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3ZE3

Crystal structure of the integral membrane diacylglycerol kinase - delta7

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0001727molecular_functionlipid kinase activity
A0004143molecular_functionATP-dependent diacylglycerol kinase activity
A0005524molecular_functionATP binding
A0005886cellular_componentplasma membrane
A0006629biological_processlipid metabolic process
A0006654biological_processphosphatidic acid biosynthetic process
A0008610biological_processlipid biosynthetic process
A0008654biological_processphospholipid biosynthetic process
A0009411biological_processresponse to UV
A0016020cellular_componentmembrane
A0016301molecular_functionkinase activity
A0016740molecular_functiontransferase activity
A0042802molecular_functionidentical protein binding
A0046872molecular_functionmetal ion binding
B0000166molecular_functionnucleotide binding
B0001727molecular_functionlipid kinase activity
B0004143molecular_functionATP-dependent diacylglycerol kinase activity
B0005524molecular_functionATP binding
B0005886cellular_componentplasma membrane
B0006629biological_processlipid metabolic process
B0006654biological_processphosphatidic acid biosynthetic process
B0008610biological_processlipid biosynthetic process
B0008654biological_processphospholipid biosynthetic process
B0009411biological_processresponse to UV
B0016020cellular_componentmembrane
B0016301molecular_functionkinase activity
B0016740molecular_functiontransferase activity
B0042802molecular_functionidentical protein binding
B0046872molecular_functionmetal ion binding
C0000166molecular_functionnucleotide binding
C0001727molecular_functionlipid kinase activity
C0004143molecular_functionATP-dependent diacylglycerol kinase activity
C0005524molecular_functionATP binding
C0005886cellular_componentplasma membrane
C0006629biological_processlipid metabolic process
C0006654biological_processphosphatidic acid biosynthetic process
C0008610biological_processlipid biosynthetic process
C0008654biological_processphospholipid biosynthetic process
C0009411biological_processresponse to UV
C0016020cellular_componentmembrane
C0016301molecular_functionkinase activity
C0016740molecular_functiontransferase activity
C0042802molecular_functionidentical protein binding
C0046872molecular_functionmetal ion binding
D0000166molecular_functionnucleotide binding
D0001727molecular_functionlipid kinase activity
D0004143molecular_functionATP-dependent diacylglycerol kinase activity
D0005524molecular_functionATP binding
D0005886cellular_componentplasma membrane
D0006629biological_processlipid metabolic process
D0006654biological_processphosphatidic acid biosynthetic process
D0008610biological_processlipid biosynthetic process
D0008654biological_processphospholipid biosynthetic process
D0009411biological_processresponse to UV
D0016020cellular_componentmembrane
D0016301molecular_functionkinase activity
D0016740molecular_functiontransferase activity
D0042802molecular_functionidentical protein binding
D0046872molecular_functionmetal ion binding
E0000166molecular_functionnucleotide binding
E0001727molecular_functionlipid kinase activity
E0004143molecular_functionATP-dependent diacylglycerol kinase activity
E0005524molecular_functionATP binding
E0005886cellular_componentplasma membrane
E0006629biological_processlipid metabolic process
E0006654biological_processphosphatidic acid biosynthetic process
E0008610biological_processlipid biosynthetic process
E0008654biological_processphospholipid biosynthetic process
E0009411biological_processresponse to UV
E0016020cellular_componentmembrane
E0016301molecular_functionkinase activity
E0016740molecular_functiontransferase activity
E0042802molecular_functionidentical protein binding
E0046872molecular_functionmetal ion binding
F0000166molecular_functionnucleotide binding
F0001727molecular_functionlipid kinase activity
F0004143molecular_functionATP-dependent diacylglycerol kinase activity
F0005524molecular_functionATP binding
F0005886cellular_componentplasma membrane
F0006629biological_processlipid metabolic process
F0006654biological_processphosphatidic acid biosynthetic process
F0008610biological_processlipid biosynthetic process
F0008654biological_processphospholipid biosynthetic process
F0009411biological_processresponse to UV
F0016020cellular_componentmembrane
F0016301molecular_functionkinase activity
F0016740molecular_functiontransferase activity
F0042802molecular_functionidentical protein binding
F0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA F 1122
ChainResidue
DLEU64
DASP107
DHOH2044
FSER60
FLEU64
FHOH2024

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE NA E 1122
ChainResidue
EHOH2020
DSER60
ESER61
ETHR111

site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN D 1122
ChainResidue
DGLU28
DGLU76
DFLC1123
DACT1124

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE FLC D 1123
ChainResidue
DGLU76
DZN1122
DACT1124
DHOH2048

site_idAC5
Number of Residues8
DetailsBINDING SITE FOR RESIDUE ACT D 1124
ChainResidue
DGLU28
DGLU69
DASN72
DSER73
DGLU76
DZN1122
DFLC1123
DHOH2047

site_idAC6
Number of Residues11
DetailsBINDING SITE FOR RESIDUE 78N B 1122
ChainResidue
AALA13
AALA14
ASER17
A78N1123
A78N1124
BSER98
BVAL101
BLEU102
BILE105
BILE110
B78N1123

site_idAC7
Number of Residues9
DetailsBINDING SITE FOR RESIDUE 78N B 1123
ChainResidue
AARG9
A78N1124
BGLU34
BVAL65
BGLU69
BALA108
BTRP112
BALA113
B78N1122

site_idAC8
Number of Residues12
DetailsBINDING SITE FOR RESIDUE 78M D 1125
ChainResidue
AGLN33
AGLU34
A78M1126
CTRP117
C78N1122
DTRP25
DALA29
DARG32
DGLN33
DVAL36
DHOH2017
DHOH2049

site_idAC9
Number of Residues10
DetailsBINDING SITE FOR RESIDUE 78N C 1122
ChainResidue
A78M1126
BALA46
BARG55
BHOH2010
CILE110
CILE114
CTRP117
CSER118
DGLN33
D78M1125

site_idBC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE 78N A 1122
ChainResidue
ATRP18
AARG22
ATRP25
AILE26
ALEU39
AMET63
AMET66

site_idBC2
Number of Residues10
DetailsBINDING SITE FOR RESIDUE 78M D 1126
ChainResidue
AALA30
APHE31
AGLU34
AGLU69
ALEU102
AILE105
AHOH2012
DARG22
DTRP25
DHOH2050

site_idBC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE 78M D 1127
ChainResidue
BTRP47
BHOH2006
BHOH2008
DLEU102
DVAL109
DALA113
DHOH2018
DHOH2043

site_idBC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE 78N C 1123
ChainResidue
ALEU40
ATRP47
A78M1126
CGLU34
CGLU69
CTRP112

site_idBC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE 78M D 1128
ChainResidue
ATRP117
BGLY35
BVAL36
DTRP47
DLEU48
DASP49
DPHE120

site_idBC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE 78N A 1123
ChainResidue
AVAL42
AALA46
AARG55
A78N1124
AHOH2016
B78N1122

site_idBC7
Number of Residues9
DetailsBINDING SITE FOR RESIDUE 78N A 1124
ChainResidue
AVAL50
AASP51
AALA52
AARG55
A78N1123
BILE114
BTRP117
B78N1122
B78N1123

site_idBC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE 78M A 1125
ChainResidue
AILE110
ATRP117
DALA46
DTRP47
DARG55

site_idBC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE 78M A 1126
ChainResidue
ACYS41
APHE120
AHOH2015
CLEU102
CILE105
C78N1122
C78N1123
DLEU39
D78M1125

Functional Information from PROSITE/UniProt
site_idPS01069
Number of Residues12
DetailsDAGK_PROKAR Prokaryotic diacylglycerol kinase signature. ElLNSAIEavVD
ChainResidueDetails
AGLU69-ASP80

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues150
DetailsTransmembrane: {"description":"Helical","evidences":[{"source":"PubMed","id":"12379131","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues10
DetailsTopological domain: {"description":"Periplasmic","evidences":[{"source":"PubMed","id":"12379131","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues150
DetailsTopological domain: {"description":"Cytoplasmic","evidences":[{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues138
DetailsTransmembrane: {"description":"Helical","evidences":[{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues12
DetailsTopological domain: {"description":"Periplasmic","evidences":[{"source":"PubMed","id":"15919996","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues6
DetailsActive site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues5
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues29
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"DEC-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of the integral membrane diacylglycerol kinase with Zn-Amppcp bound and its catalytic mechanism.","authors":["Li D.","Caffrey M."]}}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25055873","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI11
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25055873","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI12
Number of Residues15
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"JUN-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of an integral membrane enzyme determined by X-ray free electron laser femtocrystallography.","authors":["Li D.","Howe N.","Caffrey M."]}}]}
ChainResidueDetails

site_idSWS_FT_FI13
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25055873","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"JUN-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of an integral membrane enzyme determined by X-ray free electron laser femtocrystallography.","authors":["Li D.","Howe N.","Caffrey M."]}}]}
ChainResidueDetails

site_idSWS_FT_FI14
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"DEC-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of the integral membrane diacylglycerol kinase with Zn-Amppcp bound and its catalytic mechanism.","authors":["Li D.","Caffrey M."]}}]}
ChainResidueDetails

site_idSWS_FT_FI15
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI16
Number of Residues30
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"23676677","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"25055873","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26960129","evidenceCode":"ECO:0000305"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"DEC-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of the integral membrane diacylglycerol kinase with Zn-Amppcp bound and its catalytic mechanism.","authors":["Li D.","Caffrey M."]}}]}
ChainResidueDetails

238582

PDB entries from 2025-07-09

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