3EXE
Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004738 | molecular_function | pyruvate dehydrogenase activity |
| A | 0004739 | molecular_function | pyruvate dehydrogenase (acetyl-transferring) activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005730 | cellular_component | nucleolus |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0006006 | biological_process | glucose metabolic process |
| A | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| A | 0006090 | biological_process | pyruvate metabolic process |
| A | 0006099 | biological_process | tricarboxylic acid cycle |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016624 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor |
| A | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
| A | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| A | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| A | 0046872 | molecular_function | metal ion binding |
| A | 1902494 | cellular_component | catalytic complex |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004739 | molecular_function | pyruvate dehydrogenase (acetyl-transferring) activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005759 | cellular_component | mitochondrial matrix |
| B | 0006006 | biological_process | glucose metabolic process |
| B | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| B | 0006099 | biological_process | tricarboxylic acid cycle |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
| B | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0004738 | molecular_function | pyruvate dehydrogenase activity |
| C | 0004739 | molecular_function | pyruvate dehydrogenase (acetyl-transferring) activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005730 | cellular_component | nucleolus |
| C | 0005739 | cellular_component | mitochondrion |
| C | 0005759 | cellular_component | mitochondrial matrix |
| C | 0006006 | biological_process | glucose metabolic process |
| C | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| C | 0006090 | biological_process | pyruvate metabolic process |
| C | 0006099 | biological_process | tricarboxylic acid cycle |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016624 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor |
| C | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
| C | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| C | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| C | 0046872 | molecular_function | metal ion binding |
| C | 1902494 | cellular_component | catalytic complex |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0004739 | molecular_function | pyruvate dehydrogenase (acetyl-transferring) activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005739 | cellular_component | mitochondrion |
| D | 0005759 | cellular_component | mitochondrial matrix |
| D | 0006006 | biological_process | glucose metabolic process |
| D | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| D | 0006099 | biological_process | tricarboxylic acid cycle |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
| D | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0004738 | molecular_function | pyruvate dehydrogenase activity |
| E | 0004739 | molecular_function | pyruvate dehydrogenase (acetyl-transferring) activity |
| E | 0005515 | molecular_function | protein binding |
| E | 0005634 | cellular_component | nucleus |
| E | 0005730 | cellular_component | nucleolus |
| E | 0005739 | cellular_component | mitochondrion |
| E | 0005759 | cellular_component | mitochondrial matrix |
| E | 0006006 | biological_process | glucose metabolic process |
| E | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| E | 0006090 | biological_process | pyruvate metabolic process |
| E | 0006099 | biological_process | tricarboxylic acid cycle |
| E | 0016491 | molecular_function | oxidoreductase activity |
| E | 0016624 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor |
| E | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
| E | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| E | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| E | 0046872 | molecular_function | metal ion binding |
| E | 1902494 | cellular_component | catalytic complex |
| F | 0003824 | molecular_function | catalytic activity |
| F | 0004739 | molecular_function | pyruvate dehydrogenase (acetyl-transferring) activity |
| F | 0005515 | molecular_function | protein binding |
| F | 0005634 | cellular_component | nucleus |
| F | 0005654 | cellular_component | nucleoplasm |
| F | 0005739 | cellular_component | mitochondrion |
| F | 0005759 | cellular_component | mitochondrial matrix |
| F | 0006006 | biological_process | glucose metabolic process |
| F | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| F | 0006099 | biological_process | tricarboxylic acid cycle |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
| F | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| F | 0046872 | molecular_function | metal ion binding |
| G | 0004738 | molecular_function | pyruvate dehydrogenase activity |
| G | 0004739 | molecular_function | pyruvate dehydrogenase (acetyl-transferring) activity |
| G | 0005515 | molecular_function | protein binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005730 | cellular_component | nucleolus |
| G | 0005739 | cellular_component | mitochondrion |
| G | 0005759 | cellular_component | mitochondrial matrix |
| G | 0006006 | biological_process | glucose metabolic process |
| G | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| G | 0006090 | biological_process | pyruvate metabolic process |
| G | 0006099 | biological_process | tricarboxylic acid cycle |
| G | 0016491 | molecular_function | oxidoreductase activity |
| G | 0016624 | molecular_function | oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor |
| G | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
| G | 0043231 | cellular_component | intracellular membrane-bounded organelle |
| G | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| G | 0046872 | molecular_function | metal ion binding |
| G | 1902494 | cellular_component | catalytic complex |
| H | 0003824 | molecular_function | catalytic activity |
| H | 0004739 | molecular_function | pyruvate dehydrogenase (acetyl-transferring) activity |
| H | 0005515 | molecular_function | protein binding |
| H | 0005634 | cellular_component | nucleus |
| H | 0005654 | cellular_component | nucleoplasm |
| H | 0005739 | cellular_component | mitochondrion |
| H | 0005759 | cellular_component | mitochondrial matrix |
| H | 0006006 | biological_process | glucose metabolic process |
| H | 0006086 | biological_process | acetyl-CoA biosynthetic process from pyruvate |
| H | 0006099 | biological_process | tricarboxylic acid cycle |
| H | 0016491 | molecular_function | oxidoreductase activity |
| H | 0034604 | molecular_function | pyruvate dehydrogenase (NAD+) activity |
| H | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| H | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN C 1001 |
| Chain | Residue |
| C | ASP167 |
| C | ASN196 |
| C | TYR198 |
| C | TPP1002 |
| C | HOH2234 |
| site_id | AC2 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE TPP C 1002 |
| Chain | Residue |
| B | GLN88 |
| C | TYR89 |
| C | ARG90 |
| C | GLY136 |
| C | VAL138 |
| C | GLY166 |
| C | ASP167 |
| C | GLY168 |
| C | ALA169 |
| C | ASN196 |
| C | TYR198 |
| C | GLY199 |
| C | MET200 |
| C | HIS263 |
| C | MN1001 |
| C | HOH2200 |
| C | HOH2222 |
| C | HOH2234 |
| C | HOH2277 |
| C | HOH2489 |
| B | GLU28 |
| B | ILE57 |
| B | GLU59 |
| B | PHE85 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K B 1003 |
| Chain | Residue |
| B | ALA160 |
| B | ILE161 |
| B | ASP163 |
| B | HOH2133 |
| B | HOH2301 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN A 1004 |
| Chain | Residue |
| A | ASP167 |
| A | ASN196 |
| A | TYR198 |
| A | TPP1005 |
| A | HOH2039 |
| site_id | AC5 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE TPP A 1005 |
| Chain | Residue |
| A | TYR89 |
| A | ARG90 |
| A | GLY136 |
| A | VAL138 |
| A | GLY166 |
| A | ASP167 |
| A | GLY168 |
| A | ALA169 |
| A | ASN196 |
| A | TYR198 |
| A | GLY199 |
| A | HIS263 |
| A | MN1004 |
| A | HOH2039 |
| A | HOH2043 |
| A | HOH2122 |
| A | HOH2149 |
| A | HOH2346 |
| D | GLU28 |
| D | ILE57 |
| D | GLU59 |
| D | PHE85 |
| D | GLN88 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K D 1006 |
| Chain | Residue |
| D | ARG75 |
| D | ALA160 |
| D | ILE161 |
| D | ASP163 |
| D | HOH2065 |
| D | HOH2159 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN G 1007 |
| Chain | Residue |
| G | ASP167 |
| G | ASN196 |
| G | TYR198 |
| G | TPP1008 |
| G | HOH2294 |
| site_id | AC8 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE TPP G 1008 |
| Chain | Residue |
| F | GLU28 |
| F | ILE57 |
| F | GLU59 |
| F | MET81 |
| F | PHE85 |
| F | GLN88 |
| G | TYR89 |
| G | ARG90 |
| G | GLY136 |
| G | VAL138 |
| G | GLY166 |
| G | ASP167 |
| G | GLY168 |
| G | ALA169 |
| G | ASN196 |
| G | TYR198 |
| G | GLY199 |
| G | MET200 |
| G | HIS263 |
| G | MN1007 |
| G | HOH2062 |
| G | HOH2249 |
| G | HOH2294 |
| G | HOH2355 |
| G | HOH2447 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K F 1009 |
| Chain | Residue |
| F | ALA160 |
| F | ILE161 |
| F | ASP163 |
| F | HOH2116 |
| F | HOH2636 |
| F | ARG75 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN E 1010 |
| Chain | Residue |
| E | ASP167 |
| E | ASN196 |
| E | TYR198 |
| E | TPP1011 |
| E | HOH2223 |
| site_id | BC2 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE TPP E 1011 |
| Chain | Residue |
| E | TYR89 |
| E | ARG90 |
| E | GLY136 |
| E | VAL138 |
| E | GLY166 |
| E | ASP167 |
| E | GLY168 |
| E | ALA169 |
| E | ASN196 |
| E | TYR198 |
| E | GLY199 |
| E | MET200 |
| E | HIS263 |
| E | MN1010 |
| E | HOH2130 |
| E | HOH2179 |
| E | HOH2223 |
| E | HOH2391 |
| E | HOH2500 |
| H | GLU28 |
| H | ILE57 |
| H | GLU59 |
| H | PHE85 |
| H | GLN88 |
| site_id | BC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K H 1012 |
| Chain | Residue |
| H | ALA160 |
| H | ILE161 |
| H | ASP163 |
| H | HOH2386 |
| H | HOH2397 |
| site_id | BC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL A 1101 |
| Chain | Residue |
| A | LYS153 |
| A | TRP185 |
| A | LEU187 |
| A | HOH2650 |
| A | HOH2946 |
| A | HOH3205 |
| B | ASP49 |
| B | ILE53 |
| site_id | BC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL C 1102 |
| Chain | Residue |
| C | LYS153 |
| C | TRP185 |
| C | HOH2477 |
| C | HOH2998 |
| C | HOH3876 |
| D | ASP49 |
| D | ILE53 |
| D | HOH2905 |
| site_id | BC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL E 1103 |
| Chain | Residue |
| E | LYS153 |
| E | LEU187 |
| E | HOH2656 |
| E | HOH3689 |
| E | HOH3731 |
| F | ASP49 |
| F | ILE53 |
| site_id | BC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL G 1104 |
| Chain | Residue |
| G | LYS153 |
| G | LEU187 |
| G | HOH3129 |
| G | HOH3379 |
| H | ASP49 |
| H | ILE53 |
| H | HOH2848 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12651851 |
| Chain | Residue | Details |
| B | GLU59 | |
| G | LYS34 | |
| G | LYS215 | |
| G | LYS284 | |
| D | GLU59 | |
| F | GLU59 | |
| H | GLU59 | |
| C | LYS215 | |
| C | LYS284 | |
| E | LYS34 | |
| E | LYS215 | |
| E | LYS284 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | SITE: Important for interaction with DLAT => ECO:0000269|PubMed:20160912 |
| Chain | Residue | Details |
| B | ASP289 | |
| D | ASP289 | |
| F | ASP289 | |
| H | ASP289 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q9D051 |
| Chain | Residue | Details |
| B | TYR37 | |
| D | TYR37 | |
| F | TYR37 | |
| H | TYR37 | |
| E | LYS248 | |
| E | LYS356 | |
| G | LYS248 | |
| G | LYS356 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q9D051 |
| Chain | Residue | Details |
| B | LYS324 | |
| D | LYS324 | |
| F | LYS324 | |
| H | LYS324 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P35486 |
| Chain | Residue | Details |
| A | SER266 | |
| C | SER266 | |
| E | SER266 | |
| G | SER266 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine; by PDK1, PDK2, PDK3 and PDK4 => ECO:0000269|PubMed:11486000, ECO:0000269|PubMed:19081061 |
| Chain | Residue | Details |
| A | SER271 | |
| C | SER271 | |
| E | SER271 | |
| G | SER271 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P35486 |
| Chain | Residue | Details |
| A | TYR272 | |
| C | TYR272 | |
| E | TYR272 | |
| G | TYR272 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS292 | |
| C | LYS292 | |
| E | LYS292 | |
| G | LYS292 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P35486 |
| Chain | Residue | Details |
| A | LYS307 | |
| C | LYS307 | |
| E | LYS307 | |
| G | LYS307 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| A | HIS263 |
| site_id | CSA10 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| D | GLU59 | |
| D | HIS128 |
| site_id | CSA11 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| F | GLU59 | |
| F | HIS128 |
| site_id | CSA12 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| H | GLU59 | |
| H | HIS128 |
| site_id | CSA2 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| C | HIS263 |
| site_id | CSA3 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| E | HIS263 |
| site_id | CSA4 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| G | HIS263 |
| site_id | CSA5 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| B | GLU59 |
| site_id | CSA6 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| D | GLU59 |
| site_id | CSA7 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| F | GLU59 |
| site_id | CSA8 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| H | GLU59 |
| site_id | CSA9 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1dtw |
| Chain | Residue | Details |
| B | GLU59 | |
| B | HIS128 |
