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4EK2

The structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to deoxyadenosine monophosphate

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
A0016310biological_processphosphorylation
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
B0016310biological_processphosphorylation
B0016740molecular_functiontransferase activity
B0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL A 201
ChainResidue
ALYS11
ATYR51
AHIS117

site_idAC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE DMS A 202
ChainResidue
ADA203
AHOH430
AGLU4
AARG5
APRO122
AALA125
AARG126
AILE129

site_idAC3
Number of Residues11
DetailsBINDING SITE FOR RESIDUE DA A 203
ChainResidue
AALA2
ALEU3
ADMS202
AHOH349
AHOH429
AHOH430
BPHE59
BLEU63
BTHR93
BASP112
BHOH399

site_idAC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE CL B 201
ChainResidue
BLYS11
BTYR51
BHIS117

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 202
ChainResidue
BPHE50
BTYR51
BVAL53
BHIS54
BGLU128

site_idAC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE DMS B 203
ChainResidue
BGLU4
BARG5
BPRO122
BARG126

Functional Information from PROSITE/UniProt
site_idPS00469
Number of Residues9
DetailsNDPK Nucleoside diphosphate kinase (NDPK) active site signature. NavHGSDAP
ChainResidueDetails
AASN114-PRO122

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Pros-phosphohistidine intermediate => ECO:0000255|HAMAP-Rule:MF_00451
ChainResidueDetails
AHIS117
BHIS117

site_idSWS_FT_FI2
Number of Residues12
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00451
ChainResidueDetails
ALYS11
BTHR93
BARG104
BASN114
APHE59
AARG87
ATHR93
AARG104
AASN114
BLYS11
BPHE59
BARG87

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PDB entries from 2024-04-24

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