Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3ZE3

Crystal structure of the integral membrane diacylglycerol kinase - delta7

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0001727	molecular_function	lipid kinase activity
A	0004143	molecular_function	ATP-dependent diacylglycerol kinase activity
A	0005524	molecular_function	ATP binding
A	0005886	cellular_component	plasma membrane
A	0006629	biological_process	lipid metabolic process
A	0006654	biological_process	phosphatidic acid biosynthetic process
A	0008610	biological_process	lipid biosynthetic process
A	0008654	biological_process	phospholipid biosynthetic process
A	0009411	biological_process	response to UV
A	0016020	cellular_component	membrane
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0042802	molecular_function	identical protein binding
A	0046872	molecular_function	metal ion binding
B	0000166	molecular_function	nucleotide binding
B	0001727	molecular_function	lipid kinase activity
B	0004143	molecular_function	ATP-dependent diacylglycerol kinase activity
B	0005524	molecular_function	ATP binding
B	0005886	cellular_component	plasma membrane
B	0006629	biological_process	lipid metabolic process
B	0006654	biological_process	phosphatidic acid biosynthetic process
B	0008610	biological_process	lipid biosynthetic process
B	0008654	biological_process	phospholipid biosynthetic process
B	0009411	biological_process	response to UV
B	0016020	cellular_component	membrane
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0042802	molecular_function	identical protein binding
B	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide binding
C	0001727	molecular_function	lipid kinase activity
C	0004143	molecular_function	ATP-dependent diacylglycerol kinase activity
C	0005524	molecular_function	ATP binding
C	0005886	cellular_component	plasma membrane
C	0006629	biological_process	lipid metabolic process
C	0006654	biological_process	phosphatidic acid biosynthetic process
C	0008610	biological_process	lipid biosynthetic process
C	0008654	biological_process	phospholipid biosynthetic process
C	0009411	biological_process	response to UV
C	0016020	cellular_component	membrane
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0042802	molecular_function	identical protein binding
C	0046872	molecular_function	metal ion binding
D	0000166	molecular_function	nucleotide binding
D	0001727	molecular_function	lipid kinase activity
D	0004143	molecular_function	ATP-dependent diacylglycerol kinase activity
D	0005524	molecular_function	ATP binding
D	0005886	cellular_component	plasma membrane
D	0006629	biological_process	lipid metabolic process
D	0006654	biological_process	phosphatidic acid biosynthetic process
D	0008610	biological_process	lipid biosynthetic process
D	0008654	biological_process	phospholipid biosynthetic process
D	0009411	biological_process	response to UV
D	0016020	cellular_component	membrane
D	0016301	molecular_function	kinase activity
D	0016740	molecular_function	transferase activity
D	0042802	molecular_function	identical protein binding
D	0046872	molecular_function	metal ion binding
E	0000166	molecular_function	nucleotide binding
E	0001727	molecular_function	lipid kinase activity
E	0004143	molecular_function	ATP-dependent diacylglycerol kinase activity
E	0005524	molecular_function	ATP binding
E	0005886	cellular_component	plasma membrane
E	0006629	biological_process	lipid metabolic process
E	0006654	biological_process	phosphatidic acid biosynthetic process
E	0008610	biological_process	lipid biosynthetic process
E	0008654	biological_process	phospholipid biosynthetic process
E	0009411	biological_process	response to UV
E	0016020	cellular_component	membrane
E	0016301	molecular_function	kinase activity
E	0016740	molecular_function	transferase activity
E	0042802	molecular_function	identical protein binding
E	0046872	molecular_function	metal ion binding
F	0000166	molecular_function	nucleotide binding
F	0001727	molecular_function	lipid kinase activity
F	0004143	molecular_function	ATP-dependent diacylglycerol kinase activity
F	0005524	molecular_function	ATP binding
F	0005886	cellular_component	plasma membrane
F	0006629	biological_process	lipid metabolic process
F	0006654	biological_process	phosphatidic acid biosynthetic process
F	0008610	biological_process	lipid biosynthetic process
F	0008654	biological_process	phospholipid biosynthetic process
F	0009411	biological_process	response to UV
F	0016020	cellular_component	membrane
F	0016301	molecular_function	kinase activity
F	0016740	molecular_function	transferase activity
F	0042802	molecular_function	identical protein binding
F	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA F 1122

Chain	Residue
D	LEU64
D	ASP107
D	HOH2044
F	SER60
F	LEU64
F	HOH2024

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NA E 1122

Chain	Residue
E	HOH2020
D	SER60
E	SER61
E	THR111

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 1122

Chain	Residue
D	GLU28
D	GLU76
D	FLC1123
D	ACT1124

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE FLC D 1123

Chain	Residue
D	GLU76
D	ZN1122
D	ACT1124
D	HOH2048

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ACT D 1124

Chain	Residue
D	GLU28
D	GLU69
D	ASN72
D	SER73
D	GLU76
D	ZN1122
D	FLC1123
D	HOH2047

site_id	AC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE 78N B 1122

Chain	Residue
A	ALA13
A	ALA14
A	SER17
A	78N1123
A	78N1124
B	SER98
B	VAL101
B	LEU102
B	ILE105
B	ILE110
B	78N1123

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 78N B 1123

Chain	Residue
A	ARG9
A	78N1124
B	GLU34
B	VAL65
B	GLU69
B	ALA108
B	TRP112
B	ALA113
B	78N1122

site_id	AC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE 78M D 1125

Chain	Residue
A	GLN33
A	GLU34
A	78M1126
C	TRP117
C	78N1122
D	TRP25
D	ALA29
D	ARG32
D	GLN33
D	VAL36
D	HOH2017
D	HOH2049

site_id	AC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE 78N C 1122

Chain	Residue
A	78M1126
B	ALA46
B	ARG55
B	HOH2010
C	ILE110
C	ILE114
C	TRP117
C	SER118
D	GLN33
D	78M1125

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE 78N A 1122

Chain	Residue
A	TRP18
A	ARG22
A	TRP25
A	ILE26
A	LEU39
A	MET63
A	MET66

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE 78M D 1126

Chain	Residue
A	ALA30
A	PHE31
A	GLU34
A	GLU69
A	LEU102
A	ILE105
A	HOH2012
D	ARG22
D	TRP25
D	HOH2050

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE 78M D 1127

Chain	Residue
B	TRP47
B	HOH2006
B	HOH2008
D	LEU102
D	VAL109
D	ALA113
D	HOH2018
D	HOH2043

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE 78N C 1123

Chain	Residue
A	LEU40
A	TRP47
A	78M1126
C	GLU34
C	GLU69
C	TRP112

site_id	BC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE 78M D 1128

Chain	Residue
A	TRP117
B	GLY35
B	VAL36
D	TRP47
D	LEU48
D	ASP49
D	PHE120

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE 78N A 1123

Chain	Residue
A	VAL42
A	ALA46
A	ARG55
A	78N1124
A	HOH2016
B	78N1122

site_id	BC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 78N A 1124

Chain	Residue
A	VAL50
A	ASP51
A	ALA52
A	ARG55
A	78N1123
B	ILE114
B	TRP117
B	78N1122
B	78N1123

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE 78M A 1125

Chain	Residue
A	ILE110
A	TRP117
D	ALA46
D	TRP47
D	ARG55

site_id	BC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 78M A 1126

Chain	Residue
A	CYS41
A	PHE120
A	HOH2015
C	LEU102
C	ILE105
C	78N1122
C	78N1123
D	LEU39
D	78M1125

Functional Information from PROSITE/UniProt

site_id	PS01069
Number of Residues	12
Details	DAGK_PROKAR Prokaryotic diacylglycerol kinase signature. ElLNSAIEavVD

Chain	Residue	Details
A	GLU69-ASP80

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	150
Details	Transmembrane: {"description":"Helical","evidences":[{"source":"PubMed","id":"12379131","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	10
Details	Topological domain: {"description":"Periplasmic","evidences":[{"source":"PubMed","id":"12379131","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	150
Details	Topological domain: {"description":"Cytoplasmic","evidences":[{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	138
Details	Transmembrane: {"description":"Helical","evidences":[{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	12
Details	Topological domain: {"description":"Periplasmic","evidences":[{"source":"PubMed","id":"15919996","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	6
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25012698","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"26894538","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	5
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	29
Details	Binding 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."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	6
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	12
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	15
Details	Binding 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."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	6
Details	Binding 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."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	6
Details	Binding 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."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	6
Details	Binding 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"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	30
Details	Binding 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."]}}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)