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6G2N

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

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005829cellular_componentcytosol
A0006139biological_processnucleobase-containing compound metabolic process
A0006204biological_processIMP catabolic process
A0006249biological_processdCMP catabolic process
A0008252molecular_functionnucleotidase activity
A0008253molecular_function5'-nucleotidase activity
A0008254molecular_function3'-nucleotidase activity
A0009117biological_processnucleotide metabolic process
A0009223biological_processpyrimidine deoxyribonucleotide catabolic process
A0009264biological_processdeoxyribonucleotide catabolic process
A0016311biological_processdephosphorylation
A0016787molecular_functionhydrolase activity
A0016791molecular_functionphosphatase activity
A0019103molecular_functionpyrimidine nucleotide binding
A0042802molecular_functionidentical protein binding
A0046038biological_processGMP catabolic process
A0046045biological_processTMP catabolic process
A0046050biological_processUMP catabolic process
A0046055biological_processdGMP catabolic process
A0046059biological_processdAMP catabolic process
A0046074biological_processdTMP catabolic process
A0046079biological_processdUMP catabolic process
A0046872molecular_functionmetal ion binding
A0070062cellular_componentextracellular exosome
B0000166molecular_functionnucleotide binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005829cellular_componentcytosol
B0006139biological_processnucleobase-containing compound metabolic process
B0006204biological_processIMP catabolic process
B0006249biological_processdCMP catabolic process
B0008252molecular_functionnucleotidase activity
B0008253molecular_function5'-nucleotidase activity
B0008254molecular_function3'-nucleotidase activity
B0009117biological_processnucleotide metabolic process
B0009223biological_processpyrimidine deoxyribonucleotide catabolic process
B0009264biological_processdeoxyribonucleotide catabolic process
B0016311biological_processdephosphorylation
B0016787molecular_functionhydrolase activity
B0016791molecular_functionphosphatase activity
B0019103molecular_functionpyrimidine nucleotide binding
B0042802molecular_functionidentical protein binding
B0046038biological_processGMP catabolic process
B0046045biological_processTMP catabolic process
B0046050biological_processUMP catabolic process
B0046055biological_processdGMP catabolic process
B0046059biological_processdAMP catabolic process
B0046074biological_processdTMP catabolic process
B0046079biological_processdUMP catabolic process
B0046872molecular_functionmetal ion binding
B0070062cellular_componentextracellular exosome
Functional Information from PDB Data
site_idAC1
Number of Residues6
Detailsbinding site for residue MG A 301
ChainResidue
AASP14
AASP16
AASP149
AO84302
AHOH408
AHOH409

site_idAC2
Number of Residues24
Detailsbinding site for residue O84 A 302
ChainResidue
APHE48
AALA50
ATYR69
ASER104
ALEU106
ALEU107
AARG136
ALYS138
AMG301
AHOH402
AHOH404
AHOH406
AHOH408
AHOH409
AHOH411
AHOH419
AHOH430
AHOH442
AHOH459
AHOH490
AHOH512
AASP14
AASP16
APHE22

site_idAC3
Number of Residues6
Detailsbinding site for residue MG B 301
ChainResidue
BASP14
BASP16
BASP149
BO84302
BHOH420
BHOH421

site_idAC4
Number of Residues23
Detailsbinding site for residue O84 B 302
ChainResidue
BASP14
BASP16
BPHE22
BPHE48
BLEU49
BALA50
BTYR69
BSER104
BPRO105
BLEU106
BLEU107
BARG136
BLYS138
BMG301
BHOH403
BHOH409
BHOH411
BHOH420
BHOH421
BHOH458
BHOH465
BHOH480
BHOH492

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsActive site: {"description":"Nucleophile","evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues2
DetailsActive site: {"description":"Proton donor","evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues10
DetailsBinding site: {}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues2
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues4
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

246333

PDB entries from 2025-12-17

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