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2B8P

Crystal structure of Acanthamoeba polyphaga mimivirus NDK, the first viral nucleoside diphosphate kinase

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0004550molecular_functionnucleoside diphosphate kinase activity
A0005524molecular_functionATP binding
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
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 Residues6
DetailsBINDING SITE FOR RESIDUE SO4 A 5000
ChainResidue
ALYS9
ATYR50
AARG86
AARG99
AASN109
AHIS112

site_idAC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO4 B 5001
ChainResidue
BARG99
BASN109
BHIS112
BHOH5036
AHOH5037
BLYS9
BTYR50

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 A 5002
ChainResidue
AASN91
AILE92
AARG99
AILE106
AHOH5030

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 B 5003
ChainResidue
AARG107
BHIS53
BGLN56
BTYR58

Functional Information from PROSITE/UniProt
site_idPS00469
Number of Residues9
DetailsNDPK Nucleoside diphosphate kinase (NDPK) active site signature. NliHASDSE
ChainResidueDetails
AASN109-GLU117

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Pros-phosphohistidine intermediate => ECO:0000255|PROSITE-ProRule:PRU10030
ChainResidueDetails
AHIS112
BHIS112

site_idSWS_FT_FI2
Number of Residues10
DetailsBINDING:
ChainResidueDetails
ALYS9
BASN109
ATYR58
AARG86
AARG99
AASN109
BLYS9
BTYR58
BARG86
BARG99

Catalytic Information from CSA
site_idCSA1
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
AASN109
ALYS9

site_idCSA2
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
BASN109
BLYS9

site_idCSA3
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
ATYR50
ALYS9

site_idCSA4
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
BTYR50
BLYS9

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PDB entries from 2025-06-11

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