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2O3S.cif
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2O3S.cif
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data_2O3S
#
_entry.id 2O3S
#
_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 2O3S
RCSB RCSB040650
#
loop_
_database_PDB_rev.num
_database_PDB_rev.date
_database_PDB_rev.date_original
_database_PDB_rev.status
_database_PDB_rev.replaces
_database_PDB_rev.mod_type
1 2006-12-12 2006-12-01 ? 2O3S 0
2 2006-12-19 ? ? 2O3S 1
3 2007-04-03 ? ? 2O3S 1
4 2009-02-24 ? ? 2O3S 1
#
loop_
_database_PDB_rev_record.rev_num
_database_PDB_rev_record.type
_database_PDB_rev_record.details
2 SEQADV ?
3 JRNL ?
4 VERSN ?
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.db_id
_pdbx_database_related.details
_pdbx_database_related.content_type
PDB 1YH3 'wildtype protein' unspecified
PDB 2O3Q 'E226Q mutant complexed with cADPR' unspecified
PDB 2O3R 'E226D mutant complexed with cADPR' unspecified
PDB 2O3T 'E226Q mutant complexed with cGDPR' unspecified
PDB 2O3U 'E226Q mutant complexed with NGD' unspecified
#
_pdbx_database_status.status_code REL
_pdbx_database_status.entry_id 2O3S
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_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
'Liu, Q.' 1
'Kriksunov, I.A.' 2
'Graeff, R.' 3
'Lee, H.C.' 4
'Hao, Q.' 5
#
_citation.id primary
_citation.title
'Structural basis for formation and hydrolysis of the calcium messenger cyclic ADP-ribose by human CD38'
_citation.journal_abbrev J.Biol.Chem.
_citation.journal_volume 282
_citation.page_first 5853
_citation.page_last 5861
_citation.year 2007
_citation.journal_id_ASTM JBCHA3
_citation.country US
_citation.journal_id_ISSN 0021-9258
_citation.journal_id_CSD 0071
_citation.book_publisher ?
_citation.pdbx_database_id_PubMed 17182614
_citation.pdbx_database_id_DOI 10.1074/jbc.M609093200
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
primary 'Liu, Q.' 1
primary 'Kriksunov, I.A.' 2
primary 'Graeff, R.' 3
primary 'Lee, H.C.' 4
primary 'Hao, Q.' 5
#
_cell.entry_id 2O3S
_cell.length_a 42.350
_cell.length_b 53.786
_cell.length_c 66.826
_cell.angle_alpha 104.97
_cell.angle_beta 91.71
_cell.angle_gamma 95.04
_cell.Z_PDB 2
_cell.pdbx_unique_axis ?
_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.entry_id 2O3S
_symmetry.space_group_name_H-M 'P 1'
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.cell_setting ?
_symmetry.Int_Tables_number ?
_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 man 'ADP-ribosyl cyclase 1' 30298.529 2 ? 'R45F, Q49T, N100D, N164D, N209D, N219D, E226G'
'Extracellular domain, residues 45-300' 3.2.2.5
2 non-polymer syn 'CYCLIC ADENOSINE DIPHOSPHATE-RIBOSE' 541.304 2 ? ? ? ?
3 water nat water 18.015 662 ? ? ? ?
#
loop_
_entity_keywords.entity_id
_entity_keywords.text
1 ?
2 ?
3 ?
#
loop_
_entity_name_com.entity_id
_entity_name_com.name
1
;Cyclic ADP-ribose hydrolase 1, cADPr hydrolase 1, Lymphocyte differentiation antigen CD38, T10, Acute lymphoblastic leukemia cells antigen CD38
;
2 ?
3 ?
#
_entity_poly.entity_id 1
_entity_poly.type 'polypeptide(L)'
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code
;KREAEAFWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVP
CNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAE
AACDVVHVMLDGSRSKIFDKDSTFGSVGVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNI
YRPDKFLQCVKNPEDSSCTSEI
;
_entity_poly.pdbx_seq_one_letter_code_can
;KREAEAFWRQTWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCDITEEDYQPLMKLGTQTVP
CNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFDTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAE
AACDVVHVMLDGSRSKIFDKDSTFGSVGVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNI
YRPDKFLQCVKNPEDSSCTSEI
;
_entity_poly.pdbx_strand_id A,B
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 LYS n
1 2 ARG n
1 3 GLU n
1 4 ALA n
1 5 GLU n
1 6 ALA n
1 7 PHE n
1 8 TRP n
1 9 ARG n
1 10 GLN n
1 11 THR n
1 12 TRP n
1 13 SER n
1 14 GLY n
1 15 PRO n
1 16 GLY n
1 17 THR n
1 18 THR n
1 19 LYS n
1 20 ARG n
1 21 PHE n
1 22 PRO n
1 23 GLU n
1 24 THR n
1 25 VAL n
1 26 LEU n
1 27 ALA n
1 28 ARG n
1 29 CYS n
1 30 VAL n
1 31 LYS n
1 32 TYR n
1 33 THR n
1 34 GLU n
1 35 ILE n
1 36 HIS n
1 37 PRO n
1 38 GLU n
1 39 MET n
1 40 ARG n
1 41 HIS n
1 42 VAL n
1 43 ASP n
1 44 CYS n
1 45 GLN n
1 46 SER n
1 47 VAL n
1 48 TRP n
1 49 ASP n
1 50 ALA n
1 51 PHE n
1 52 LYS n
1 53 GLY n
1 54 ALA n
1 55 PHE n
1 56 ILE n
1 57 SER n
1 58 LYS n
1 59 HIS n
1 60 PRO n
1 61 CYS n
1 62 ASP n
1 63 ILE n
1 64 THR n
1 65 GLU n
1 66 GLU n
1 67 ASP n
1 68 TYR n
1 69 GLN n
1 70 PRO n
1 71 LEU n
1 72 MET n
1 73 LYS n
1 74 LEU n
1 75 GLY n
1 76 THR n
1 77 GLN n
1 78 THR n
1 79 VAL n
1 80 PRO n
1 81 CYS n
1 82 ASN n
1 83 LYS n
1 84 ILE n
1 85 LEU n
1 86 LEU n
1 87 TRP n
1 88 SER n
1 89 ARG n
1 90 ILE n
1 91 LYS n
1 92 ASP n
1 93 LEU n
1 94 ALA n
1 95 HIS n
1 96 GLN n
1 97 PHE n
1 98 THR n
1 99 GLN n
1 100 VAL n
1 101 GLN n
1 102 ARG n
1 103 ASP n
1 104 MET n
1 105 PHE n
1 106 THR n
1 107 LEU n
1 108 GLU n
1 109 ASP n
1 110 THR n
1 111 LEU n
1 112 LEU n
1 113 GLY n
1 114 TYR n
1 115 LEU n
1 116 ALA n
1 117 ASP n
1 118 ASP n
1 119 LEU n
1 120 THR n
1 121 TRP n
1 122 CYS n
1 123 GLY n
1 124 GLU n
1 125 PHE n
1 126 ASP n
1 127 THR n
1 128 SER n
1 129 LYS n
1 130 ILE n
1 131 ASN n
1 132 TYR n
1 133 GLN n
1 134 SER n
1 135 CYS n
1 136 PRO n
1 137 ASP n
1 138 TRP n
1 139 ARG n
1 140 LYS n
1 141 ASP n
1 142 CYS n
1 143 SER n
1 144 ASN n
1 145 ASN n
1 146 PRO n
1 147 VAL n
1 148 SER n
1 149 VAL n
1 150 PHE n
1 151 TRP n
1 152 LYS n
1 153 THR n
1 154 VAL n
1 155 SER n
1 156 ARG n
1 157 ARG n
1 158 PHE n
1 159 ALA n
1 160 GLU n
1 161 ALA n
1 162 ALA n
1 163 CYS n
1 164 ASP n
1 165 VAL n
1 166 VAL n
1 167 HIS n
1 168 VAL n
1 169 MET n
1 170 LEU n
1 171 ASP n
1 172 GLY n
1 173 SER n
1 174 ARG n
1 175 SER n
1 176 LYS n
1 177 ILE n
1 178 PHE n
1 179 ASP n
1 180 LYS n
1 181 ASP n
1 182 SER n
1 183 THR n
1 184 PHE n
1 185 GLY n
1 186 SER n
1 187 VAL n
1 188 GLY n
1 189 VAL n
1 190 HIS n
1 191 ASN n
1 192 LEU n
1 193 GLN n
1 194 PRO n
1 195 GLU n
1 196 LYS n
1 197 VAL n
1 198 GLN n
1 199 THR n
1 200 LEU n
1 201 GLU n
1 202 ALA n
1 203 TRP n
1 204 VAL n
1 205 ILE n
1 206 HIS n
1 207 GLY n
1 208 GLY n
1 209 ARG n
1 210 GLU n
1 211 ASP n
1 212 SER n
1 213 ARG n
1 214 ASP n
1 215 LEU n
1 216 CYS n
1 217 GLN n
1 218 ASP n
1 219 PRO n
1 220 THR n
1 221 ILE n
1 222 LYS n
1 223 GLU n
1 224 LEU n
1 225 GLU n
1 226 SER n
1 227 ILE n
1 228 ILE n
1 229 SER n
1 230 LYS n
1 231 ARG n
1 232 ASN n
1 233 ILE n
1 234 GLN n
1 235 PHE n
1 236 SER n
1 237 CYS n
1 238 LYS n
1 239 ASN n
1 240 ILE n
1 241 TYR n
1 242 ARG n
1 243 PRO n
1 244 ASP n
1 245 LYS n
1 246 PHE n
1 247 LEU n
1 248 GLN n
1 249 CYS n
1 250 VAL n
1 251 LYS n
1 252 ASN n
1 253 PRO n
1 254 GLU n
1 255 ASP n
1 256 SER n
1 257 SER n
1 258 CYS n
1 259 THR n
1 260 SER n
1 261 GLU n
1 262 ILE n
#
_entity_src_gen.entity_id 1
_entity_src_gen.gene_src_common_name human
_entity_src_gen.gene_src_genus Homo
_entity_src_gen.pdbx_gene_src_gene CD38
_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 'Pichia pastoris'
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 4922
_entity_src_gen.host_org_genus Pichia
_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 X-33
_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 pPICZaA
_entity_src_gen.plasmid_details ?
_entity_src_gen.pdbx_description ?
#
_struct_ref.id 1
_struct_ref.db_name UNP
_struct_ref.db_code CD38_HUMAN
_struct_ref.pdbx_db_accession P28907
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code
;RWRQQWSGPGTTKRFPETVLARCVKYTEIHPEMRHVDCQSVWDAFKGAFISKHPCNITEEDYQPLMKLGTQTVPCNKILLWSRIKDLAHQFTQVQRDMFTLEDTLLGYLADDLTWCGEFNTSKINYQSCPDWRKDCSNNPVSVFWKTVSRRFAEAACDVVHVMLNGSRSKIFDKNSTFGSVEVHNLQPEKVQTLEAWVIHGGREDSRDLCQDPTIKELESIISKRNIQFSCKNIYRPDKFLQCVKNPEDSSCTSEI
;
_struct_ref.pdbx_align_begin 45
_struct_ref.biol_id .
#
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.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
1 1 2O3S A 7 ? 262 ? P28907 45 300 45 300
2 1 2O3S B 7 ? 262 ? P28907 45 300 45 300
#
loop_
_struct_ref_seq_dif.align_id
_struct_ref_seq_dif.pdbx_pdb_id_code
_struct_ref_seq_dif.mon_id
_struct_ref_seq_dif.pdbx_pdb_strand_id
_struct_ref_seq_dif.seq_num
_struct_ref_seq_dif.pdbx_seq_db_name
_struct_ref_seq_dif.pdbx_seq_db_accession_code
_struct_ref_seq_dif.db_mon_id
_struct_ref_seq_dif.pdbx_seq_db_seq_num
_struct_ref_seq_dif.details
_struct_ref_seq_dif.pdbx_auth_seq_num
_struct_ref_seq_dif.pdbx_ordinal
_struct_ref_seq_dif.pdbx_pdb_ins_code
1 2O3S LYS A 1 UNP P28907 ? ? 'CLONING ARTIFACT' 39 1 ?
1 2O3S ARG A 2 UNP P28907 ? ? 'CLONING ARTIFACT' 40 2 ?
1 2O3S GLU A 3 UNP P28907 ? ? 'CLONING ARTIFACT' 41 3 ?
1 2O3S ALA A 4 UNP P28907 ? ? 'CLONING ARTIFACT' 42 4 ?
1 2O3S GLU A 5 UNP P28907 ? ? 'CLONING ARTIFACT' 43 5 ?
1 2O3S ALA A 6 UNP P28907 ? ? 'CLONING ARTIFACT' 44 6 ?
1 2O3S PHE A 7 UNP P28907 ARG 45 ENGINEERED 45 7 ?
1 2O3S THR A 11 UNP P28907 GLN 49 ENGINEERED 49 8 ?
1 2O3S ASP A 62 UNP P28907 ASN 100 ENGINEERED 100 9 ?
1 2O3S ASP A 126 UNP P28907 ASN 164 ENGINEERED 164 10 ?
1 2O3S ASP A 171 UNP P28907 ASN 209 ENGINEERED 209 11 ?
1 2O3S ASP A 181 UNP P28907 ASN 219 ENGINEERED 219 12 ?
1 2O3S GLY A 188 UNP P28907 GLU 226 ENGINEERED 226 13 ?
2 2O3S LYS B 1 UNP P28907 ? ? 'CLONING ARTIFACT' 39 14 ?
2 2O3S ARG B 2 UNP P28907 ? ? 'CLONING ARTIFACT' 40 15 ?
2 2O3S GLU B 3 UNP P28907 ? ? 'CLONING ARTIFACT' 41 16 ?
2 2O3S ALA B 4 UNP P28907 ? ? 'CLONING ARTIFACT' 42 17 ?
2 2O3S GLU B 5 UNP P28907 ? ? 'CLONING ARTIFACT' 43 18 ?
2 2O3S ALA B 6 UNP P28907 ? ? 'CLONING ARTIFACT' 44 19 ?
2 2O3S PHE B 7 UNP P28907 ARG 45 ENGINEERED 45 20 ?
2 2O3S THR B 11 UNP P28907 GLN 49 ENGINEERED 49 21 ?
2 2O3S ASP B 62 UNP P28907 ASN 100 ENGINEERED 100 22 ?
2 2O3S ASP B 126 UNP P28907 ASN 164 ENGINEERED 164 23 ?
2 2O3S ASP B 171 UNP P28907 ASN 209 ENGINEERED 209 24 ?
2 2O3S ASP B 181 UNP P28907 ASN 219 ENGINEERED 219 25 ?
2 2O3S GLY B 188 UNP P28907 GLU 226 ENGINEERED 226 26 ?
#
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
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.191
TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.228
ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.210
GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.146
THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.120
SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093
GLY 'PEPTIDE LINKING' y GLYCINE ? 'C2 H5 N O2' 75.067
PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.132
LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.197
GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.130
VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.147
LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.174
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
TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.191
ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.174
HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.164
MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.207
ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.104
ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.119
CXR NON-POLYMER . 'CYCLIC ADENOSINE DIPHOSPHATE-RIBOSE' 'CYCLIC ADP-RIBOSE' 'C15 H21 N5 O13 P2' 541.304
HOH NON-POLYMER . WATER ? 'H2 O' 18.015
#
_exptl.entry_id 2O3S
_exptl.method 'X-RAY DIFFRACTION'
_exptl.crystals_number 1
#
_exptl_crystal.id 1
_exptl_crystal.density_meas ?
_exptl_crystal.density_Matthews 2.41
_exptl_crystal.density_percent_sol 49.02
_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.temp 300
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.pH 6.0
_exptl_crystal_grow.pdbx_details '100 mM MES, 13% PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K'
_exptl_crystal_grow.pdbx_pH_range .
#
_diffrn.id 1
_diffrn.ambient_temp 100
_diffrn.ambient_temp_details ?
_diffrn.crystal_id 1
#
_diffrn_detector.diffrn_id 1
_diffrn_detector.detector CCD
_diffrn_detector.type 'ADSC QUANTUM 210'
_diffrn_detector.pdbx_collection_date 2005-07-11
_diffrn_detector.details ?
#
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.monochromator 'Si 111 CHANNEL'
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_scattering_type x-ray
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 0.977
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.diffrn_id 1
_diffrn_source.source SYNCHROTRON
_diffrn_source.type 'CHESS BEAMLINE A1'
_diffrn_source.pdbx_synchrotron_site CHESS
_diffrn_source.pdbx_synchrotron_beamline A1
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_wavelength_list 0.977
#
_reflns.entry_id 2O3S
_reflns.observed_criterion_sigma_F 2.0
_reflns.observed_criterion_sigma_I 2.0
_reflns.d_resolution_high 1.50
_reflns.d_resolution_low 50
_reflns.number_all 89701
_reflns.number_obs 78040
_reflns.percent_possible_obs 87.0
_reflns.pdbx_Rmerge_I_obs ?
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_sigmaI ?
_reflns.B_iso_Wilson_estimate ?
_reflns.pdbx_redundancy ?
_reflns.R_free_details ?
_reflns.limit_h_max ?
_reflns.limit_h_min ?
_reflns.limit_k_max ?
_reflns.limit_k_min ?
_reflns.limit_l_max ?
_reflns.limit_l_min ?
_reflns.observed_criterion_F_max ?
_reflns.observed_criterion_F_min ?
_reflns.pdbx_chi_squared ?
_reflns.pdbx_scaling_rejects ?
_reflns.pdbx_ordinal 1
_reflns.pdbx_diffrn_id 1
#
_reflns_shell.d_res_high 1.50
_reflns_shell.d_res_low 1.55
_reflns_shell.percent_possible_all 41.2
_reflns_shell.Rmerge_I_obs 0.389
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.meanI_over_sigI_obs ?
_reflns_shell.pdbx_redundancy ?
_reflns_shell.percent_possible_obs ?
_reflns_shell.number_unique_all ?
_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 2O3S
_computing.pdbx_data_reduction_ii HKL-3000
_computing.pdbx_data_reduction_ds HKL-3000
_computing.data_collection 'ADSC QUANTUM'
_computing.structure_solution MOLREP
_computing.structure_refinement 'REFMAC 5.3.0017'
_computing.pdbx_structure_refinement_method ?
#
_refine.entry_id 2O3S
_refine.ls_number_reflns_obs 74166
_refine.ls_number_reflns_all 85572
_refine.pdbx_ls_sigma_I 0
_refine.pdbx_ls_sigma_F 0
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.ls_d_res_low 20.00
_refine.ls_d_res_high 1.50
_refine.ls_percent_reflns_obs 86.67
_refine.ls_R_factor_obs 0.19128
_refine.ls_R_factor_all 0.19128
_refine.ls_R_factor_R_work 0.18887
_refine.ls_R_factor_R_free 0.23826
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_percent_reflns_R_free 4.9
_refine.ls_number_reflns_R_free 3850
_refine.ls_number_parameters ?
_refine.ls_number_restraints ?
_refine.occupancy_min ?
_refine.occupancy_max ?
_refine.correlation_coeff_Fo_to_Fc 0.963
_refine.correlation_coeff_Fo_to_Fc_free 0.942
_refine.B_iso_mean 40.066
_refine.aniso_B[1][1] -0.64
_refine.aniso_B[2][2] 0.15
_refine.aniso_B[3][3] 0.96
_refine.aniso_B[1][2] 0.43
_refine.aniso_B[1][3] 0.33
_refine.aniso_B[2][3] 0.73
_refine.solvent_model_details 'BABINET MODEL WITH MASK'
_refine.solvent_model_param_ksol ?
_refine.solvent_model_param_bsol ?
_refine.pdbx_solvent_vdw_probe_radii 1.20
_refine.pdbx_solvent_ion_probe_radii 0.80
_refine.pdbx_solvent_shrinkage_radii 0.80
_refine.pdbx_ls_cross_valid_method THROUGHOUT
_refine.details ?
_refine.pdbx_starting_model 'PDB entry 1YH3'
_refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT'
_refine.pdbx_isotropic_thermal_model ?
_refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD'
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_R_Free_selection_details RANDOM
_refine.pdbx_overall_ESU_R 0.091
_refine.pdbx_overall_ESU_R_Free 0.098
_refine.overall_SU_ML 0.063
_refine.overall_SU_B 3.265
_refine.ls_redundancy_reflns_obs ?
_refine.B_iso_min ?
_refine.B_iso_max ?
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.overall_SU_R_free ?
_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 4076
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 70
_refine_hist.number_atoms_solvent 662
_refine_hist.number_atoms_total 4808
_refine_hist.d_res_high 1.50
_refine_hist.d_res_low 20.00
#
loop_
_refine_ls_restr.type
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.weight
_refine_ls_restr.number
_refine_ls_restr.pdbx_refine_id
r_bond_refined_d 0.021 0.022 ? 4269 'X-RAY DIFFRACTION'
r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION'
r_angle_refined_deg 1.654 1.955 ? 5810 'X-RAY DIFFRACTION'
r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION'
r_dihedral_angle_1_deg 5.945 5.000 ? 502 'X-RAY DIFFRACTION'
r_dihedral_angle_2_deg 35.407 24.216 ? 204 'X-RAY DIFFRACTION'
r_dihedral_angle_3_deg 15.502 15.000 ? 728 'X-RAY DIFFRACTION'
r_dihedral_angle_4_deg 21.199 15.000 ? 26 'X-RAY DIFFRACTION'
r_chiral_restr 0.142 0.200 ? 626 'X-RAY DIFFRACTION'
r_gen_planes_refined 0.008 0.020 ? 3210 'X-RAY DIFFRACTION'
r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION'
r_nbd_refined 0.231 0.200 ? 1802 'X-RAY DIFFRACTION'
r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION'
r_nbtor_refined 0.303 0.200 ? 2824 'X-RAY DIFFRACTION'
r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION'
r_xyhbond_nbd_refined 0.186 0.200 ? 454 'X-RAY DIFFRACTION'
r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION'
r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION'
r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION'
r_symmetry_vdw_refined 0.350 0.200 ? 70 'X-RAY DIFFRACTION'
r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION'
r_symmetry_hbond_refined 0.247 0.200 ? 53 'X-RAY DIFFRACTION'
r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION'
r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION'
r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION'
r_mcbond_it 1.368 1.500 ? 2626 'X-RAY DIFFRACTION'
r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION'
r_mcangle_it 1.870 2.000 ? 4102 'X-RAY DIFFRACTION'
r_scbond_it 2.785 3.000 ? 1955 'X-RAY DIFFRACTION'
r_scangle_it 4.223 4.500 ? 1708 'X-RAY DIFFRACTION'
r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION'
r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION'
r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION'
#
_refine_ls_shell.pdbx_total_number_of_bins_used 20
_refine_ls_shell.d_res_high 1.50
_refine_ls_shell.d_res_low 1.543
_refine_ls_shell.number_reflns_R_work 2295
_refine_ls_shell.R_factor_R_work 0.237
_refine_ls_shell.percent_reflns_obs 36.77
_refine_ls_shell.R_factor_R_free 0.278
_refine_ls_shell.R_factor_R_free_error ?
_refine_ls_shell.percent_reflns_R_free ?
_refine_ls_shell.number_reflns_R_free 133
_refine_ls_shell.number_reflns_all ?
_refine_ls_shell.R_factor_all ?
_refine_ls_shell.number_reflns_obs ?
_refine_ls_shell.redundancy_reflns_obs ?
_refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION'
#
_struct.entry_id 2O3S
_struct.title
'Structural Basis for Formation and Hydrolysis of Calcium Messenger Cyclic ADP-ribose by Human CD38'
_struct.pdbx_descriptor 'ADP-ribosyl cyclase 1 (E.C.3.2.2.5)'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 2O3S
_struct_keywords.pdbx_keywords HYDROLASE
_struct_keywords.text
'Human CD38 E226G mutant, the catalytic pocket, cADPR formation and hydrolysis, substrate binding, HYDROLASE'
#
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 ?
#
loop_
_struct_biol.id
_struct_biol.details
_struct_biol.pdbx_parent_biol_id
1 'There are two biological units in the crystallographic asymmetric unit.' ?
2 ? ?
#
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 ARG A 20 ? HIS A 36 ? ARG A 58 HIS A 74 1 ? 17
HELX_P HELX_P2 2 PRO A 37 ? ARG A 40 ? PRO A 75 ARG A 78 5 ? 4
HELX_P HELX_P3 3 ASP A 43 ? ILE A 56 ? ASP A 81 ILE A 94 1 ? 14
HELX_P HELX_P4 4 THR A 64 ? ASP A 67 ? THR A 102 ASP A 105 5 ? 4
HELX_P HELX_P5 5 TYR A 68 ? GLY A 75 ? TYR A 106 GLY A 113 1 ? 8
HELX_P HELX_P6 6 PRO A 80 ? LYS A 83 ? PRO A 118 LYS A 121 5 ? 4
HELX_P HELX_P7 7 ILE A 90 ? VAL A 100 ? ILE A 128 VAL A 138 1 ? 11
HELX_P HELX_P8 8 THR A 106 ? ASP A 109 ? THR A 144 ASP A 147 5 ? 4
HELX_P HELX_P9 9 THR A 110 ? ASP A 117 ? THR A 148 ASP A 155 1 ? 8
HELX_P HELX_P10 10 ASN A 145 ? ALA A 162 ? ASN A 183 ALA A 200 1 ? 18
HELX_P HELX_P11 11 SER A 182 ? VAL A 187 ? SER A 220 VAL A 225 1 ? 6
HELX_P HELX_P12 12 VAL A 187 ? LEU A 192 ? VAL A 225 LEU A 230 1 ? 6
HELX_P HELX_P13 13 ASP A 214 ? GLN A 217 ? ASP A 252 GLN A 255 5 ? 4
HELX_P HELX_P14 14 ASP A 218 ? ARG A 231 ? ASP A 256 ARG A 269 1 ? 14
HELX_P HELX_P15 15 ARG A 242 ? ASN A 252 ? ARG A 280 ASN A 290 1 ? 11
HELX_P HELX_P16 16 ARG B 20 ? HIS B 36 ? ARG B 58 HIS B 74 1 ? 17
HELX_P HELX_P17 17 PRO B 37 ? ARG B 40 ? PRO B 75 ARG B 78 5 ? 4
HELX_P HELX_P18 18 ASP B 43 ? ILE B 56 ? ASP B 81 ILE B 94 1 ? 14
HELX_P HELX_P19 19 GLU B 65 ? ASP B 67 ? GLU B 103 ASP B 105 5 ? 3
HELX_P HELX_P20 20 TYR B 68 ? GLY B 75 ? TYR B 106 GLY B 113 1 ? 8
HELX_P HELX_P21 21 ILE B 90 ? GLN B 101 ? ILE B 128 GLN B 139 1 ? 12
HELX_P HELX_P22 22 THR B 106 ? ASP B 109 ? THR B 144 ASP B 147 5 ? 4
HELX_P HELX_P23 23 THR B 110 ? ASP B 117 ? THR B 148 ASP B 155 1 ? 8
HELX_P HELX_P24 24 ASN B 145 ? GLU B 160 ? ASN B 183 GLU B 198 1 ? 16
HELX_P HELX_P25 25 SER B 186 ? ASN B 191 ? SER B 224 ASN B 229 1 ? 6
HELX_P HELX_P26 26 ASP B 214 ? GLN B 217 ? ASP B 252 GLN B 255 5 ? 4
HELX_P HELX_P27 27 ASP B 218 ? ARG B 231 ? ASP B 256 ARG B 269 1 ? 14
HELX_P HELX_P28 28 ARG B 242 ? ASN B 252 ? ARG B 280 ASN B 290 1 ? 11
#
_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
disulf1 disulf ? A CYS 29 SG ? ? ? 1_555 A CYS 44 SG ? ? A CYS 67 A CYS 82 1_555 ? ? ? ? ? ? ? 2.118 ?
disulf2 disulf ? A CYS 61 SG ? ? ? 1_555 A CYS 142 SG ? ? A CYS 99 A CYS 180 1_555 ? ? ? ? ? ? ? 2.094 ?
disulf3 disulf ? A CYS 81 SG ? ? ? 1_555 A CYS 163 SG ? ? A CYS 119 A CYS 201 1_555 ? ? ? ? ? ? ? 2.061 ?
disulf4 disulf ? A CYS 122 SG ? ? ? 1_555 A CYS 135 SG ? ? A CYS 160 A CYS 173 1_555 ? ? ? ? ? ? ? 2.112 ?
disulf5 disulf ? A CYS 216 SG ? ? ? 1_555 A CYS 237 SG ? ? A CYS 254 A CYS 275 1_555 ? ? ? ? ? ? ? 2.117 ?
disulf6 disulf ? A CYS 249 SG ? ? ? 1_555 A CYS 258 SG ? ? A CYS 287 A CYS 296 1_555 ? ? ? ? ? ? ? 2.048 ?
disulf7 disulf ? B CYS 29 SG ? ? ? 1_555 B CYS 44 SG ? ? B CYS 67 B CYS 82 1_555 ? ? ? ? ? ? ? 2.084 ?
disulf8 disulf ? B CYS 61 SG ? ? ? 1_555 B CYS 142 SG ? ? B CYS 99 B CYS 180 1_555 ? ? ? ? ? ? ? 2.111 ?
disulf9 disulf ? B CYS 81 SG ? ? ? 1_555 B CYS 163 SG ? ? B CYS 119 B CYS 201 1_555 ? ? ? ? ? ? ? 2.058 ?
disulf10 disulf ? B CYS 122 SG ? ? ? 1_555 B CYS 135 SG ? ? B CYS 160 B CYS 173 1_555 ? ? ? ? ? ? ? 2.130 ?
disulf11 disulf ? B CYS 216 SG ? ? ? 1_555 B CYS 237 SG ? ? B CYS 254 B CYS 275 1_555 ? ? ? ? ? ? ? 2.040 ?
disulf12 disulf ? B CYS 249 SG ? ? ? 1_555 B CYS 258 SG ? ? B CYS 287 B CYS 296 1_555 ? ? ? ? ? ? ? 2.679 ?
#
_struct_conn_type.id disulf
_struct_conn_type.criteria ?
_struct_conn_type.reference ?
#
loop_
_struct_sheet.id
_struct_sheet.type
_struct_sheet.number_strands
_struct_sheet.details
A ? 2 ?
B ? 4 ?
C ? 2 ?
D ? 4 ?
#
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
B 1 2 ? parallel
B 2 3 ? parallel
B 3 4 ? parallel
C 1 2 ? anti-parallel
D 1 2 ? parallel
D 2 3 ? parallel
D 3 4 ? 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 GLY A 14 ? PRO A 15 ? ? GLY A 52 PRO A 53
A 2 SER A 134 ? CYS A 135 ? ? SER A 172 CYS A 173
B 1 LEU A 85 ? SER A 88 ? ? LEU A 123 SER A 126
B 2 ASP A 164 ? ASP A 171 ? ? ASP A 202 ASP A 209
B 3 VAL A 197 ? ILE A 205 ? ? VAL A 235 ILE A 243
B 4 GLN A 234 ? ILE A 240 ? ? GLN A 272 ILE A 278
C 1 GLY B 14 ? PRO B 15 ? ? GLY B 52 PRO B 53
C 2 SER B 134 ? CYS B 135 ? ? SER B 172 CYS B 173
D 1 LEU B 85 ? SER B 88 ? ? LEU B 123 SER B 126
D 2 ASP B 164 ? ASP B 171 ? ? ASP B 202 ASP B 209
D 3 VAL B 197 ? ILE B 205 ? ? VAL B 235 ILE B 243
D 4 GLN B 234 ? ILE B 240 ? ? GLN B 272 ILE B 278
#
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