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4YIK

Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PVU

Functional Information from GO Data
ChainGOidnamespacecontents
A0008253molecular_function5'-nucleotidase activity
A0009264biological_processdeoxyribonucleotide catabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues6
Detailsbinding site for residue MG A 301
ChainResidue
AASP41
AASP43
AASP176
A2O2306
AHOH465
AHOH448

site_idAC2
Number of Residues9
Detailsbinding site for residue GOL A 302
ChainResidue
ATHR124
AASP125
AVAL126
AGLN158
AHOH585
AHOH414
ASER27
AASN28
AALA119

site_idAC3
Number of Residues9
Detailsbinding site for residue GOL A 303
ChainResidue
AGLY110
AGLU113
AALA114
ATRP214
AALA215
AASP216
ATRP218
AHOH620
AHOH406

site_idAC4
Number of Residues6
Detailsbinding site for residue GOL A 304
ChainResidue
ATRP76
AARG177
APRO178
AASP179
AHOH403
AHOH423

site_idAC5
Number of Residues8
Detailsbinding site for residue GOL A 305
ChainResidue
AARG37
ASER169
AALA170
AASP171
ASER188
AHOH440
AHOH592
AHOH429

site_idAC6
Number of Residues24
Detailsbinding site for residue 2O2 A 306
ChainResidue
AASP41
AASP43
APHE49
APHE75
ATRP76
AVAL77
ATRP96
ASER131
AILE133
ALYS134
AARG163
AMG301
ATRS307
AHOH573
AHOH465
AHOH422
AHOH448
AHOH410
AHOH418
AHOH442
AHOH480
AHOH427
AHOH474
AHOH438

site_idAC7
Number of Residues6
Detailsbinding site for residue TRS A 307
ChainResidue
AASP43
APHE49
APHE102
AILE133
A2O2306
AHOH410

site_idAC8
Number of Residues10
Detailsbinding site for residue PEG A 308
ChainResidue
AARG72
AARG73
ACYS197
AHIS198
AASN199
AGLN200
AHIS201
ALEU202
AHOH432
AHOH560

site_idAC9
Number of Residues9
Detailsbinding site for residue PEG A 309
ChainResidue
AGLU148
AARG210
AHIS212
AASP216
AHOH407
AHOH411
AHOH446
AHOH452
AHOH471

site_idAD1
Number of Residues9
Detailsbinding site for residue PEG A 310
ChainResidue
AASN28
AALA29
AGLY33
AARG34
AALA35
AASP125
AALA183
AHOH484
AHOH598

site_idAD2
Number of Residues7
Detailsbinding site for residue PEG A 311
ChainResidue
AARG208
AARG209
AHOH445
AHOH529
APHE103
ALYS149
APRO207

site_idAD3
Number of Residues6
Detailsbinding site for residue PEG A 312
ChainResidue
AGLU104
ALYS149
AHOH428
AHOH413
AHOH564
AHOH420

site_idAD4
Number of Residues7
Detailsbinding site for residue PO4 A 313
ChainResidue
APRO178
AASP179
AILE180
ATRP189
AHIS191
AARG208
AHOH576

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsActive site: {"description":"Nucleophile"}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues1
DetailsActive site: {"description":"Proton donor","evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12352955","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues8
DetailsBinding site: {}
ChainResidueDetails

Catalytic Information from CSA
site_idMCSA1
Number of Residues3
DetailsM-CSA 812
ChainResidueDetails
AASP41covalently attached, metal ligand, nucleofuge, nucleophile
AASP43metal ligand
AASP176metal ligand

239803

PDB entries from 2025-08-06

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