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3Q86

Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with GTP

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0004550molecular_functionnucleoside diphosphate kinase activity
A0005524molecular_functionATP binding
A0005737cellular_componentcytoplasm
A0006183biological_processGTP biosynthetic process
A0006228biological_processUTP biosynthetic process
A0006241biological_processCTP biosynthetic process
A0009117biological_processnucleotide metabolic process
A0016301molecular_functionkinase activity
A0016740molecular_functiontransferase activity
A0046872molecular_functionmetal ion binding
B0000166molecular_functionnucleotide binding
B0004550molecular_functionnucleoside diphosphate kinase activity
B0005524molecular_functionATP binding
B0005737cellular_componentcytoplasm
B0006183biological_processGTP biosynthetic process
B0006228biological_processUTP biosynthetic process
B0006241biological_processCTP biosynthetic process
B0009117biological_processnucleotide metabolic process
B0016301molecular_functionkinase activity
B0016740molecular_functiontransferase activity
B0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues15
DetailsBINDING SITE FOR RESIDUE GTP A 158
ChainResidue
ALYS9
AGLU149
AMG159
AHOH206
AHOH218
AHOH227
BHOH210
ATYR49
AHIS52
APHE57
ATHR91
AVAL109
AGLY110
AASN112
AHIS115

site_idAC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MG A 159
ChainResidue
ATHR91
AARG102
AGTP158

site_idAC3
Number of Residues20
DetailsBINDING SITE FOR RESIDUE GTP B 158
ChainResidue
BLYS9
BTYR49
BHIS52
BPHE57
BTHR91
BARG102
BVAL109
BGLY110
BASN112
BHIS115
BGLY116
BMG159
BHOH179
BHOH195
BHOH196
BHOH208
BHOH209
BHOH210
BHOH211
BHOH212

site_idAC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MG B 159
ChainResidue
BGTP158
BHOH195
BHOH196

Functional Information from PROSITE/UniProt
site_idPS00469
Number of Residues9
DetailsNDPK Nucleoside diphosphate kinase (NDPK) active site signature. NiiHGSDSL
ChainResidueDetails
AASN112-LEU120

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsActive site: {"description":"Pros-phosphohistidine intermediate","evidences":[{"source":"HAMAP-Rule","id":"MF_00451","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00451","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

247536

PDB entries from 2026-01-14

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