)(DC)(DA)(DT)(DG)(DT)(DC)(DC)(DG)' CGGACATGTCCG E,F
2 'polypeptide(L)' no no
;SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
;
;SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVV
RRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILT
IITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKG
;
A,B
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 DC n
1 2 DG n
1 3 DG n
1 4 DA n
1 5 DC n
1 6 DA n
1 7 DT n
1 8 DG n
1 9 DT n
1 10 DC n
1 11 DC n
1 12 DG n
2 1 SER n
2 2 SER n
2 3 SER n
2 4 VAL n
2 5 PRO n
2 6 SER n
2 7 GLN n
2 8 LYS n
2 9 THR n
2 10 TYR n
2 11 GLN n
2 12 GLY n
2 13 SER n
2 14 TYR n
2 15 GLY n
2 16 PHE n
2 17 ARG n
2 18 LEU n
2 19 GLY n
2 20 PHE n
2 21 LEU n
2 22 HIS n
2 23 SER n
2 24 GLY n
2 25 THR n
2 26 ALA n
2 27 LYS n
2 28 SER n
2 29 VAL n
2 30 THR n
2 31 CYS n
2 32 THR n
2 33 TYR n
2 34 SER n
2 35 PRO n
2 36 ALA n
2 37 LEU n
2 38 ASN n
2 39 LYS n
2 40 MET n
2 41 PHE n
2 42 CYS n
2 43 GLN n
2 44 LEU n
2 45 ALA n
2 46 LYS n
2 47 THR n
2 48 CYS n
2 49 PRO n
2 50 VAL n
2 51 GLN n
2 52 LEU n
2 53 TRP n
2 54 VAL n
2 55 ASP n
2 56 SER n
2 57 THR n
2 58 PRO n
2 59 PRO n
2 60 PRO n
2 61 GLY n
2 62 THR n
2 63 ARG n
2 64 VAL n
2 65 ARG n
2 66 ALA n
2 67 MET n
2 68 ALA n
2 69 ILE n
2 70 TYR n
2 71 LYS n
2 72 GLN n
2 73 SER n
2 74 GLN n
2 75 HIS n
2 76 MET n
2 77 THR n
2 78 GLU n
2 79 VAL n
2 80 VAL n
2 81 ARG n
2 82 ARG n
2 83 CYS n
2 84 PRO n
2 85 HIS n
2 86 HIS n
2 87 GLU n
2 88 ARG n
2 89 CYS n
2 90 SER n
2 91 ASP n
2 92 SER n
2 93 ASP n
2 94 GLY n
2 95 LEU n
2 96 ALA n
2 97 PRO n
2 98 PRO n
2 99 GLN n
2 100 HIS n
2 101 LEU n
2 102 ILE n
2 103 ARG n
2 104 VAL n
2 105 GLU n
2 106 GLY n
2 107 ASN n
2 108 LEU n
2 109 ARG n
2 110 VAL n
2 111 GLU n
2 112 TYR n
2 113 LEU n
2 114 ASP n
2 115 ASP n
2 116 ARG n
2 117 ASN n
2 118 THR n
2 119 PHE n
2 120 ARG n
2 121 HIS n
2 122 SER n
2 123 VAL n
2 124 VAL n
2 125 VAL n
2 126 PRO n
2 127 TYR n
2 128 GLU n
2 129 PRO n
2 130 PRO n
2 131 GLU n
2 132 VAL n
2 133 GLY n
2 134 SER n
2 135 ASP n
2 136 CYS n
2 137 THR n
2 138 THR n
2 139 ILE n
2 140 HIS n
2 141 TYR n
2 142 ASN n
2 143 TYR n
2 144 MET n
2 145 CYS n
2 146 ASN n
2 147 SER n
2 148 SER n
2 149 CYS n
2 150 MET n
2 151 GLY n
2 152 GLY n
2 153 MET n
2 154 ASN n
2 155 ARG n
2 156 ARG n
2 157 PRO n
2 158 ILE n
2 159 LEU n
2 160 THR n
2 161 ILE n
2 162 ILE n
2 163 THR n
2 164 LEU n
2 165 GLU n
2 166 ASP n
2 167 SER n
2 168 SER n
2 169 GLY n
2 170 ASN n
2 171 LEU n
2 172 LEU n
2 173 GLY n
2 174 ARG n
2 175 ASN n
2 176 SER n
2 177 PHE n
2 178 GLU n
2 179 VAL n
2 180 ARG n
2 181 VAL n
2 182 CYS n
2 183 ALA n
2 184 CYS n
2 185 PRO n
2 186 GLY n
2 187 ARG n
2 188 ASP n
2 189 ARG n
2 190 ARG n
2 191 THR n
2 192 GLU n
2 193 GLU n
2 194 GLU n
2 195 ASN n
2 196 LEU n
2 197 ARG n
2 198 LYS n
2 199 LYS n
2 200 GLY n
#
_entity_src_gen.entity_id 2
_entity_src_gen.gene_src_common_name human
_entity_src_gen.gene_src_genus Homo
_entity_src_gen.pdbx_gene_src_gene ?
_entity_src_gen.gene_src_species ?
_entity_src_gen.gene_src_strain ?
_entity_src_gen.gene_src_tissue ?
_entity_src_gen.gene_src_tissue_fraction ?
_entity_src_gen.gene_src_details ?
_entity_src_gen.pdbx_gene_src_fragment ?
_entity_src_gen.pdbx_gene_src_scientific_name 'Homo sapiens'
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606
_entity_src_gen.pdbx_gene_src_variant ?
_entity_src_gen.pdbx_gene_src_cell_line ?
_entity_src_gen.pdbx_gene_src_atcc ?
_entity_src_gen.pdbx_gene_src_organ ?
_entity_src_gen.pdbx_gene_src_organelle ?
_entity_src_gen.pdbx_gene_src_cell ?
_entity_src_gen.pdbx_gene_src_cellular_location ?
_entity_src_gen.host_org_common_name ?
_entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli'
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562
_entity_src_gen.host_org_genus Escherichia
_entity_src_gen.pdbx_host_org_gene ?
_entity_src_gen.pdbx_host_org_organ ?
_entity_src_gen.host_org_species ?
_entity_src_gen.pdbx_host_org_tissue ?
_entity_src_gen.pdbx_host_org_tissue_fraction ?
_entity_src_gen.pdbx_host_org_strain ?
_entity_src_gen.pdbx_host_org_variant ?
_entity_src_gen.pdbx_host_org_cell_line ?
_entity_src_gen.pdbx_host_org_atcc ?
_entity_src_gen.pdbx_host_org_culture_collection ?
_entity_src_gen.pdbx_host_org_cell ?
_entity_src_gen.pdbx_host_org_organelle ?
_entity_src_gen.pdbx_host_org_cellular_location ?
_entity_src_gen.pdbx_host_org_vector_type plasmid
_entity_src_gen.pdbx_host_org_vector ?
_entity_src_gen.plasmid_name Pet27b
_entity_src_gen.plasmid_details ?
_entity_src_gen.pdbx_description ?
#
loop_
_struct_ref.id
_struct_ref.db_name
_struct_ref.db_code
_struct_ref.pdbx_db_accession
_struct_ref.entity_id
_struct_ref.pdbx_align_begin
_struct_ref.biol_id
1 UNP P53_HUMAN P04637 2 94 .
2 PDB 2ADY 2ADY 1 ? .
#
loop_
_struct_ref_seq.align_id
_struct_ref_seq.ref_id
_struct_ref_seq.pdbx_PDB_id_code
_struct_ref_seq.pdbx_strand_id
_struct_ref_seq.seq_align_beg
_struct_ref_seq.pdbx_seq_align_beg_ins_code
_struct_ref_seq.seq_align_end
_struct_ref_seq.pdbx_seq_align_end_ins_code
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.db_align_beg
_struct_ref_seq.db_align_end
_struct_ref_seq.details
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
1 1 2ADY A 1 ? 200 ? P04637 94 293 ? 94 293
2 1 2ADY B 1 ? 200 ? P04637 94 293 ? 94 293
3 2 2ADY E 1 ? 12 ? 2ADY 1 12 ? 1 12
4 2 2ADY F 1 ? 12 ? 2ADY 1 12 ? 1 12
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.199
DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.224
DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.224
DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.211
SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093
VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.147
PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.132
GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.146
LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.197
THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.120
TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.191
GLY 'PEPTIDE LINKING' y GLYCINE ? 'C2 H5 N O2' 75.067
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.191
ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.210
LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.174
HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.164
ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.094
CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.154
ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.119
MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.207
TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.228
ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.104
ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.174
GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.130
ZN NON-POLYMER . 'ZINC ION' ? 'ZN 2' 65.380
HOH NON-POLYMER . WATER ? 'H2 O' 18.015
#
_exptl.entry_id 2ADY
_exptl.crystals_number 1
_exptl.method 'X-RAY DIFFRACTION'
#
_exptl_crystal.id 1
_exptl_crystal.density_Matthews 2.3
_exptl_crystal.density_meas ?
_exptl_crystal.density_percent_sol 46.
_exptl_crystal.description ?
_exptl_crystal.F_000 ?
_exptl_crystal.preparation ?
#
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP'
_exptl_crystal_grow.pH 6.2
_exptl_crystal_grow.temp 293
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.pdbx_details 'Ammonium Fluoride, PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K'
_exptl_crystal_grow.pdbx_pH_range .
#
loop_
_exptl_crystal_grow_comp.crystal_id
_exptl_crystal_grow_comp.id
_exptl_crystal_grow_comp.sol_id
_exptl_crystal_grow_comp.name
_exptl_crystal_grow_comp.conc
_exptl_crystal_grow_comp.volume
_exptl_crystal_grow_comp.details
1 1 1 'Ammonium Fluoride' ? ? ?
1 2 1 'PEG 3350' ? ? ?
1 3 1 H2O ? ? ?
1 4 2 'Ammonium Fluoride' ? ? ?
1 5 2 'PEG 3350' ? ? ?
1 6 2 H2O ? ? ?
#
_diffrn.id 1
_diffrn.ambient_temp 100
_diffrn.ambient_temp_details ?
_diffrn.crystal_id 1
#
_diffrn_detector.diffrn_id 1
_diffrn_detector.detector 'IMAGE PLATE'
_diffrn_detector.type 'RIGAKU RAXIS IV++'
_diffrn_detector.pdbx_collection_date 2004-10-05
_diffrn_detector.details 'Osmic Inc. MSC - Blue Confocal Mirrors'
#
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.monochromator 'Osmic Inc. MSC - Blue Confocal Mirrors'
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.pdbx_scattering_type x-ray
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 1.5418
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.diffrn_id 1
_diffrn_source.source 'ROTATING ANODE'
_diffrn_source.type 'RIGAKU RUH3R'
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_wavelength_list 1.5418
_diffrn_source.pdbx_synchrotron_site ?
_diffrn_source.pdbx_synchrotron_beamline ?
#
_reflns.entry_id 2ADY
_reflns.observed_criterion_sigma_F 0
_reflns.observed_criterion_sigma_I 0
_reflns.d_resolution_high 2.5
_reflns.d_resolution_low 38.
_reflns.number_all 16113
_reflns.number_obs 15517
_reflns.percent_possible_obs 96.2
_reflns.pdbx_Rmerge_I_obs 0.114
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_sigmaI 12.8
_reflns.B_iso_Wilson_estimate 44.5
_reflns.pdbx_redundancy 4.2
_reflns.R_free_details ?
_reflns.pdbx_chi_squared ?
_reflns.pdbx_scaling_rejects ?
_reflns.pdbx_ordinal 1
_reflns.pdbx_diffrn_id 1
#
_reflns_shell.d_res_high 2.5
_reflns_shell.d_res_low 2.56
_reflns_shell.percent_possible_obs ?
_reflns_shell.percent_possible_all 98.4
_reflns_shell.Rmerge_I_obs 0.443
_reflns_shell.meanI_over_sigI_obs 2.9
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.pdbx_redundancy 4.0
_reflns_shell.number_unique_all 1029
_reflns_shell.number_measured_all ?
_reflns_shell.number_measured_obs ?
_reflns_shell.number_unique_obs ?
_reflns_shell.pdbx_chi_squared ?
_reflns_shell.pdbx_ordinal 1
_reflns_shell.pdbx_diffrn_id 1
#
_computing.entry_id 2ADY
_computing.pdbx_data_reduction_ii DENZO
_computing.pdbx_data_reduction_ds SCALEPACK
_computing.data_collection ?
_computing.structure_solution CNS
_computing.structure_refinement 'REFMAC 5.2.0005'
_computing.pdbx_structure_refinement_method ?
#
_refine.ls_d_res_high 2.500
_refine.ls_d_res_low 37.530
_refine.pdbx_ls_sigma_F 0.00
_refine.ls_percent_reflns_obs 96.310
_refine.ls_number_reflns_obs 15517
_refine.pdbx_ls_cross_valid_method THROUGHOUT
_refine.pdbx_R_Free_selection_details RANDOM
_refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS'
_refine.ls_R_factor_all 0.169
_refine.ls_R_factor_R_work 0.164
_refine.ls_R_factor_R_free 0.251
_refine.ls_percent_reflns_R_free 5.000
_refine.ls_number_reflns_R_free 773
_refine.B_iso_mean 36.501
_refine.aniso_B[1][1] -0.770
_refine.aniso_B[2][2] -0.680
_refine.aniso_B[3][3] 1.300
_refine.aniso_B[1][2] 0.000
_refine.aniso_B[1][3] -1.440
_refine.aniso_B[2][3] 0.000
_refine.correlation_coeff_Fo_to_Fc 0.949
_refine.correlation_coeff_Fo_to_Fc_free 0.882
_refine.pdbx_overall_ESU_R_Free 0.327
_refine.overall_SU_ML 0.236
_refine.overall_SU_B 10.455
_refine.solvent_model_details 'BABINET MODEL WITH MASK'
_refine.pdbx_solvent_vdw_probe_radii 1.200
_refine.pdbx_solvent_ion_probe_radii 0.800
_refine.pdbx_solvent_shrinkage_radii 0.800
_refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD'
_refine.entry_id 2ADY
_refine.pdbx_ls_sigma_I ?
_refine.ls_number_reflns_all 16113
_refine.ls_R_factor_obs 0.169
_refine.ls_redundancy_reflns_obs ?
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.ls_number_parameters ?
_refine.ls_number_restraints ?
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT'
_refine.pdbx_starting_model 'PDB ENTRY 1TSR'
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.solvent_model_param_bsol ?
_refine.solvent_model_param_ksol ?
_refine.occupancy_max ?
_refine.occupancy_min ?
_refine.pdbx_isotropic_thermal_model ISOTROPIC
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.overall_SU_R_free ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.pdbx_overall_ESU_R ?
_refine.ls_wR_factor_R_free ?
_refine.ls_wR_factor_R_work ?
_refine.overall_FOM_free_R_set ?
_refine.overall_FOM_work_R_set ?
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine.pdbx_diffrn_id 1
#
_refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine_hist.cycle_id LAST
_refine_hist.pdbx_number_atoms_protein 3088
_refine_hist.pdbx_number_atoms_nucleic_acid 486
_refine_hist.pdbx_number_atoms_ligand 2
_refine_hist.number_atoms_solvent 213
_refine_hist.number_atoms_total 3789
_refine_hist.d_res_high 2.500
_refine_hist.d_res_low 37.530
#
loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.weight
_refine_ls_restr.pdbx_refine_id
r_bond_refined_d 3706 0.016 0.021 ? 'X-RAY DIFFRACTION'
r_angle_refined_deg 5126 1.999 2.128 ? 'X-RAY DIFFRACTION'
r_dihedral_angle_1_deg 395 7.137 5.000 ? 'X-RAY DIFFRACTION'
r_dihedral_angle_2_deg 147 35.826 22.381 ? 'X-RAY DIFFRACTION'
r_dihedral_angle_3_deg 525 20.083 15.000 ? 'X-RAY DIFFRACTION'
r_dihedral_angle_4_deg 35 20.202 15.000 ? 'X-RAY DIFFRACTION'
r_chiral_restr 561 0.109 0.200 ? 'X-RAY DIFFRACTION'
r_gen_planes_refined 2697 0.007 0.020 ? 'X-RAY DIFFRACTION'
r_nbd_refined 1764 0.237 0.200 ? 'X-RAY DIFFRACTION'
r_nbtor_refined 2407 0.318 0.200 ? 'X-RAY DIFFRACTION'
r_xyhbond_nbd_refined 286 0.222 0.200 ? 'X-RAY DIFFRACTION'
r_symmetry_vdw_refined 76 0.265 0.200 ? 'X-RAY DIFFRACTION'
r_symmetry_hbond_refined 16 0.273 0.200 ? 'X-RAY DIFFRACTION'
r_mcbond_it 2031 2.412 3.000 ? 'X-RAY DIFFRACTION'
r_mcangle_it 3217 3.909 5.000 ? 'X-RAY DIFFRACTION'
r_scbond_it 2046 5.961 7.000 ? 'X-RAY DIFFRACTION'
r_scangle_it 1908 8.094 10.000 ? 'X-RAY DIFFRACTION'
#
_refine_ls_shell.d_res_high 2.497
_refine_ls_shell.d_res_low 2.562
_refine_ls_shell.pdbx_total_number_of_bins_used 20
_refine_ls_shell.percent_reflns_obs 91.020
_refine_ls_shell.number_reflns_R_work 973
_refine_ls_shell.R_factor_R_work 0.184
_refine_ls_shell.R_factor_R_free 0.314
_refine_ls_shell.percent_reflns_R_free ?
_refine_ls_shell.number_reflns_R_free 51
_refine_ls_shell.R_factor_R_free_error ?
_refine_ls_shell.redundancy_reflns_obs ?
_refine_ls_shell.number_reflns_all ?
_refine_ls_shell.number_reflns_obs ?
_refine_ls_shell.R_factor_all ?
_refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION'
#
_struct.entry_id 2ADY
_struct.title 'Structural Basis of DNA Recognition by p53 Tetramers (complex IV)'
_struct.pdbx_descriptor 'Cellular tumor antigen p53/DNA Complex'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 2ADY
_struct_keywords.pdbx_keywords APOPTOSIS/DNA
_struct_keywords.text 'Protein-DNA complexes, APOPTOSIS-DNA COMPLEX'
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 1 ?
C N N 2 ?
D N N 2 ?
E N N 3 ?
F N N 3 ?
G N N 4 ?
H N N 4 ?
I N N 4 ?
J N N 4 ?
#
_struct_biol.id 1
_struct_biol.pdbx_parent_biol_id ?
_struct_biol.details ?
#
loop_
_struct_conf.conf_type_id
_struct_conf.id
_struct_conf.pdbx_PDB_helix_id
_struct_conf.beg_label_comp_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.pdbx_beg_PDB_ins_code
_struct_conf.end_label_comp_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
_struct_conf.pdbx_end_PDB_ins_code
_struct_conf.beg_auth_comp_id
_struct_conf.beg_auth_asym_id
_struct_conf.beg_auth_seq_id
_struct_conf.end_auth_comp_id
_struct_conf.end_auth_asym_id
_struct_conf.end_auth_seq_id
_struct_conf.pdbx_PDB_helix_class
_struct_conf.details
_struct_conf.pdbx_PDB_helix_length
HELX_P HELX_P1 1 CYS C 83 ? ARG C 88 ? CYS A 176 ARG A 181 1 ? 6
HELX_P HELX_P2 2 CYS C 184 ? ASN C 195 ? CYS A 277 ASN A 288 1 ? 12
HELX_P HELX_P3 3 CYS D 83 ? ARG D 88 ? CYS B 176 ARG B 181 1 ? 6
HELX_P HELX_P4 4 CYS D 184 ? ASN D 195 ? CYS B 277 ASN B 288 1 ? 12
#
_struct_conf_type.id HELX_P
_struct_conf_type.criteria ?
_struct_conf_type.reference ?
#
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc1 metalc ? E ZN . ZN ? ? ? 1_555 C CYS 83 SG ? ? A ZN 1 A CYS 176 1_555 ? ? ? ? ? ? ? 2.410 ?
metalc2 metalc ? E ZN . ZN ? ? ? 1_555 C HIS 86 ND1 ? ? A ZN 1 A HIS 179 1_555 ? ? ? ? ? ? ? 2.102 ?
metalc3 metalc ? E ZN . ZN ? ? ? 1_555 C CYS 145 SG ? ? A ZN 1 A CYS 238 1_555 ? ? ? ? ? ? ? 2.307 ?
metalc4 metalc ? E ZN . ZN ? ? ? 1_555 C CYS 149 SG ? ? A ZN 1 A CYS 242 1_555 ? ? ? ? ? ? ? 2.294 ?
metalc5 metalc ? F ZN . ZN ? ? ? 1_555 D CYS 83 SG ? ? B ZN 1 B CYS 176 1_555 ? ? ? ? ? ? ? 2.467 ?
metalc6 metalc ? F ZN . ZN ? ? ? 1_555 D HIS 86 ND1 ? ? B ZN 1 B HIS 179 1_555 ? ? ? ? ? ? ? 2.076 ?
metalc7 metalc ? F ZN . ZN ? ? ? 1_555 D CYS 145 SG ? ? B ZN 1 B CYS 238 1_555 ? ? ? ? ? ? ? 2.230 ?
metalc8 metalc ? F ZN . ZN ? ? ? 1_555 D CYS 149 SG ? ? B ZN 1 B CYS 242 1_555 ? ? ? ? ? ? ? 2.265 ?
hydrog1 hydrog ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? E DC 1 F DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog2 hydrog ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? E DC 1 F DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog3 hydrog ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? E DC 1 F DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog4 hydrog ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? E DG 2 F DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog5 hydrog ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? E DG 2 F DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog6 hydrog ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? E DG 2 F DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog7 hydrog ? A DG 3 N1 ? ? ? 1_555 B DC 10 N3 ? ? E DG 3 F DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog8 hydrog ? A DG 3 N2 ? ? ? 1_555 B DC 10 O2 ? ? E DG 3 F DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog9 hydrog ? A DG 3 O6 ? ? ? 1_555 B DC 10 N4 ? ? E DG 3 F DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog10 hydrog ? A DA 4 N1 ? ? ? 1_555 B DT 9 N3 ? ? E DA 4 F DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog11 hydrog ? A DA 4 N6 ? ? ? 1_555 B DT 9 O4 ? ? E DA 4 F DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog12 hydrog ? A DC 5 N3 ? ? ? 1_555 B DG 8 N1 ? ? E DC 5 F DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog13 hydrog ? A DC 5 N4 ? ? ? 1_555 B DG 8 O6 ? ? E DC 5 F DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog14 hydrog ? A DC 5 O2 ? ? ? 1_555 B DG 8 N2 ? ? E DC 5 F DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog15 hydrog ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? E DA 6 F DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog16 hydrog ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? E DA 6 F DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog17 hydrog ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? E DT 7 F DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog18 hydrog ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? E DT 7 F DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog19 hydrog ? A DG 8 N1 ? ? ? 1_555 B DC 5 N3 ? ? E DG 8 F DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog20 hydrog ? A DG 8 N2 ? ? ? 1_555 B DC 5 O2 ? ? E DG 8 F DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog21 hydrog ? A DG 8 O6 ? ? ? 1_555 B DC 5 N4 ? ? E DG 8 F DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog22 hydrog ? A DT 9 N3 ? ? ? 1_555 B DA 4 N1 ? ? E DT 9 F DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog23 hydrog ? A DT 9 O4 ? ? ? 1_555 B DA 4 N6 ? ? E DT 9 F DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog24 hydrog ? A DC 10 N3 ? ? ? 1_555 B DG 3 N1 ? ? E DC 10 F DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog25 hydrog ? A DC 10 N4 ? ? ? 1_555 B DG 3 O6 ? ? E DC 10 F DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog26 hydrog ? A DC 10 O2 ? ? ? 1_555 B DG 3 N2 ? ? E DC 10 F DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog27 hydrog ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? E DC 11 F DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog28 hydrog ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? E DC 11 F DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
hydrog29 hydrog ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? E DC 11 F DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ?
#
loop_
_struct_conn_type.id
_struct_conn_type.criteria
_struct_conn_type.reference
metalc ? ?
hydrog 'For hydrogen bonding between nucleic acid bases, donor to acceptor distance of 2.2 -3.5 Angstroms was used.' ?
#
loop_
_struct_sheet.id
_struct_sheet.type
_struct_sheet.number_strands
_struct_sheet.details
A ? 4 ?
B ? 7 ?
C ? 4 ?
D ? 7 ?
#
loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
A 1 2 ? anti-parallel
A 2 3 ? anti-parallel
A 3 4 ? anti-parallel
B 1 2 ? anti-parallel
B 2 3 ? parallel
B 3 4 ? anti-parallel
B 4 5 ? anti-parallel
B 5 6 ? anti-parallel
B 6 7 ? anti-parallel
C 1 2 ? anti-parallel
C 2 3 ? anti-parallel
C 3 4 ? anti-parallel
D 1 2 ? anti-parallel
D 2 3 ? parallel
D 3 4 ? anti-parallel
D 4 5 ? anti-parallel
D 5 6 ? anti-parallel
D 6 7 ? anti-parallel
#
loop_
_struct_sheet_range.sheet_id
_struct_sheet_range.id
_struct_sheet_range.beg_label_comp_id
_struct_sheet_range.beg_label_asym_id
_struct_sheet_range.beg_label_seq_id
_struct_sheet_range.pdbx_beg_PDB_ins_code
_struct_sheet_range.end_label_comp_id
_struct_sheet_range.end_label_asym_id
_struct_sheet_range.end_label_seq_id
_struct_sheet_range.pdbx_end_PDB_ins_code
_struct_sheet_range.symmetry
_struct_sheet_range.beg_auth_comp_id
_struct_sheet_range.beg_auth_asym_id
_struct_sheet_range.beg_auth_seq_id
_struct_sheet_range.end_auth_comp_id
_struct_sheet_range.end_auth_asym_id
_struct_sheet_range.end_auth_seq_id
A 1 ARG C 17 ? PHE C 20 ? ? ARG A 110 PHE A 113
A 2 CYS C 48 ? TRP C 53 ? ? CYS A 141 TRP A 146
A 3 THR C 137 ? TYR C 143 ? ? THR A 230 TYR A 236
A 4 ILE C 102 ? GLU C 105 ? ? ILE A 195 GLU A 198
B 1 CYS C 31 ? SER C 34 ? ? CYS A 124 SER A 127
B 2 LYS C 39 ? CYS C 42 ? ? LYS A 132 CYS A 135
B 3 LEU C 171 ? VAL C 181 ? ? LEU A 264 VAL A 274
B 4 ILE C 158 ? GLU C 165 ? ? ILE A 251 GLU A 258
B 5 ARG C 63 ? TYR C 70 ? ? ARG A 156 TYR A 163
B 6 HIS C 121 ? PRO C 126 ? ? HIS A 214 PRO A 219
B 7 GLU C 111 ? ASP C 114 ? ? GLU A 204 ASP A 207
C 1 ARG D 17 ? GLY D 19 ? ? ARG B 110 GLY B 112
C 2 CYS D 48 ? TRP D 53 ? ? CYS B 141 TRP B 146
C 3 CYS D 136 ? TYR D 143 ? ? CYS B 229 TYR B 236
C 4 ILE D 102 ? VAL D 104 ? ? ILE B 195 VAL B 197
D 1 CYS D 31 ? SER D 34 ? ? CYS B 124 SER B 127
D 2 LYS D 39 ? CYS D 42 ? ? LYS B 132 CYS B 135
D 3 LEU D 171 ? VAL D 181 ? ? LEU B 264 VAL B 274
D 4 ILE D 158 ? GLU D 165 ? ? ILE B 251 GLU B 258
D 5 ARG D 63 ? TYR D 70 ? ? ARG B 156 TYR B 163
D 6 HIS D 121 ? PRO D 126 ? ? HIS B 214 PRO B 219
D 7 GLU D 111 ? ASP D 114 ? ? GLU B 204 ASP B 207
#
loop_
_pdbx_struct_sheet_hbond.sheet_id
_pdbx_struct_sheet_hbond.range_id_1
_pdbx_struct_sheet_hbond.range_id_2
_pdbx_struct_sheet_hbond.range_1_label_atom_id
_pdbx_struct_sheet_hbond.range_1_label_comp_id
_pdbx_struct_sheet_hbond.range_1_label_asym_id
_pdbx_struct_sheet_hbond.range_1_label_seq_id
_pdbx_struct_sheet_hbond.range_1_PDB_ins_code
_pdbx_struct_sheet_hbond.range_1_auth_atom_id
_pdbx_struct_sheet_hbond.range_1_auth_comp_id
_pdbx_struct_sheet_hbond.range_1_auth_asym_id
_pdbx_struct_sheet_hbond.range_1_auth_seq_id
_pdbx_struct_sheet_hbond.range_2_label_atom_id
_pdbx_struct_sheet_hbond.range_2_label_comp_id
_pdbx_struct_sheet_hbond.range_2_label_asym_id
_pdbx_struct_sheet_hbond.range_2_label_seq_id
_pdbx_struct_sheet_hbond.range_2_PDB_ins_code
_pdbx_struct_sheet_hbond.range_2_auth_atom_id
_pdbx_struct_sheet_hbond.range_2_auth_comp_id
_pdbx_struct_sheet_hbond.range_2_auth_asym_id
_pdbx_struct_sheet_hbond.range_2_auth_seq_id
A 1 2 N ARG C 17 ? N ARG A 110 O TRP C 53 ? O TRP A 146
A 2 3 N VAL C 50 ? N VAL A 143 O ILE C 139 ? O ILE A 232
A 3 4 O ASN C 142 ? O ASN A 235 N ARG C 103 ? N ARG A 196
B 1 2 N THR C 32 ? N THR A 125 O PHE C 41 ? O PHE A 134
B 2 3 N MET C 40 ? N MET A 133 O GLU C 178 ? O GLU A 271
B 3 4 O PHE C 177 ? O PHE A 270 N THR C 160 ? N THR A 253
B 4 5 O THR C 163 ? O THR A 256 N ARG C 65 ? N ARG A 158
B 5 6 N VAL C 64 ? N VAL A 157 O VAL C 125 ? O VAL A 218
B 6 7 O SER C 122 ? O SER A 215 N LEU C 113 ? N LEU A 206
C 1 2 N GLY D 19 ? N GLY B 112 O GLN D 51 ? O GLN B 144
C 2 3 N LEU D 52 ? N LEU B 145 O THR D 137 ? O THR B 230
C 3 4 O ASN D 142 ? O ASN B 235 N ARG D 103 ? N ARG B 196
D 1 2 N THR D 32 ? N THR B 125 O PHE D 41 ? O PHE B 134
D 2 3 N MET D 40 ? N MET B 133 O GLU D 178 ? O GLU B 271
D 3 4 O VAL D 179 ? O VAL B 272 N ILE D 158 ? N ILE B 251
D 4 5 O ILE D 161 ? O ILE B 254 N MET D 67 ? N MET B 160
D 5 6 N VAL D 64 ? N VAL B 157 O VAL D 125 ? O VAL B 218
D 6 7 O VAL D 124 ? O VAL B 217 N GLU D 111 ? N GLU B 204
#
loop_
_struct_site.id
_struct_site.details
_struct_site.pdbx_evidence_code
AC1 'BINDING SITE FOR RESIDUE ZN A 1' SOFTWARE
AC2 'BINDING SITE FOR RESIDUE ZN B 1' SOFTWARE
#
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.pdbx_num_res
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.pdbx_auth_ins_code
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_atom_id
_struct_site_gen.label_alt_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 AC1 4 CYS C 83 ? CYS A 176 . . 1_555 ?
2 AC1 4 HIS C 86 ? HIS A 179 . . 1_555 ?
3 AC1 4 CYS C 145 ? CYS A 238 . . 1_555 ?
4 AC1 4 CYS C 149 ? CYS A 242 . . 1_555 ?
5 AC2 4 CYS D 83 ? CYS B 176 . . 1_555 ?
6 AC2 4 HIS D 86 ? HIS B 179 . . 1_555 ?
7 AC2 4 CYS D 145 ? CYS B 238 . . 1_555 ?
8 AC2 4 CYS D 149 ? CYS B 242 . . 1_555 ?
#
_atom_sites.entry_id 2ADY
_atom_sites.Cartn_transform_axes ?
_atom_sites.fract_transf_matrix[1][1] 0.01087
_atom_sites.fract_transf_matrix[1][2] 0.00000
_atom_sites.fract_transf_matrix[1][3] 0.00056
_atom_sites.fract_transf_matrix[2][1] 0.00000
_atom_sites.fract_transf_matrix[2][2] 0.01473
_atom_sites.fract_transf_matrix[2][3] 0.00000
_atom_sites.fract_transf_matrix[3][1] 0.00000