4D2E
Crystal structure of an integral membrane kinase - v2.3
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 | 4 |
| Details | BINDING SITE FOR RESIDUE NA D 1122 |
| Chain | Residue |
| D | ASP107 |
| D | HOH2016 |
| D | HOH2017 |
| D | HOH2032 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE FLC D 1123 |
| Chain | Residue |
| D | GLU28 |
| D | GLU76 |
| D | FLC1124 |
| D | ZN1126 |
| site_id | AC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE FLC D 1124 |
| Chain | Residue |
| D | GLU28 |
| D | ALA30 |
| D | GLU69 |
| D | GLU76 |
| D | FLC1123 |
| D | ZN1126 |
| D | 78N1128 |
| D | HOH2009 |
| B | ASP49 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE 78M A 1122 |
| Chain | Residue |
| A | TRP25 |
| A | ILE26 |
| A | MET63 |
| A | 78M1123 |
| A | 78M1124 |
| A | HOH2008 |
| C | 78N1126 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE 78M A 1123 |
| Chain | Residue |
| A | 78M1122 |
| A | HOH2003 |
| C | TRP47 |
| C | 78M1123 |
| C | 78N1126 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE 78M D 1125 |
| Chain | Residue |
| B | GLY35 |
| B | VAL36 |
| D | TRP47 |
| D | LEU48 |
| D | ASP49 |
| D | PHE120 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE 78M A 1124 |
| Chain | Residue |
| A | ALA46 |
| A | ARG55 |
| A | 78M1122 |
| B | ILE110 |
| B | ILE114 |
| B | 78N1121 |
| B | 78N1123 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE 78M A 1125 |
| Chain | Residue |
| A | LEU48 |
| A | GLY121 |
| C | LEU102 |
| C | ILE105 |
| C | 78M1123 |
| C | 78N1124 |
| C | 78N1125 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE 78M C 1122 |
| Chain | Residue |
| A | TRP47 |
| C | GLU34 |
| C | VAL65 |
| C | GLU69 |
| C | ALA108 |
| C | TRP112 |
| C | 78M1123 |
| C | 78N1126 |
| site_id | BC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE 78M C 1123 |
| Chain | Residue |
| A | VAL43 |
| A | TRP47 |
| A | LEU48 |
| A | 78M1123 |
| A | 78M1125 |
| C | LEU40 |
| C | ILE44 |
| C | 78M1122 |
| C | 78N1126 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN D 1126 |
| Chain | Residue |
| D | GLU28 |
| D | GLU76 |
| D | FLC1123 |
| D | FLC1124 |
| site_id | BC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE 78N C 1124 |
| Chain | Residue |
| A | GLN33 |
| A | VAL62 |
| A | 78M1125 |
| C | TRP117 |
| C | 78N1125 |
| D | TRP25 |
| D | ARG32 |
| D | VAL36 |
| site_id | BC4 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE 78N C 1125 |
| Chain | Residue |
| A | 78M1125 |
| B | ALA46 |
| B | ALA52 |
| B | ARG55 |
| C | ILE114 |
| C | TRP117 |
| C | SER118 |
| C | 78N1124 |
| D | GLN33 |
| D | VAL36 |
| D | LEU39 |
| D | LEU40 |
| site_id | BC5 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE 78N D 1127 |
| Chain | Residue |
| D | TRP25 |
| D | ILE26 |
| D | MET66 |
| A | ALA30 |
| A | PHE31 |
| A | GLU34 |
| A | GLU69 |
| A | VAL101 |
| A | LEU102 |
| A | ILE105 |
| A | 78N1126 |
| D | ARG22 |
| site_id | BC6 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE 78N D 1128 |
| Chain | Residue |
| B | TRP47 |
| B | ASP49 |
| B | HOH2002 |
| D | ALA30 |
| D | GLN33 |
| D | GLU34 |
| D | LEU102 |
| D | ILE105 |
| D | VAL109 |
| D | FLC1124 |
| D | HOH2018 |
| site_id | BC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE 78N B 1121 |
| Chain | Residue |
| A | ILE10 |
| A | ALA13 |
| A | ALA14 |
| A | SER17 |
| A | 78M1124 |
| B | SER98 |
| B | VAL101 |
| B | LEU102 |
| B | 78N1123 |
| site_id | BC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE 78N A 1126 |
| Chain | Residue |
| A | ILE106 |
| A | VAL109 |
| A | ALA113 |
| A | ILE114 |
| A | TRP117 |
| D | LEU39 |
| D | 78N1127 |
| site_id | BC9 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE 78N C 1126 |
| Chain | Residue |
| A | TRP25 |
| A | LEU39 |
| A | LEU40 |
| A | 78M1122 |
| A | 78M1123 |
| C | CYS41 |
| C | TRP47 |
| C | TRP112 |
| C | 78M1122 |
| C | 78M1123 |
| site_id | CC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE 78N E 1122 |
| Chain | Residue |
| E | CYS41 |
| E | VAL62 |
| E | GLU69 |
| E | TRP112 |
| E | HOH2005 |
| site_id | CC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE 78N B 1122 |
| Chain | Residue |
| B | GLU34 |
| B | ALA37 |
| B | GLU69 |
| B | ILE105 |
| B | TRP112 |
| site_id | CC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE 78N B 1123 |
| Chain | Residue |
| A | 78M1124 |
| B | VAL109 |
| B | ILE114 |
| B | TRP117 |
| B | 78N1121 |
| site_id | CC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE 78N C 1127 |
| Chain | Residue |
| A | ASP107 |
| C | ARG55 |
| C | MET63 |
| C | HOH2001 |
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 | 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 | 9 |
| 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 | 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_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 |
