SIFTS
Sift was used to list the aminoacids of the input PBD, to obtain the entire secuence first and second structure and the accession ids.
GET https://www.ebi.ac.uk/pdbe/api/mappings/{pdb_id}
GET https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/{pdb_id}
GET https://www.ebi.ac.uk/pdbe/api/pdb/entry/summary/{pdb_id}
GET https://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/{pdb_id}
GET https://www.ebi.ac.uk/pdbe/api/pdb/entry/secondary_structure/{pdb_id}
GET https://www.ebi.ac.uk/pdbe/api/pdb/entry/residue_listing/{pdb_id}
MOBIDB
MobiDB was used to obtain the missing residues of the PDB
GET https://mobidb.bio.unipd.it/api/download?acc={acc}
UNIPROT
Uniprot was used to get the uniprot id of each aminoacids of the PDB sequence
GET https://rest.uniprot.org/uniprotkb/search?size=1&query={pdb_id}
[
{
"pdb_id": "String",
"related_uniprot_accessions": [
"String"
],
"summary": [
{
"related_structures": [],
"split_entry": [],
"title": "String",
"release_date": "String",
"experimental_method": [
"String"
],
"experimental_method_class": [
"String"
],
"revision_date": "String",
"entry_authors": [
"String",
"String",
"String"
],
"deposition_site": null,
"number_of_entities": {
"polypeptide": int,
"dna": int,
"ligand": int,
"dna/rna": int,
"rna": int,
"sugar": int,
"water": int,
"other": int,
"carbohydrate_polymer": int
},
"processing_site": null,
"deposition_date": "String",
"assemblies": [
{
"assembly_id": "String",
"form": "String",
"preferred": boolean,
"name": "String"
},
{
"assembly_id": "String",
"form": "String",
"preferred": false,
"name": "String"
}
]
}
],
"pdb_sequence": "String",
"chains": [
{
"chain_id": "String",
"residues": [
{
"name": "String",
"number": int
}
],
"secondary_structure": {}
}
],
"missing_residues_in_pdb": {
"derived-missing_residues-mobi-1thj_A": {
"source_id": "String",
"regions": [
[int]
],
"content_fraction": float,
"content_count": int,
"uniprot_source": "String"
}
}
}
]
[
{
"pdb_id": "1THJ",
"related_uniprot_accessions": [
"P40881"
],
"summary": [
{
"related_structures": [],
"split_entry": [],
"title": "CARBONIC ANHYDRASE FROM METHANOSARCINA",
"release_date": "19961014",
"experimental_method": [
"X-ray diffraction"
],
"experimental_method_class": [
"x-ray"
],
"revision_date": "20110713",
"entry_authors": [
"Kisker, C.",
"Schindelin, H.",
"Rees, D.C."
],
"deposition_site": null,
"number_of_entities": {
"polypeptide": 1,
"dna": 0,
"ligand": 1,
"dna/rna": 0,
"rna": 0,
"sugar": 0,
"water": 1,
"other": 0,
"carbohydrate_polymer": 0
},
"processing_site": null,
"deposition_date": "19960402",
"assemblies": [
{
"assembly_id": "1",
"form": "homo",
"preferred": true,
"name": "trimer"
},
{
"assembly_id": "2",
"form": "homo",
"preferred": false,
"name": "hexamer"
}
]
}
],
"pdb_sequence": "MQEITVDEFSNIRENPVTPWNPEPSAPVIDPTAYIDPEASVIGEVTIGANVMVSPMASIRSDEGMPIFVGDRSNVQDGVVLHALETINEEGEPIEDNIVEVDGKEYAVYIGNNVSLAHQSQVHGPAAVGDDTFIGMQAFVFKSKVGNNCVLEPRSAAIGVTIPDGRYIPAGMVVTSQAEADKLPEVTDDYAYSHTNEAVVYVNVHLAEGYKETS",
"chains": [
{
"chain_id": "A",
"residues": [
{
"name": "MET",
"number": 0
},
{
"name": "GLN",
"number": 1
},
{
"name": "GLU",
"number": 2
},
{
"name": "ILE",
"number": 3
},
{
"name": "THR",
"number": 4
},
{
"name": "VAL",
"number": 5
},
{
"name": "ASP",
"number": 6
},
{
"name": "GLU",
"number": 7
},
{
"name": "PHE",
"number": 8
},
{
"name": "SER",
"number": 9
},
{
"name": "ASN",
"number": 10
},
{
"name": "ILE",
"number": 11
},
{
"name": "ARG",
"number": 12
},
{
"name": "GLU",
"number": 13
},
{
"name": "ASN",
"number": 14
},
{
"name": "PRO",
"number": 15
},
{
"name": "VAL",
"number": 16
},
{
"name": "THR",
"number": 17
},
{
"name": "PRO",
"number": 18
},
{
"name": "TRP",
"number": 19
},
{
"name": "ASN",
"number": 20
},
{
"name": "PRO",
"number": 21
},
{
"name": "GLU",
"number": 22
},
{
"name": "PRO",
"number": 23
},
{
"name": "SER",
"number": 24
},
{
"name": "ALA",
"number": 25
},
{
"name": "PRO",
"number": 26
},
{
"name": "VAL",
"number": 27
},
{
"name": "ILE",
"number": 28
},
{
"name": "ASP",
"number": 29
},
{
"name": "PRO",
"number": 30
},
{
"name": "THR",
"number": 31
},
{
"name": "ALA",
"number": 32
},
{
"name": "TYR",
"number": 33
},
{
"name": "ILE",
"number": 34
},
{
"name": "ASP",
"number": 35
},
{
"name": "PRO",
"number": 36
},
{
"name": "GLU",
"number": 37
},
{
"name": "ALA",
"number": 38
},
{
"name": "SER",
"number": 39
},
{
"name": "VAL",
"number": 40
},
{
"name": "ILE",
"number": 41
},
{
"name": "GLY",
"number": 42
},
{
"name": "GLU",
"number": 43
},
{
"name": "VAL",
"number": 44
},
{
"name": "THR",
"number": 45
},
{
"name": "ILE",
"number": 46
},
{
"name": "GLY",
"number": 47
},
{
"name": "ALA",
"number": 48
},
{
"name": "ASN",
"number": 49
},
{
"name": "VAL",
"number": 50
},
{
"name": "MET",
"number": 51
},
{
"name": "VAL",
"number": 52
},
{
"name": "SER",
"number": 53
},
{
"name": "PRO",
"number": 54
},
{
"name": "MET",
"number": 55
},
{
"name": "ALA",
"number": 56
},
{
"name": "SER",
"number": 57
},
{
"name": "ILE",
"number": 58
},
{
"name": "ARG",
"number": 59
},
{
"name": "SER",
"number": 60
},
{
"name": "ASP",
"number": 61
},
{
"name": "GLU",
"number": 62
},
{
"name": "GLY",
"number": 63
},
{
"name": "MET",
"number": 64
},
{
"name": "PRO",
"number": 65
},
{
"name": "ILE",
"number": 66
},
{
"name": "PHE",
"number": 67
},
{
"name": "VAL",
"number": 68
},
{
"name": "GLY",
"number": 69
},
{
"name": "ASP",
"number": 70
},
{
"name": "ARG",
"number": 71
},
{
"name": "SER",
"number": 72
},
{
"name": "ASN",
"number": 73
},
{
"name": "VAL",
"number": 74
},
{
"name": "GLN",
"number": 75
},
{
"name": "ASP",
"number": 76
},
{
"name": "GLY",
"number": 77
},
{
"name": "VAL",
"number": 78
},
{
"name": "VAL",
"number": 79
},
{
"name": "LEU",
"number": 80
},
{
"name": "HIS",
"number": 81
},
{
"name": "ALA",
"number": 82
},
{
"name": "LEU",
"number": 83
},
{
"name": "GLU",
"number": 84
},
{
"name": "THR",
"number": 85
},
{
"name": "ILE",
"number": 86
},
{
"name": "ASN",
"number": 87
},
{
"name": "GLU",
"number": 88
},
{
"name": "GLU",
"number": 89
},
{
"name": "GLY",
"number": 90
},
{
"name": "GLU",
"number": 91
},
{
"name": "PRO",
"number": 92
},
{
"name": "ILE",
"number": 93
},
{
"name": "GLU",
"number": 94
},
{
"name": "ASP",
"number": 95
},
{
"name": "ASN",
"number": 96
},
{
"name": "ILE",
"number": 97
},
{
"name": "VAL",
"number": 98
},
{
"name": "GLU",
"number": 99
},
{
"name": "VAL",
"number": 100
},
{
"name": "ASP",
"number": 101
},
{
"name": "GLY",
"number": 102
},
{
"name": "LYS",
"number": 103
},
{
"name": "GLU",
"number": 104
},
{
"name": "TYR",
"number": 105
},
{
"name": "ALA",
"number": 106
},
{
"name": "VAL",
"number": 107
},
{
"name": "TYR",
"number": 108
},
{
"name": "ILE",
"number": 109
},
{
"name": "GLY",
"number": 110
},
{
"name": "ASN",
"number": 111
},
{
"name": "ASN",
"number": 112
},
{
"name": "VAL",
"number": 113
},
{
"name": "SER",
"number": 114
},
{
"name": "LEU",
"number": 115
},
{
"name": "ALA",
"number": 116
},
{
"name": "HIS",
"number": 117
},
{
"name": "GLN",
"number": 118
},
{
"name": "SER",
"number": 119
},
{
"name": "GLN",
"number": 120
},
{
"name": "VAL",
"number": 121
},
{
"name": "HIS",
"number": 122
},
{
"name": "GLY",
"number": 123
},
{
"name": "PRO",
"number": 124
},
{
"name": "ALA",
"number": 125
},
{
"name": "ALA",
"number": 126
},
{
"name": "VAL",
"number": 127
},
{
"name": "GLY",
"number": 128
},
{
"name": "ASP",
"number": 129
},
{
"name": "ASP",
"number": 130
},
{
"name": "THR",
"number": 131
},
{
"name": "PHE",
"number": 132
},
{
"name": "ILE",
"number": 133
},
{
"name": "GLY",
"number": 134
},
{
"name": "MET",
"number": 135
},
{
"name": "GLN",
"number": 136
},
{
"name": "ALA",
"number": 137
},
{
"name": "PHE",
"number": 138
},
{
"name": "VAL",
"number": 139
},
{
"name": "PHE",
"number": 140
},
{
"name": "LYS",
"number": 141
},
{
"name": "SER",
"number": 142
},
{
"name": "LYS",
"number": 143
},
{
"name": "VAL",
"number": 144
},
{
"name": "GLY",
"number": 145
},
{
"name": "ASN",
"number": 146
},
{
"name": "ASN",
"number": 147
},
{
"name": "CYS",
"number": 148
},
{
"name": "VAL",
"number": 149
},
{
"name": "LEU",
"number": 150
},
{
"name": "GLU",
"number": 151
},
{
"name": "PRO",
"number": 152
},
{
"name": "ARG",
"number": 153
},
{
"name": "SER",
"number": 154
},
{
"name": "ALA",
"number": 155
},
{
"name": "ALA",
"number": 156
},
{
"name": "ILE",
"number": 157
},
{
"name": "GLY",
"number": 158
},
{
"name": "VAL",
"number": 159
},
{
"name": "THR",
"number": 160
},
{
"name": "ILE",
"number": 161
},
{
"name": "PRO",
"number": 162
},
{
"name": "ASP",
"number": 163
},
{
"name": "GLY",
"number": 164
},
{
"name": "ARG",
"number": 165
},
{
"name": "TYR",
"number": 166
},
{
"name": "ILE",
"number": 167
},
{
"name": "PRO",
"number": 168
},
{
"name": "ALA",
"number": 169
},
{
"name": "GLY",
"number": 170
},
{
"name": "MET",
"number": 171
},
{
"name": "VAL",
"number": 172
},
{
"name": "VAL",
"number": 173
},
{
"name": "THR",
"number": 174
},
{
"name": "SER",
"number": 175
},
{
"name": "GLN",
"number": 176
},
{
"name": "ALA",
"number": 177
},
{
"name": "GLU",
"number": 178
},
{
"name": "ALA",
"number": 179
},
{
"name": "ASP",
"number": 180
},
{
"name": "LYS",
"number": 181
},
{
"name": "LEU",
"number": 182
},
{
"name": "PRO",
"number": 183
},
{
"name": "GLU",
"number": 184
},
{
"name": "VAL",
"number": 185
},
{
"name": "THR",
"number": 186
},
{
"name": "ASP",
"number": 187
},
{
"name": "ASP",
"number": 188
},
{
"name": "TYR",
"number": 189
},
{
"name": "ALA",
"number": 190
},
{
"name": "TYR",
"number": 191
},
{
"name": "SER",
"number": 192
},
{
"name": "HIS",
"number": 193
},
{
"name": "THR",
"number": 194
},
{
"name": "ASN",
"number": 195
},
{
"name": "GLU",
"number": 196
},
{
"name": "ALA",
"number": 197
},
{
"name": "VAL",
"number": 198
},
{
"name": "VAL",
"number": 199
},
{
"name": "TYR",
"number": 200
},
{
"name": "VAL",
"number": 201
},
{
"name": "ASN",
"number": 202
},
{
"name": "VAL",
"number": 203
},
{
"name": "HIS",
"number": 204
},
{
"name": "LEU",
"number": 205
},
{
"name": "ALA",
"number": 206
},
{
"name": "GLU",
"number": 207
},
{
"name": "GLY",
"number": 208
},
{
"name": "TYR",
"number": 209
},
{
"name": "LYS",
"number": 210
},
{
"name": "GLU",
"number": 211
},
{
"name": "THR",
"number": 212
},
{
"name": "SER",
"number": 213
}
],
"secondary_structure": {}
},
{
"chain_id": "C",
"residues": [
{
"name": "MET",
"number": 0
},
{
"name": "GLN",
"number": 1
},
{
"name": "GLU",
"number": 2
},
{
"name": "ILE",
"number": 3
},
{
"name": "THR",
"number": 4
},
{
"name": "VAL",
"number": 5
},
{
"name": "ASP",
"number": 6
},
{
"name": "GLU",
"number": 7
},
{
"name": "PHE",
"number": 8
},
{
"name": "SER",
"number": 9
},
{
"name": "ASN",
"number": 10
},
{
"name": "ILE",
"number": 11
},
{
"name": "ARG",
"number": 12
},
{
"name": "GLU",
"number": 13
},
{
"name": "ASN",
"number": 14
},
{
"name": "PRO",
"number": 15
},
{
"name": "VAL",
"number": 16
},
{
"name": "THR",
"number": 17
},
{
"name": "PRO",
"number": 18
},
{
"name": "TRP",
"number": 19
},
{
"name": "ASN",
"number": 20
},
{
"name": "PRO",
"number": 21
},
{
"name": "GLU",
"number": 22
},
{
"name": "PRO",
"number": 23
},
{
"name": "SER",
"number": 24
},
{
"name": "ALA",
"number": 25
},
{
"name": "PRO",
"number": 26
},
{
"name": "VAL",
"number": 27
},
{
"name": "ILE",
"number": 28
},
{
"name": "ASP",
"number": 29
},
{
"name": "PRO",
"number": 30
},
{
"name": "THR",
"number": 31
},
{
"name": "ALA",
"number": 32
},
{
"name": "TYR",
"number": 33
},
{
"name": "ILE",
"number": 34
},
{
"name": "ASP",
"number": 35
},
{
"name": "PRO",
"number": 36
},
{
"name": "GLU",
"number": 37
},
{
"name": "ALA",
"number": 38
},
{
"name": "SER",
"number": 39
},
{
"name": "VAL",
"number": 40
},
{
"name": "ILE",
"number": 41
},
{
"name": "GLY",
"number": 42
},
{
"name": "GLU",
"number": 43
},
{
"name": "VAL",
"number": 44
},
{
"name": "THR",
"number": 45
},
{
"name": "ILE",
"number": 46
},
{
"name": "GLY",
"number": 47
},
{
"name": "ALA",
"number": 48
},
{
"name": "ASN",
"number": 49
},
{
"name": "VAL",
"number": 50
},
{
"name": "MET",
"number": 51
},
{
"name": "VAL",
"number": 52
},
{
"name": "SER",
"number": 53
},
{
"name": "PRO",
"number": 54
},
{
"name": "MET",
"number": 55
},
{
"name": "ALA",
"number": 56
},
{
"name": "SER",
"number": 57
},
{
"name": "ILE",
"number": 58
},
{
"name": "ARG",
"number": 59
},
{
"name": "SER",
"number": 60
},
{
"name": "ASP",
"number": 61
},
{
"name": "GLU",
"number": 62
},
{
"name": "GLY",
"number": 63
},
{
"name": "MET",
"number": 64
},
{
"name": "PRO",
"number": 65
},
{
"name": "ILE",
"number": 66
},
{
"name": "PHE",
"number": 67
},
{
"name": "VAL",
"number": 68
},
{
"name": "GLY",
"number": 69
},
{
"name": "ASP",
"number": 70
},
{
"name": "ARG",
"number": 71
},
{
"name": "SER",
"number": 72
},
{
"name": "ASN",
"number": 73
},
{
"name": "VAL",
"number": 74
},
{
"name": "GLN",
"number": 75
},
{
"name": "ASP",
"number": 76
},
{
"name": "GLY",
"number": 77
},
{
"name": "VAL",
"number": 78
},
{
"name": "VAL",
"number": 79
},
{
"name": "LEU",
"number": 80
},
{
"name": "HIS",
"number": 81
},
{
"name": "ALA",
"number": 82
},
{
"name": "LEU",
"number": 83
},
{
"name": "GLU",
"number": 84
},
{
"name": "THR",
"number": 85
},
{
"name": "ILE",
"number": 86
},
{
"name": "ASN",
"number": 87
},
{
"name": "GLU",
"number": 88
},
{
"name": "GLU",
"number": 89
},
{
"name": "GLY",
"number": 90
},
{
"name": "GLU",
"number": 91
},
{
"name": "PRO",
"number": 92
},
{
"name": "ILE",
"number": 93
},
{
"name": "GLU",
"number": 94
},
{
"name": "ASP",
"number": 95
},
{
"name": "ASN",
"number": 96
},
{
"name": "ILE",
"number": 97
},
{
"name": "VAL",
"number": 98
},
{
"name": "GLU",
"number": 99
},
{
"name": "VAL",
"number": 100
},
{
"name": "ASP",
"number": 101
},
{
"name": "GLY",
"number": 102
},
{
"name": "LYS",
"number": 103
},
{
"name": "GLU",
"number": 104
},
{
"name": "TYR",
"number": 105
},
{
"name": "ALA",
"number": 106
},
{
"name": "VAL",
"number": 107
},
{
"name": "TYR",
"number": 108
},
{
"name": "ILE",
"number": 109
},
{
"name": "GLY",
"number": 110
},
{
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],
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}
}
]