Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

4NFL

Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor NPB-T

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
APO4302
AHOH401
AHOH402

site_idAC2
Number of Residues15
DetailsBINDING SITE FOR RESIDUE PO4 A 302
ChainResidue
ATHR130
ASER131
ALYS143
ALYS165
AMG301
A2JW303
AGOL310
AGOL311
AHOH401
AHOH402
AHOH418
AHOH680
AASP41
AMET42
AASP43

site_idAC3
Number of Residues19
DetailsBINDING SITE FOR RESIDUE 2JW A 303
ChainResidue
APHE75
ATRP76
AVAL77
ATRP96
ASER131
AILE133
ALYS134
AARG163
AARG177
APO4302
AHOH402
AHOH429
AHOH455
AHOH542
AHOH600
AHOH678
AHOH679
AHOH681
AHOH683

site_idAC4
Number of Residues11
DetailsBINDING SITE FOR RESIDUE TRS A 304
ChainResidue
ATYR138
ATRP214
AALA215
AASP216
AASP217
ATRP218
ALYS219
AGOL309
AHOH578
AHOH638
AHOH689

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL A 305
ChainResidue
AASP48
AGLY51
AARG55
APRO86
AHOH408

site_idAC6
Number of Residues9
DetailsBINDING SITE FOR RESIDUE GOL A 306
ChainResidue
ASER27
AASN28
AALA119
ATHR124
AASP125
AVAL126
AGLN158
AHOH541
AHOH653

site_idAC7
Number of Residues10
DetailsBINDING SITE FOR RESIDUE GOL A 307
ChainResidue
AASN100
APHE103
ATYR141
APEG312
AHOH420
AHOH506
AHOH592
AHOH642
AHOH655
AHOH687

site_idAC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL A 308
ChainResidue
APHE75
ATRP76
AARG177
APRO178
AASP179
AHOH480
AHOH572
AHOH588

site_idAC9
Number of Residues10
DetailsBINDING SITE FOR RESIDUE GOL A 309
ChainResidue
AGLY110
AGLU113
AALA114
ATRP214
AALA215
ATRP218
ATRS304
AHOH447
AHOH496
AHOH571

site_idBC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL A 310
ChainResidue
AHOH523
AHOH678
AASP43
AGLU50
APHE75
APO4302
AGOL311
AHOH402

site_idBC2
Number of Residues11
DetailsBINDING SITE FOR RESIDUE GOL A 311
ChainResidue
APHE75
ATRP76
ASER131
APRO132
AARG163
APO4302
AGOL310
AHOH461
AHOH515
AHOH542
AHOH680

site_idBC3
Number of Residues11
DetailsBINDING SITE FOR RESIDUE PEG A 312
ChainResidue
APHE103
ALYS149
APRO207
AARG208
AARG209
AGOL307
APEG317
AHOH473
AHOH644
AHOH655
AHOH687

site_idBC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PEG A 313
ChainResidue
AASN28
AALA29
AGLY33
AALA35
AASP125
AALA183
AHOH568

site_idBC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PEG A 314
ChainResidue
ALYS56
AASN100
AGLU104
AHOH424
AHOH471
AHOH684

site_idBC6
Number of Residues12
DetailsBINDING SITE FOR RESIDUE PEG A 315
ChainResidue
AARG72
AARG73
AGLY74
ACYS197
AHIS198
AASN199
AGLN200
AHIS201
ALEU202
AHOH433
AHOH589
AHOH623

site_idBC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PEG A 316
ChainResidue
APRO178
AASP179
AILE180
AHIS191
AHOH682

site_idBC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PEG A 317
ChainResidue
AGLU148
ALYS149
ALEU204
APRO206
AARG208
APEG312
AHOH446
AHOH470

site_idBC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PEG A 318
ChainResidue
AASP48
AGLY51
ALEU69
AGLU90
AHOH422
AHOH615

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsACT_SITE: Nucleophile
ChainResidueDetails
AASP41

site_idSWS_FT_FI2
Number of Residues1
DetailsACT_SITE: Proton donor => ECO:0000305
ChainResidueDetails
AASP43

site_idSWS_FT_FI3
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:12352955
ChainResidueDetails
AASP41
AASP176

site_idSWS_FT_FI4
Number of Residues8
DetailsBINDING:
ChainResidueDetails
AASP43
APHE49
APHE75
ATRP76
AVAL77
ATRP96
ATHR130
ALYS165

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

222415

PDB entries from 2024-07-10

PDB statisticsPDBj update infoContact PDBjnumon