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4L6C

Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor pib-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
AHOH417
AHOH418

site_idAC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 A 302
ChainResidue
ATHR130
ASER131
ALYS165
AMG301
A0BT303
AHOH417
AHOH439
AASP41
AMET42
AASP43

site_idAC3
Number of Residues13
DetailsBINDING SITE FOR RESIDUE 0BT A 303
ChainResidue
APHE75
ATRP76
AVAL77
ATRP96
AILE133
ALYS134
AARG163
APO4302
AHOH415
AHOH418
AHOH447
AHOH449
AHOH567

site_idAC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE GOL A 304
ChainResidue
AARG73
AGLY74
AHIS198
AASN199
AGLN200
AHIS201
ALEU202
AHOH471
AHOH500

site_idAC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE GOL A 305
ChainResidue
ASER27
AASN28
AALA119
ATHR124
AASP125
AVAL126
AGLN158
AGOL309
AHOH490

site_idAC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL A 306
ChainResidue
ATRP76
AARG177
APRO178
AASP179

site_idAC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL A 307
ChainResidue
ATYR138
ATRP214
AALA215
AASP216
AASP217
ATRP218
ALYS219
AHOH510

site_idAC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL A 308
ChainResidue
AASP48
ALEU108
AALA196
ACYS197
AHOH436
AHOH484
AHOH511

site_idAC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE GOL A 309
ChainResidue
AASP154
AGLN158
AGOL305

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL A 310
ChainResidue
AARG37
ASER169
AALA170
AASP171
AGLU184
AHOH470

site_idBC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO A 311
ChainResidue
APRO65
APHE66
AHOH448

site_idBC3
Number of Residues9
DetailsBINDING SITE FOR RESIDUE EDO A 312
ChainResidue
AASN28
AALA29
AGLY33
AARG34
AALA35
AASP125
AALA183
APRO185
AHOH538

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

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PDB entries from 2025-06-11

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