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3EMT

Crystal structure of the mimivirus NDK +Kpn-R107G double mutant complexed with dGDP

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 Residues3
DetailsBINDING SITE FOR RESIDUE MG A 202
ChainResidue
ADGI201
AHOH233
AHOH236

site_idAC2
Number of Residues18
DetailsBINDING SITE FOR RESIDUE DGI A 201
ChainResidue
AARG103
AILE110
AASN113
AMG202
AHOH213
AHOH229
AHOH232
AHOH236
AHOH242
AHOH252
AHOH280
AHOH282
ALYS9
ATYR50
AHIS53
ATYR58
AARG86
ATHR92

site_idAC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MG B 202
ChainResidue
BDGI201
BHOH224
BHOH269

site_idAC4
Number of Residues16
DetailsBINDING SITE FOR RESIDUE DGI B 201
ChainResidue
BLYS9
BTYR50
BHIS53
BTYR58
BARG86
BTHR92
BARG103
BILE110
BASN113
BMG202
BHOH205
BHOH211
BHOH265
BHOH269
BHOH274
BHOH278

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

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PDB entries from 2025-12-17

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