Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5D56

In meso in situ serial X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K

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 78M A 201

Chain	Residue
A	ARG22
A	TRP25
A	VAL38
A	MET63
A	MET66
A	78M202

site_id	AC2
Number of Residues	6
Details	binding site for residue 78M A 202

Chain	Residue
A	78M204
A	HOH303
B	78M202
A	ALA46
A	ARG55
A	78M201

site_id	AC3
Number of Residues	7
Details	binding site for residue 78M A 203

Chain	Residue
A	ARG9
B	GLU34
B	VAL65
B	GLU69
B	ALA108
B	TRP112
B	78M202

site_id	AC4
Number of Residues	8
Details	binding site for residue 78M A 204

Chain	Residue
A	ILE10
A	ALA13
A	ALA14
A	SER17
A	78M202
B	GLU69
B	SER98
B	VAL101

site_id	AC5
Number of Residues	4
Details	binding site for residue 78M B 201

Chain	Residue
B	TRP47
B	ASP49
D	LEU102
D	ILE105

site_id	AC6
Number of Residues	4
Details	binding site for residue 78M B 202

Chain	Residue
A	78M202
A	78M203
B	ALA113
B	TRP117

site_id	AC7
Number of Residues	8
Details	binding site for residue 78M B 203

Chain	Residue
A	LEU116
B	ALA46
B	ARG55
C	ILE114
C	TRP117
D	ALA37
D	LEU40
D	78M204

site_id	AC8
Number of Residues	6
Details	binding site for residue 78M C 201

Chain	Residue
A	LEU40
A	TRP47
C	GLU34
C	ILE44
C	MET66
C	GLU69

site_id	AC9
Number of Residues	4
Details	binding site for residue ZN D 201

Chain	Residue
D	GLU28
D	GLU76
D	FLC202
D	ACT203

site_id	AD1
Number of Residues	2
Details	binding site for residue FLC D 202

Chain	Residue
D	GLU76
D	ZN201

site_id	AD2
Number of Residues	5
Details	binding site for residue ACT D 203

Chain	Residue
D	GLU28
D	GLU69
D	SER73
D	GLU76
D	ZN201

site_id	AD3
Number of Residues	8
Details	binding site for residue 78M D 204

Chain	Residue
A	GLN33
A	GLU34
A	CYS41
B	78M203
C	TRP117
D	ARG32
D	GLN33
D	VAL36

site_id	AD4
Number of Residues	5
Details	binding site for residue 78M D 205

Chain	Residue
B	GLY35
B	VAL36
D	TRP47
D	ASP49
D	PHE120

site_id	AD5
Number of Residues	10
Details	binding site for residue 78M D 206

Chain	Residue
A	ALA30
A	GLU34
A	GLU69
D	LEU21
D	ARG22
D	TRP25
D	ILE26
D	VAL42
E	ILE103
E	ILE110

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	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	8
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	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_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)