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2DXD

Crystal structure of nucleoside diphosphate kinase in complex with ATP analog

Functional Information from GO Data
ChainGOidnamespacecontents
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
A0009142biological_processnucleoside triphosphate biosynthetic process
A0016301molecular_functionkinase activity
A0046872molecular_functionmetal ion 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
B0009142biological_processnucleoside triphosphate biosynthetic process
B0016301molecular_functionkinase activity
B0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CL A 701
ChainResidue
AGLY95
AALA96
AALA102
AALA103
AHOH877
AHOH923

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE CL B 702
ChainResidue
BALA103
BHOH884
BGLY95
BALA96
BALA102

site_idAC3
Number of Residues9
DetailsBINDING SITE FOR RESIDUE AMP A 501
ChainResidue
ALYS15
AHIS58
APHE63
ATHR97
AILE119
AASN121
AHOH763
AHOH782
AHOH871

site_idAC4
Number of Residues12
DetailsBINDING SITE FOR RESIDUE AMP B 502
ChainResidue
BLYS15
BTYR55
BHIS58
BPHE63
BTHR97
BARG108
BILE119
BASN121
BHOH723
BHOH755
BHOH790
BHOH905

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
DetailsACT_SITE: Pros-phosphohistidine intermediate => ECO:0000255|HAMAP-Rule:MF_00451
ChainResidueDetails
AHIS124
BHIS124

site_idSWS_FT_FI2
Number of Residues10
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00451
ChainResidueDetails
ALYS15
APHE63
AARG91
ATHR97
AARG108
BLYS15
BPHE63
BARG91
BTHR97
BARG108

219869

PDB entries from 2024-05-15

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