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 | 0004143 | molecular_function | ATP-dependent diacylglycerol kinase activity |
A | 0005524 | molecular_function | ATP binding |
A | 0005886 | cellular_component | plasma membrane |
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 | 0016310 | biological_process | phosphorylation |
A | 0042802 | molecular_function | identical protein binding |
A | 0046872 | molecular_function | metal ion binding |
B | 0004143 | molecular_function | ATP-dependent diacylglycerol kinase activity |
B | 0005524 | molecular_function | ATP binding |
B | 0005886 | cellular_component | plasma membrane |
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 | 0016310 | biological_process | phosphorylation |
B | 0042802 | molecular_function | identical protein binding |
B | 0046872 | molecular_function | metal ion binding |
C | 0004143 | molecular_function | ATP-dependent diacylglycerol kinase activity |
C | 0005524 | molecular_function | ATP binding |
C | 0005886 | cellular_component | plasma membrane |
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 | 0016310 | biological_process | phosphorylation |
C | 0042802 | molecular_function | identical protein binding |
C | 0046872 | molecular_function | metal ion binding |
D | 0004143 | molecular_function | ATP-dependent diacylglycerol kinase activity |
D | 0005524 | molecular_function | ATP binding |
D | 0005886 | cellular_component | plasma membrane |
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 | 0016310 | biological_process | phosphorylation |
D | 0042802 | molecular_function | identical protein binding |
D | 0046872 | molecular_function | metal ion binding |
E | 0004143 | molecular_function | ATP-dependent diacylglycerol kinase activity |
E | 0005524 | molecular_function | ATP binding |
E | 0005886 | cellular_component | plasma membrane |
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 | 0016310 | biological_process | phosphorylation |
E | 0042802 | molecular_function | identical protein binding |
E | 0046872 | molecular_function | metal ion binding |
F | 0004143 | molecular_function | ATP-dependent diacylglycerol kinase activity |
F | 0005524 | molecular_function | ATP binding |
F | 0005886 | cellular_component | plasma membrane |
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 | 0016310 | biological_process | phosphorylation |
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 | 174 |
Details | TOPO_DOM: Cytoplasmic => ECO:0000269|PubMed:8071224 |
Chain | Residue | Details |
A | ALA1-ALA30 | |
B | ALA1-ALA30 | |
C | ALA1-ALA30 | |
D | ALA1-ALA30 | |
E | ALA1-ALA30 | |
F | ALA1-ALA30 |
site_id | SWS_FT_FI2 |
Number of Residues | 198 |
Details | TRANSMEM: Helical => ECO:0000305|PubMed:12379131, ECO:0000305|PubMed:8071224 |
Chain | Residue | Details |
A | PHE31-TRP47 | |
E | ASP51-VAL68 | |
F | PHE31-TRP47 | |
F | ASP51-VAL68 | |
A | ASP51-VAL68 | |
B | PHE31-TRP47 | |
B | ASP51-VAL68 | |
C | PHE31-TRP47 | |
C | ASP51-VAL68 | |
D | PHE31-TRP47 | |
D | ASP51-VAL68 | |
E | PHE31-TRP47 |
site_id | SWS_FT_FI3 |
Number of Residues | 12 |
Details | TOPO_DOM: Periplasmic => ECO:0000305|PubMed:12379131, ECO:0000305|PubMed:8071224 |
Chain | Residue | Details |
A | LEU48-VAL50 | |
B | LEU48-VAL50 | |
C | LEU48-VAL50 | |
D | LEU48-VAL50 | |
E | LEU48-VAL50 | |
F | LEU48-VAL50 |
site_id | SWS_FT_FI4 |
Number of Residues | 150 |
Details | TOPO_DOM: Cytoplasmic => ECO:0000305|PubMed:8071224 |
Chain | Residue | Details |
A | GLU69-LYS94 | |
B | GLU69-LYS94 | |
C | GLU69-LYS94 | |
D | GLU69-LYS94 | |
E | GLU69-LYS94 | |
F | GLU69-LYS94 |
site_id | SWS_FT_FI5 |
Number of Residues | 138 |
Details | TRANSMEM: Helical => ECO:0000305|PubMed:8071224 |
Chain | Residue | Details |
A | ASP95-SER118 | |
B | ASP95-SER118 | |
C | ASP95-SER118 | |
D | ASP95-SER118 | |
E | ASP95-SER118 | |
F | ASP95-SER118 |
site_id | SWS_FT_FI6 |
Number of Residues | 12 |
Details | TOPO_DOM: Periplasmic => ECO:0000269|PubMed:15919996, ECO:0000269|PubMed:8071224 |
Chain | Residue | Details |
A | HIS119-GLY121 | |
B | HIS119-GLY121 | |
C | HIS119-GLY121 | |
D | HIS119-GLY121 | |
E | HIS119-GLY121 | |
F | HIS119-GLY121 |
site_id | SWS_FT_FI7 |
Number of Residues | 6 |
Details | ACT_SITE: Proton acceptor => ECO:0000305|PubMed:26673816 |
Chain | Residue | Details |
A | GLU69 | |
B | GLU69 | |
C | GLU69 | |
D | GLU69 | |
E | GLU69 | |
F | GLU69 |
site_id | SWS_FT_FI8 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000305|PubMed:25012698, ECO:0000305|PubMed:26673816, ECO:0000305|PubMed:26894538 |
Chain | Residue | Details |
A | ARG9 | |
B | ARG9 | |
C | ARG9 | |
D | ARG9 | |
E | ARG9 | |
F | ARG9 |
site_id | SWS_FT_FI9 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000305|PubMed:23676677, ECO:0000305|PubMed:25012698, ECO:0000305|PubMed:26894538, ECO:0000305|PubMed:26960129 |
Chain | Residue | Details |
A | ALA13 | |
B | ALA13 | |
C | ALA13 | |
D | ALA13 | |
E | ALA13 | |
F | ALA13 |
site_id | SWS_FT_FI10 |
Number of Residues | 30 |
Details | BINDING: BINDING => ECO:0000305|PubMed:26673816, ECO:0000305|Ref.26 |
Chain | Residue | Details |
A | TYR16 | |
B | LYS94 | |
C | TYR16 | |
C | GLU28 | |
C | GLU76 | |
C | GLU85 | |
C | LYS94 | |
D | TYR16 | |
D | GLU28 | |
D | GLU76 | |
D | GLU85 | |
A | GLU28 | |
D | LYS94 | |
E | TYR16 | |
E | GLU28 | |
E | GLU76 | |
E | GLU85 | |
E | LYS94 | |
F | TYR16 | |
F | GLU28 | |
F | GLU76 | |
F | GLU85 | |
A | GLU76 | |
F | LYS94 | |
A | GLU85 | |
A | LYS94 | |
B | TYR16 | |
B | GLU28 | |
B | GLU76 | |
B | GLU85 |
site_id | SWS_FT_FI11 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000305|PubMed:23676677, ECO:0000305|PubMed:25012698, ECO:0000305|PubMed:25055873, ECO:0000305|PubMed:26673816, ECO:0000305|PubMed:26960129 |
Chain | Residue | Details |
A | ARG22 | |
B | ARG22 | |
C | ARG22 | |
D | ARG22 | |
E | ARG22 | |
F | ARG22 |
site_id | SWS_FT_FI12 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000305|PubMed:23676677, ECO:0000305|PubMed:25012698, ECO:0000305|PubMed:25055873, ECO:0000305|PubMed:26673816, ECO:0000305|PubMed:26894538, ECO:0000305|PubMed:26960129 |
Chain | Residue | Details |
A | ALA30 | |
B | ALA30 | |
C | ALA30 | |
D | ALA30 | |
E | ALA30 | |
F | ALA30 |
site_id | SWS_FT_FI13 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000305|PubMed:23676677, ECO:0000305|PubMed:25012698, ECO:0000305|PubMed:26673816, ECO:0000305|PubMed:26894538, ECO:0000305|PubMed:26960129, ECO:0000305|Ref.25 |
Chain | Residue | Details |
A | TRP47 | |
B | TRP47 | |
C | TRP47 | |
D | TRP47 | |
E | TRP47 | |
F | TRP47 |
site_id | SWS_FT_FI14 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000305|PubMed:23676677, ECO:0000305|PubMed:25012698, ECO:0000305|PubMed:25055873, ECO:0000305|PubMed:26673816, ECO:0000305|PubMed:26894538, ECO:0000305|PubMed:26960129, ECO:0000305|Ref.25 |
Chain | Residue | Details |
A | ARG55 | |
B | ARG55 | |
C | ARG55 | |
D | ARG55 | |
E | ARG55 | |
F | ARG55 |
site_id | SWS_FT_FI15 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000305|PubMed:25012698, ECO:0000305|PubMed:26673816, ECO:0000305|PubMed:26894538, ECO:0000305|PubMed:26960129, ECO:0000305|Ref.26 |
Chain | Residue | Details |
A | GLU69 | |
B | GLU69 | |
C | GLU69 | |
D | GLU69 | |
E | GLU69 | |
F | GLU69 |
site_id | SWS_FT_FI16 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000305|PubMed:23676677, ECO:0000305|PubMed:25012698, ECO:0000305|PubMed:26673816, ECO:0000305|PubMed:26894538, ECO:0000305|PubMed:26960129 |
Chain | Residue | Details |
A | SER98 | |
B | SER98 | |
C | SER98 | |
D | SER98 | |
E | SER98 | |
F | SER98 |
site_id | SWS_FT_FI17 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000305|PubMed:23676677, ECO:0000305|PubMed:25012698, ECO:0000305|PubMed:25055873, ECO:0000305|PubMed:26673816, ECO:0000305|PubMed:26894538, ECO:0000305|PubMed:26960129, ECO:0000305|Ref.26 |
Chain | Residue | Details |
A | TRP112 | |
B | TRP112 | |
C | TRP112 | |
D | TRP112 | |
E | TRP112 | |
F | TRP112 |