Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4BRB

Crystal structure of the integral membrane enzyme DgkA-ref, delta 7

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	8
Details	BINDING SITE FOR RESIDUE 78N A 1121

Chain	Residue
A	GLN33
B	78N1122
C	TRP117
D	TRP25
D	ALA29
D	ARG32
D	GLN33
D	VAL36

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE 78N A 1122

Chain	Residue
A	TRP25
A	ILE26
A	MET63
A	78N1123
A	78N1124
A	ARG22

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE 78N A 1123

Chain	Residue
A	TRP25
A	LEU40
A	78N1122
C	TRP47
C	TRP112

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE 78N A 1124

Chain	Residue
A	VAL42
A	ALA46
A	LEU48
A	ARG55
A	78N1122
A	78N1125
B	ILE110
B	ILE114

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE 78N A 1125

Chain	Residue
A	78N1124
B	ILE110
B	ILE114
B	TRP117

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE 78N B 1122

Chain	Residue
A	78N1121
B	ALA46
B	ARG55
C	ILE110
C	SER118
D	GLN33
D	LEU39
D	VAL43

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE 78N B 1123

Chain	Residue
B	GLN33
B	GLU34
B	GLU69
B	ILE105
B	ALA108
B	TRP112

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN D 1122

Chain	Residue
D	GLU28
D	GLU76
D	FLC1123
D	ACT1124

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE FLC D 1123

Chain	Residue
D	GLU28
D	GLU76
D	ZN1122
D	ACT1124

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACT D 1124

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

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE 78N D 1125

Chain	Residue
B	ILE26
B	ARG32
B	GLY35
B	VAL36
B	LEU39
B	MET63
D	TRP47
D	ASP49

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE 78N D 1126

Chain	Residue
B	TRP47
B	ASP49
B	HOH2001
D	ILE105
D	VAL109
D	ILE110

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE 78N C 1122

Chain	Residue
A	ASP107
C	VAL42
C	ALA46
C	ARG55
C	MET63

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	182
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	12
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	6
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"26673816","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
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_FI7
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_FI8
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_FI9
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_FI10
Number of Residues	20
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_FI11
Number of Residues	18
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_FI12
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_FI13
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_FI14
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_FI15
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

site_id	SWS_FT_FI16
Number of Residues	6
Details	Topological domain: {"description":"Periplasmic","evidences":[{"source":"PubMed","id":"15919996","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8071224","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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