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6G2L

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

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
AEJ8303
AHOH414
AHOH432

site_idAC2
Number of Residues3
Detailsbinding site for residue BME A 302
ChainResidue
ACYS197
AGLN200
AHOH571

site_idAC3
Number of Residues25
Detailsbinding site for residue EJ8 A 303
ChainResidue
AASP41
AASP43
APHE49
APHE75
ATRP76
AVAL77
ATRP96
ATHR130
ASER131
AILE133
ALYS134
AARG163
ALYS165
AMG301
AHOH414
AHOH416
AHOH418
AHOH425
AHOH432
AHOH435
AHOH448
AHOH469
AHOH483
AHOH522
AHOH641

site_idAC4
Number of Residues9
Detailsbinding site for residue GOL A 304
ChainResidue
ASER27
AASN28
AALA119
ATHR124
AASP125
AVAL126
AGLN158
AHOH403
AHOH577

site_idAC5
Number of Residues6
Detailsbinding site for residue GOL A 305
ChainResidue
AARG37
AALA170
AASP171
ASER188
AHOH402
AHOH502

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

247536

PDB entries from 2026-01-14

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