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6G2M

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

Functional Information from GO Data
ChainGOidnamespacecontents
A0008253molecular_function5'-nucleotidase activity
A0009264biological_processdeoxyribonucleotide catabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues4
Detailsbinding site for residue BME A 301
ChainResidue
ATHR195
AALA196
ACYS197
AGLN200

site_idAC2
Number of Residues4
Detailsbinding site for residue GOL A 302
ChainResidue
APRO65
APHE66
AHOH448
AHOH600

site_idAC3
Number of Residues8
Detailsbinding site for residue GOL A 303
ChainResidue
AALA114
ATRP214
AALA215
AASP216
ATRP218
AHOH408
AHOH608
AGLY110

site_idAC4
Number of Residues9
Detailsbinding site for residue GOL A 304
ChainResidue
AASN100
APHE103
ATYR141
AHOH428
AHOH443
AHOH578
AHOH591
AHOH647
AHOH649

site_idAC5
Number of Residues25
Detailsbinding site for residue O84 A 305
ChainResidue
AASP41
AASP43
APHE49
APHE75
ATRP76
AVAL77
ATRP96
ASER131
APRO132
AILE133
ALYS134
AARG163
ALYS165
AMG307
AHOH411
AHOH420
AHOH422
AHOH455
AHOH456
AHOH471
AHOH473
AHOH480
AHOH536
AHOH538
AHOH568

site_idAC6
Number of Residues6
Detailsbinding site for residue EDO A 306
ChainResidue
ASER27
AASN28
AALA119
ATHR124
AASP125
AVAL126

site_idAC7
Number of Residues6
Detailsbinding site for residue MG A 307
ChainResidue
AASP41
AASP43
AASP176
AO84305
AHOH422
AHOH455

site_idAC8
Number of Residues3
Detailsbinding site for residue K A 308
ChainResidue
APRO178
AILE180
AHIS191

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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