Loading
PDBj
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help

3B54

Saccharomyces cerevisiae nucleoside diphosphate kinase

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0004550molecular_functionnucleoside diphosphate kinase activity
A0005524molecular_functionATP binding
A0005737cellular_componentcytoplasm
A0005739cellular_componentmitochondrion
A0005758cellular_componentmitochondrial intermembrane space
A0005829cellular_componentcytosol
A0006183biological_processGTP biosynthetic process
A0006228biological_processUTP biosynthetic process
A0006241biological_processCTP biosynthetic process
A0006281biological_processDNA repair
A0006974biological_processDNA damage response
A0009117biological_processnucleotide metabolic process
A0009142biological_processnucleoside triphosphate biosynthetic process
A0016301molecular_functionkinase activity
A0016740molecular_functiontransferase activity
A0046872molecular_functionmetal ion binding
B0000166molecular_functionnucleotide binding
B0004550molecular_functionnucleoside diphosphate kinase activity
B0005524molecular_functionATP binding
B0005737cellular_componentcytoplasm
B0005739cellular_componentmitochondrion
B0005758cellular_componentmitochondrial intermembrane space
B0005829cellular_componentcytosol
B0006183biological_processGTP biosynthetic process
B0006228biological_processUTP biosynthetic process
B0006241biological_processCTP biosynthetic process
B0006281biological_processDNA repair
B0006974biological_processDNA damage response
B0009117biological_processnucleotide metabolic process
B0009142biological_processnucleoside triphosphate biosynthetic process
B0016301molecular_functionkinase activity
B0016740molecular_functiontransferase activity
B0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PO4 A 154
ChainResidue
AARG89
AARG106
AHIS119

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PO4 B 154
ChainResidue
BARG89
BARG106
BHIS119
BGLY120

Functional Information from PROSITE/UniProt
site_idPS00469
Number of Residues9
DetailsNDPK Nucleoside diphosphate kinase (NDPK) active site signature. NvcHGSDSV
ChainResidueDetails
AASN116-VAL124

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Pros-phosphohistidine intermediate => ECO:0000250|UniProtKB:P22392
ChainResidueDetails
AHIS119
BHIS119

site_idSWS_FT_FI2
Number of Residues12
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P22392
ChainResidueDetails
ALYS13
BTHR95
BARG106
BASN116
APHE61
AARG89
ATHR95
AARG106
AASN116
BLYS13
BPHE61
BARG89

site_idSWS_FT_FI3
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:18407956
ChainResidueDetails
ATHR95
BTHR95

Catalytic Information from CSA
site_idCSA1
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
ALYS13
AASN116

site_idCSA2
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
BLYS13
BASN116

site_idCSA3
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
ALYS13
ATYR53

site_idCSA4
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
BLYS13
BTYR53

237735

PDB entries from 2025-06-18

PDB statisticsPDBj update infoContact PDBjnumon