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3EJM

Crystal structure of the mimivirus NDK +Kpn mutant complexed with GDP

Functional Information from GO Data
ChainGOidnamespacecontents
A0004550molecular_functionnucleoside diphosphate kinase activity
A0006183biological_processGTP biosynthetic process
A0006228biological_processUTP biosynthetic process
A0006241biological_processCTP biosynthetic process
B0004550molecular_functionnucleoside diphosphate kinase activity
B0006183biological_processGTP biosynthetic process
B0006228biological_processUTP biosynthetic process
B0006241biological_processCTP biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues18
DetailsBINDING SITE FOR RESIDUE GDP A 201
ChainResidue
ALYS9
AARG111
AASN113
AMG203
AHOH213
AHOH214
AHOH234
AHOH236
AHOH248
AHOH265
ATYR50
AHIS53
ATYR58
AASN62
AARG86
ATHR92
AARG103
AILE110

site_idAC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MG A 203
ChainResidue
AGDP201
AHOH240
AHOH308

site_idAC3
Number of Residues20
DetailsBINDING SITE FOR RESIDUE GDP B 202
ChainResidue
BLYS9
BTYR50
BHIS53
BTYR58
BASN62
BARG86
BTHR92
BARG103
BILE110
BARG111
BASN113
BMG204
BHOH207
BHOH213
BHOH221
BHOH271
BHOH275
BHOH300
BHOH327
BHOH330

site_idAC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MG B 204
ChainResidue
BGDP202
BHOH306
BHOH322

Functional Information from PROSITE/UniProt
site_idPS00469
Number of Residues9
DetailsNDPK Nucleoside diphosphate kinase (NDPK) active site signature. NliHASDSE
ChainResidueDetails
AASN113-GLU121

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsActive site: {"description":"Pros-phosphohistidine intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10030","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues10
DetailsBinding site: {}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
AASN113
ALYS9

site_idCSA2
Number of Residues2
DetailsAnnotated By Reference To The Literature 1nsp
ChainResidueDetails
BASN113
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

238895

PDB entries from 2025-07-16

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