3EXF
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 | obsolete 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 | pyruvate decarboxylation to acetyl-CoA |
| 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 | obsolete 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 | 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 | pyruvate decarboxylation to acetyl-CoA |
| B | 0006099 | biological_process | tricarboxylic acid cycle |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0072522 | biological_process | purine-containing compound biosynthetic process |
| C | 0004738 | molecular_function | obsolete 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 | pyruvate decarboxylation to acetyl-CoA |
| 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 | obsolete 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 | 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 | pyruvate decarboxylation to acetyl-CoA |
| D | 0006099 | biological_process | tricarboxylic acid cycle |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0072522 | biological_process | purine-containing compound biosynthetic process |
| E | 0004738 | molecular_function | obsolete 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 | pyruvate decarboxylation to acetyl-CoA |
| 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 | obsolete 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 | 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 | pyruvate decarboxylation to acetyl-CoA |
| F | 0006099 | biological_process | tricarboxylic acid cycle |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0072522 | biological_process | purine-containing compound biosynthetic process |
| G | 0004738 | molecular_function | obsolete 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 | pyruvate decarboxylation to acetyl-CoA |
| 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 | obsolete 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 | 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 | pyruvate decarboxylation to acetyl-CoA |
| H | 0006099 | biological_process | tricarboxylic acid cycle |
| H | 0016491 | molecular_function | oxidoreductase activity |
| H | 0045254 | cellular_component | pyruvate dehydrogenase complex |
| H | 0046872 | molecular_function | metal ion binding |
| H | 0072522 | biological_process | purine-containing compound biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG A1001 |
| Chain | Residue |
| A | ASP167 |
| A | ASN196 |
| A | TYR198 |
| A | TPP1003 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K D1002 |
| Chain | Residue |
| D | ARG75 |
| D | PRO111 |
| D | ALA160 |
| D | ILE161 |
| D | ASP163 |
| site_id | AC3 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE TPP A1003 |
| 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 | MET200 |
| A | HIS263 |
| A | MG1001 |
| D | GLU28 |
| D | ILE57 |
| D | GLU59 |
| D | PHE85 |
| D | GLN88 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG C1004 |
| Chain | Residue |
| C | ASP167 |
| C | ASN196 |
| C | TYR198 |
| C | TPP1006 |
| C | HOH2002 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE K B1005 |
| Chain | Residue |
| B | ILE112 |
| B | ALA160 |
| B | ILE161 |
| B | ASP163 |
| site_id | AC6 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE TPP C1006 |
| Chain | Residue |
| B | GLU28 |
| B | ILE57 |
| B | GLU59 |
| B | PHE85 |
| B | GLN88 |
| C | TYR89 |
| C | ARG90 |
| C | GLY136 |
| C | ILE137 |
| C | VAL138 |
| C | GLY166 |
| C | ASP167 |
| C | GLY168 |
| C | ALA169 |
| C | ASN196 |
| C | TYR198 |
| C | GLY199 |
| C | MET200 |
| C | MG1004 |
| C | HOH2002 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG E1007 |
| Chain | Residue |
| E | ASP167 |
| E | ASN196 |
| E | TYR198 |
| E | TPP1009 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE K H1008 |
| Chain | Residue |
| H | PRO111 |
| H | ILE112 |
| H | VAL113 |
| H | ALA160 |
| H | ILE161 |
| H | ASP163 |
| site_id | AC9 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE TPP E1009 |
| Chain | Residue |
| E | TYR89 |
| E | ARG90 |
| E | GLY136 |
| E | VAL138 |
| E | GLY166 |
| E | ASP167 |
| E | GLY168 |
| E | ALA169 |
| E | GLN172 |
| E | ASN196 |
| E | TYR198 |
| E | GLY199 |
| E | MET200 |
| E | HIS263 |
| E | MG1007 |
| H | GLU28 |
| H | ILE57 |
| H | GLU59 |
| H | PHE85 |
| H | GLN88 |
| site_id | BC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG G1010 |
| Chain | Residue |
| G | ASP167 |
| G | ASN196 |
| G | TYR198 |
| G | TPP1012 |
| site_id | BC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K F1011 |
| Chain | Residue |
| F | ARG75 |
| F | PRO111 |
| F | ALA160 |
| F | ILE161 |
| F | ASP163 |
| site_id | BC3 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE TPP G1012 |
| Chain | Residue |
| 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 | MG1010 |
| F | GLU28 |
| F | ILE57 |
| F | GLU59 |
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 | HIS63 | |
| G | ALA128 | |
| G | TYR198 | |
| D | GLU59 | |
| F | GLU59 | |
| H | GLU59 | |
| C | ALA128 | |
| C | TYR198 | |
| E | HIS63 | |
| E | ALA128 | |
| E | TYR198 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12651851, ECO:0000269|PubMed:17474719, ECO:0007744|PDB:1NI4, ECO:0007744|PDB:2OZL |
| Chain | Residue | Details |
| B | ILE112 | |
| E | ARG90 | |
| E | GLY136 | |
| E | VAL138 | |
| G | TYR89 | |
| G | ARG90 | |
| G | GLY136 | |
| G | VAL138 | |
| D | ILE112 | |
| F | ILE112 | |
| H | ILE112 | |
| C | TYR89 | |
| C | ARG90 | |
| C | GLY136 | |
| C | VAL138 | |
| E | TYR89 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12651851, ECO:0000269|PubMed:17474719, ECO:0000269|PubMed:19081061, ECO:0007744|PDB:1NI4, ECO:0007744|PDB:2OZL, ECO:0007744|PDB:3EXE, ECO:0007744|PDB:3EXF, ECO:0007744|PDB:3EXG, ECO:0007744|PDB:3EXH, ECO:0007744|PDB:3EXI |
| Chain | Residue | Details |
| B | ALA160 | |
| B | ASP163 | |
| D | ALA160 | |
| D | ASP163 | |
| F | ALA160 | |
| F | ASP163 | |
| H | ALA160 | |
| H | ASP163 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:19081061, ECO:0007744|PDB:3EXE, ECO:0007744|PDB:3EXF, ECO:0007744|PDB:3EXG, ECO:0007744|PDB:3EXH, ECO:0007744|PDB:3EXI |
| Chain | Residue | Details |
| B | ILE161 | |
| G | GLY168 | |
| G | ALA169 | |
| G | ASN196 | |
| D | ILE161 | |
| F | ILE161 | |
| H | ILE161 | |
| C | ALA169 | |
| C | ASN196 | |
| E | GLY168 | |
| E | ALA169 | |
| E | ASN196 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12651851, ECO:0000269|PubMed:17474719, ECO:0000269|PubMed:19081061, ECO:0007744|PDB:1NI4, ECO:0007744|PDB:2OZL, ECO:0007744|PDB:3EXE |
| Chain | Residue | Details |
| B | ASN165 | |
| D | ASN165 | |
| F | ASN165 | |
| H | ASN165 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | SITE: Important for interaction with DLAT => ECO:0000269|PubMed:20160912 |
| Chain | Residue | Details |
| B | ASP289 | |
| G | LYS34 | |
| G | LYS215 | |
| G | LYS284 | |
| D | ASP289 | |
| F | ASP289 | |
| H | ASP289 | |
| C | LYS215 | |
| C | LYS284 | |
| E | LYS34 | |
| E | LYS215 | |
| E | LYS284 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q9D051 |
| Chain | Residue | Details |
| B | TYR37 | |
| D | TYR37 | |
| F | TYR37 | |
| H | TYR37 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q9D051 |
| Chain | Residue | Details |
| B | LYS324 | |
| D | LYS324 | |
| F | LYS324 | |
| H | LYS324 | |
| E | LYS248 | |
| E | LYS356 | |
| G | LYS248 | |
| G | LYS356 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine; by PDK1, PDK2, PDK3 and PDK4 => ECO:0000269|PubMed:11486000, ECO:0000269|PubMed:17474719, ECO:0000269|PubMed:19081061 |
| Chain | Residue | Details |
| A | SER264 | |
| C | SER264 | |
| E | SER264 | |
| G | SER264 |
| site_id | SWS_FT_FI10 |
| 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_FI11 |
| 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 | ALA271 | |
| C | ALA271 | |
| E | ALA271 | |
| G | ALA271 |
| site_id | SWS_FT_FI12 |
| 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_FI13 |
| 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_FI14 |
| 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 |
