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2DY9

Crystal structure of nucleoside diphosphate kinase in complex with ADP

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 Residues4
DetailsBINDING SITE FOR RESIDUE MG A 601
ChainResidue
AADP501
AHOH732
AHOH735
AHOH774

site_idAC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL A 701
ChainResidue
AALA96
AALA102
AALA103

site_idAC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL A 702
ChainResidue
AALA152
AARG150
AALA151

site_idAC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL B 703
ChainResidue
BGLY95
BALA96
BALA103

site_idAC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL B 704
ChainResidue
BARG150
BALA151
BALA152

site_idAC6
Number of Residues14
DetailsBINDING SITE FOR RESIDUE ADP A 501
ChainResidue
ALYS15
AHIS58
APHE63
ALEU67
AARG91
ATHR97
AARG108
AILE119
AASN121
AMG601
AHOH714
AHOH730
AHOH754
AHOH764

Functional Information from PROSITE/UniProt
site_idPS00469
Number of Residues9
DetailsNDPK Nucleoside diphosphate kinase (NDPK) active site signature. NviHASDSK
ChainResidueDetails
AASN121-LYS129

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 Residues10
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00451","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
ALYS15
AASN121

site_idCSA2
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
BLYS15
BASN121

site_idCSA3
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
ALYS15
ATYR55

site_idCSA4
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
BLYS15
BTYR55

246031

PDB entries from 2025-12-10

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