5D57
In meso 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 | 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 | 0016310 | biological_process | phosphorylation |
| 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 | 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 | 0016310 | biological_process | phosphorylation |
| 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 | 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 | 0016310 | biological_process | phosphorylation |
| 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 | 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 | 0016310 | biological_process | phosphorylation |
| 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 | 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 | 0016310 | biological_process | phosphorylation |
| 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 | 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 | 0016310 | biological_process | phosphorylation |
| 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 | 4 |
| Details | binding site for residue 78M A 201 |
| Chain | Residue |
| A | ALA46 |
| A | TRP47 |
| A | ASP49 |
| A | 78M205 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | binding site for residue 78M A 202 |
| Chain | Residue |
| C | 78M201 |
| D | LEU39 |
| D | 78M204 |
| A | ILE44 |
| A | PHE120 |
| B | 78M203 |
| C | ILE105 |
| C | VAL109 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue 78M A 203 |
| Chain | Residue |
| A | ARG92 |
| A | ASP95 |
| A | ILE103 |
| D | TRP18 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | binding site for residue 78M A 204 |
| Chain | Residue |
| A | TRP18 |
| A | ARG22 |
| A | TRP25 |
| A | VAL38 |
| A | LEU39 |
| A | VAL42 |
| A | MET63 |
| A | 78M205 |
| B | ILE103 |
| B | ILE110 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | binding site for residue 78M A 205 |
| Chain | Residue |
| A | ALA46 |
| A | ARG55 |
| A | 78M201 |
| A | 78M204 |
| A | 78M206 |
| A | HOH303 |
| B | ILE106 |
| B | 78M201 |
| site_id | AC6 |
| Number of Residues | 10 |
| Details | binding site for residue 78M A 206 |
| Chain | Residue |
| A | ILE10 |
| A | ALA13 |
| A | ALA14 |
| A | SER17 |
| A | 78M205 |
| B | GLU69 |
| B | SER98 |
| B | VAL101 |
| B | 78M201 |
| B | 78M202 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue 78M B 201 |
| Chain | Residue |
| A | 78M205 |
| A | 78M206 |
| B | TRP117 |
| B | 78M202 |
| site_id | AC8 |
| Number of Residues | 11 |
| Details | binding site for residue 78M B 202 |
| Chain | Residue |
| A | ARG9 |
| A | 78M206 |
| B | GLU34 |
| B | VAL62 |
| B | VAL65 |
| B | GLU69 |
| B | ILE105 |
| B | ALA108 |
| B | TRP112 |
| B | ALA113 |
| B | 78M201 |
| site_id | AC9 |
| Number of Residues | 9 |
| Details | binding site for residue 78M B 203 |
| Chain | Residue |
| A | LEU116 |
| A | 78M202 |
| B | ALA46 |
| B | ARG55 |
| B | HOH303 |
| C | ILE114 |
| D | VAL36 |
| D | ALA37 |
| D | 78M204 |
| site_id | AD1 |
| Number of Residues | 7 |
| Details | binding site for residue 78M B 204 |
| Chain | Residue |
| B | TRP47 |
| B | LEU48 |
| B | ASP49 |
| B | HOH301 |
| B | HOH302 |
| D | LEU102 |
| D | ILE105 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue 78M C 201 |
| Chain | Residue |
| A | TRP47 |
| A | 78M202 |
| C | ALA37 |
| C | CYS41 |
| C | ILE105 |
| C | 78M202 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue 78M C 202 |
| Chain | Residue |
| A | LEU40 |
| A | TRP47 |
| C | GLU34 |
| C | GLU69 |
| C | TRP112 |
| C | 78M201 |
| site_id | AD4 |
| Number of Residues | 7 |
| Details | binding site for residue 78M D 201 |
| Chain | Residue |
| A | TRP117 |
| D | ALA46 |
| D | ARG55 |
| D | ILE59 |
| D | 78M202 |
| E | ILE110 |
| E | TRP117 |
| site_id | AD5 |
| Number of Residues | 15 |
| Details | binding site for residue 78M D 202 |
| Chain | Residue |
| A | ILE105 |
| D | LEU21 |
| D | ARG22 |
| D | TRP25 |
| D | ILE26 |
| D | MET63 |
| D | 78M201 |
| D | HOH301 |
| E | ILE103 |
| E | ILE110 |
| A | ALA30 |
| A | PHE31 |
| A | GLU34 |
| A | GLU69 |
| A | LEU102 |
| site_id | AD6 |
| Number of Residues | 9 |
| Details | binding site for residue 78M D 203 |
| Chain | Residue |
| B | ILE26 |
| B | ARG32 |
| B | GLY35 |
| B | VAL36 |
| B | MET63 |
| D | TRP47 |
| D | LEU48 |
| D | ASP49 |
| D | PHE120 |
| site_id | AD7 |
| Number of Residues | 12 |
| Details | binding site for residue 78M D 204 |
| Chain | Residue |
| A | GLN33 |
| A | GLU34 |
| A | ALA37 |
| A | CYS41 |
| A | 78M202 |
| B | 78M203 |
| C | TRP117 |
| D | ARG32 |
| D | GLN33 |
| D | VAL36 |
| D | HOH301 |
| D | HOH304 |
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 | |
| E | ALA1-ALA30 | |
| F | ALA1-ALA30 | |
| C | ALA1-ALA30 | |
| D | 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 | |
| A | ASP51-VAL68 | |
| B | PHE31-TRP47 | |
| B | ASP51-VAL68 | |
| D | PHE31-TRP47 | |
| D | ASP51-VAL68 | |
| E | PHE31-TRP47 | |
| E | ASP51-VAL68 | |
| F | PHE31-TRP47 | |
| F | ASP51-VAL68 | |
| C | PHE31-TRP47 | |
| C | ASP51-VAL68 |
| 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 | |
| E | LEU48-VAL50 | |
| F | LEU48-VAL50 | |
| C | LEU48-VAL50 | |
| D | 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 | |
| C | GLU69-LYS94 | |
| D | GLU69-LYS94 | |
| E | GLU69-LYS94 | |
| F | GLU69-LYS94 | |
| B | 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 |
| B | GLU28 | |
| B | GLU76 | |
| B | GLU85 | |
| B | LYS94 | |
| C | TYR16 | |
| C | GLU28 | |
| C | GLU76 | |
| C | GLU85 | |
| C | LYS94 | |
| D | TYR16 | |
| D | GLU28 | |
| D | GLU76 | |
| D | GLU85 | |
| D | LYS94 | |
| E | TYR16 | |
| E | GLU28 | |
| E | GLU76 | |
| E | GLU85 | |
| E | LYS94 | |
| F | TYR16 | |
| F | GLU28 | |
| F | GLU76 | |
| F | GLU85 | |
| F | LYS94 | |
| A | TYR16 | |
| A | GLU28 | |
| A | GLU76 | |
| A | GLU85 | |
| A | LYS94 | |
| B | TYR16 |
| 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 |
