3JD3
Glutamate dehydrogenase in complex with NADH and GTP, open conformation
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004352 | molecular_function | glutamate dehydrogenase (NAD+) activity |
| A | 0004353 | molecular_function | glutamate dehydrogenase [NAD(P)+] activity |
| A | 0004354 | molecular_function | glutamate dehydrogenase (NADP+) activity |
| A | 0005524 | molecular_function | ATP binding |
| A | 0005525 | molecular_function | GTP binding |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005743 | cellular_component | mitochondrial inner membrane |
| A | 0005783 | cellular_component | endoplasmic reticulum |
| A | 0006520 | biological_process | amino acid metabolic process |
| A | 0006538 | biological_process | glutamate catabolic process |
| A | 0006541 | biological_process | glutamine metabolic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016639 | molecular_function | oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0072350 | biological_process | tricarboxylic acid metabolic process |
| B | 0004352 | molecular_function | glutamate dehydrogenase (NAD+) activity |
| B | 0004353 | molecular_function | glutamate dehydrogenase [NAD(P)+] activity |
| B | 0004354 | molecular_function | glutamate dehydrogenase (NADP+) activity |
| B | 0005524 | molecular_function | ATP binding |
| B | 0005525 | molecular_function | GTP binding |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005743 | cellular_component | mitochondrial inner membrane |
| B | 0005783 | cellular_component | endoplasmic reticulum |
| B | 0006520 | biological_process | amino acid metabolic process |
| B | 0006538 | biological_process | glutamate catabolic process |
| B | 0006541 | biological_process | glutamine metabolic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016639 | molecular_function | oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0072350 | biological_process | tricarboxylic acid metabolic process |
| C | 0004352 | molecular_function | glutamate dehydrogenase (NAD+) activity |
| C | 0004353 | molecular_function | glutamate dehydrogenase [NAD(P)+] activity |
| C | 0004354 | molecular_function | glutamate dehydrogenase (NADP+) activity |
| C | 0005524 | molecular_function | ATP binding |
| C | 0005525 | molecular_function | GTP binding |
| C | 0005739 | cellular_component | mitochondrion |
| C | 0005743 | cellular_component | mitochondrial inner membrane |
| C | 0005783 | cellular_component | endoplasmic reticulum |
| C | 0006520 | biological_process | amino acid metabolic process |
| C | 0006538 | biological_process | glutamate catabolic process |
| C | 0006541 | biological_process | glutamine metabolic process |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016639 | molecular_function | oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0072350 | biological_process | tricarboxylic acid metabolic process |
| D | 0004352 | molecular_function | glutamate dehydrogenase (NAD+) activity |
| D | 0004353 | molecular_function | glutamate dehydrogenase [NAD(P)+] activity |
| D | 0004354 | molecular_function | glutamate dehydrogenase (NADP+) activity |
| D | 0005524 | molecular_function | ATP binding |
| D | 0005525 | molecular_function | GTP binding |
| D | 0005739 | cellular_component | mitochondrion |
| D | 0005743 | cellular_component | mitochondrial inner membrane |
| D | 0005783 | cellular_component | endoplasmic reticulum |
| D | 0006520 | biological_process | amino acid metabolic process |
| D | 0006538 | biological_process | glutamate catabolic process |
| D | 0006541 | biological_process | glutamine metabolic process |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016639 | molecular_function | oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0072350 | biological_process | tricarboxylic acid metabolic process |
| E | 0004352 | molecular_function | glutamate dehydrogenase (NAD+) activity |
| E | 0004353 | molecular_function | glutamate dehydrogenase [NAD(P)+] activity |
| E | 0004354 | molecular_function | glutamate dehydrogenase (NADP+) activity |
| E | 0005524 | molecular_function | ATP binding |
| E | 0005525 | molecular_function | GTP binding |
| E | 0005739 | cellular_component | mitochondrion |
| E | 0005743 | cellular_component | mitochondrial inner membrane |
| E | 0005783 | cellular_component | endoplasmic reticulum |
| E | 0006520 | biological_process | amino acid metabolic process |
| E | 0006538 | biological_process | glutamate catabolic process |
| E | 0006541 | biological_process | glutamine metabolic process |
| E | 0016491 | molecular_function | oxidoreductase activity |
| E | 0016639 | molecular_function | oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor |
| E | 0042802 | molecular_function | identical protein binding |
| E | 0072350 | biological_process | tricarboxylic acid metabolic process |
| F | 0004352 | molecular_function | glutamate dehydrogenase (NAD+) activity |
| F | 0004353 | molecular_function | glutamate dehydrogenase [NAD(P)+] activity |
| F | 0004354 | molecular_function | glutamate dehydrogenase (NADP+) activity |
| F | 0005524 | molecular_function | ATP binding |
| F | 0005525 | molecular_function | GTP binding |
| F | 0005739 | cellular_component | mitochondrion |
| F | 0005743 | cellular_component | mitochondrial inner membrane |
| F | 0005783 | cellular_component | endoplasmic reticulum |
| F | 0006520 | biological_process | amino acid metabolic process |
| F | 0006538 | biological_process | glutamate catabolic process |
| F | 0006541 | biological_process | glutamine metabolic process |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0016639 | molecular_function | oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor |
| F | 0042802 | molecular_function | identical protein binding |
| F | 0072350 | biological_process | tricarboxylic acid metabolic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GTP A 601 |
| Chain | Residue |
| A | ARG261 |
| A | TYR262 |
| A | GLU292 |
| A | LYS446 |
| A | HIS450 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE NAI A 602 |
| Chain | Residue |
| A | ASN254 |
| A | GLU275 |
| A | SER276 |
| A | ALA326 |
| A | GLN330 |
| A | ALA348 |
| A | MET169 |
| A | GLN250 |
| A | PHE252 |
| A | GLY253 |
| site_id | AC3 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE NAI A 603 |
| Chain | Residue |
| A | HIS85 |
| A | ARG86 |
| A | CYS115 |
| A | ASP119 |
| A | VAL120 |
| A | PHE122 |
| A | ARG459 |
| A | GLN463 |
| B | SER204 |
| B | HIS209 |
| B | SER393 |
| B | SER444 |
| B | GLU445 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GTP B 601 |
| Chain | Residue |
| B | ARG261 |
| B | TYR262 |
| B | GLU292 |
| B | LYS446 |
| B | HIS450 |
| site_id | AC5 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE NAI B 602 |
| Chain | Residue |
| B | MET169 |
| B | GLN250 |
| B | PHE252 |
| B | GLY253 |
| B | ASN254 |
| B | GLU275 |
| B | SER276 |
| B | ALA326 |
| B | GLN330 |
| B | ALA348 |
| site_id | AC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE NAI B 603 |
| Chain | Residue |
| B | HIS85 |
| B | ARG86 |
| B | CYS115 |
| B | ASP119 |
| B | VAL120 |
| B | PHE122 |
| B | ARG459 |
| B | GLN463 |
| C | SER204 |
| C | HIS209 |
| C | SER393 |
| C | SER444 |
| C | GLU445 |
| site_id | AC7 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE NAI C 601 |
| Chain | Residue |
| A | SER204 |
| A | HIS209 |
| A | SER393 |
| A | SER444 |
| A | GLU445 |
| C | HIS85 |
| C | ARG86 |
| C | CYS115 |
| C | ASP119 |
| C | VAL120 |
| C | PHE122 |
| C | ARG459 |
| C | GLN463 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GTP C 602 |
| Chain | Residue |
| C | ARG261 |
| C | TYR262 |
| C | GLU292 |
| C | LYS446 |
| C | HIS450 |
| site_id | AC9 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE NAI C 603 |
| Chain | Residue |
| C | MET169 |
| C | GLN250 |
| C | PHE252 |
| C | GLY253 |
| C | ASN254 |
| C | GLU275 |
| C | SER276 |
| C | ALA326 |
| C | GLN330 |
| C | ALA348 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GTP D 601 |
| Chain | Residue |
| D | ARG261 |
| D | TYR262 |
| D | GLU292 |
| D | LYS446 |
| D | HIS450 |
| site_id | BC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE NAI D 602 |
| Chain | Residue |
| D | MET169 |
| D | GLN250 |
| D | PHE252 |
| D | GLY253 |
| D | ASN254 |
| D | GLU275 |
| D | SER276 |
| D | ALA326 |
| D | GLN330 |
| D | ALA348 |
| site_id | BC3 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE NAI D 603 |
| Chain | Residue |
| D | HIS85 |
| D | ARG86 |
| D | CYS115 |
| D | ASP119 |
| D | VAL120 |
| D | PHE122 |
| D | ARG459 |
| D | GLN463 |
| E | SER204 |
| E | HIS209 |
| E | SER393 |
| E | SER444 |
| E | GLU445 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GTP E 601 |
| Chain | Residue |
| E | ARG261 |
| E | TYR262 |
| E | GLU292 |
| E | LYS446 |
| E | HIS450 |
| site_id | BC5 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE NAI E 602 |
| Chain | Residue |
| E | MET169 |
| E | GLN250 |
| E | PHE252 |
| E | GLY253 |
| E | ASN254 |
| E | GLU275 |
| E | SER276 |
| E | ALA326 |
| E | GLN330 |
| E | ALA348 |
| site_id | BC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE NAI E 603 |
| Chain | Residue |
| E | HIS85 |
| E | ARG86 |
| E | CYS115 |
| E | ASP119 |
| E | VAL120 |
| E | PHE122 |
| E | ARG459 |
| E | GLN463 |
| F | SER204 |
| F | HIS209 |
| F | SER393 |
| F | SER444 |
| F | GLU445 |
| site_id | BC7 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE NAI F 601 |
| Chain | Residue |
| D | SER204 |
| D | HIS209 |
| D | SER393 |
| D | SER444 |
| D | GLU445 |
| F | HIS85 |
| F | ARG86 |
| F | CYS115 |
| F | ASP119 |
| F | VAL120 |
| F | PHE122 |
| F | ARG459 |
| F | GLN463 |
| site_id | BC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GTP F 602 |
| Chain | Residue |
| F | ARG261 |
| F | TYR262 |
| F | GLU292 |
| F | LYS446 |
| F | HIS450 |
| site_id | BC9 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE NAI F 603 |
| Chain | Residue |
| F | MET169 |
| F | GLN250 |
| F | PHE252 |
| F | GLY253 |
| F | ASN254 |
| F | GLU275 |
| F | SER276 |
| F | ALA326 |
| F | GLN330 |
| F | ALA348 |
Functional Information from PROSITE/UniProt
| site_id | PS00074 |
| Number of Residues | 14 |
| Details | GLFV_DEHYDROGENASE Glu / Leu / Phe / Val dehydrogenases active site. VpfGGAKaGvkiNP |
| Chain | Residue | Details |
| A | VAL120-PRO133 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | ACT_SITE: ACT_SITE => ECO:0000255|PROSITE-ProRule:PRU10011 |
| Chain | Residue | Details |
| A | LYS126 | |
| B | LYS126 | |
| C | LYS126 | |
| D | LYS126 | |
| E | LYS126 | |
| F | LYS126 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 66 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11254391 |
| Chain | Residue | Details |
| A | GLN84 | |
| A | SER381 | |
| A | ASN387 | |
| B | GLN84 | |
| B | LYS90 | |
| B | LYS114 | |
| B | ASP119 | |
| B | HIS195 | |
| B | HIS209 | |
| B | SER213 | |
| B | TYR262 | |
| A | LYS90 | |
| B | ARG265 | |
| B | SER381 | |
| B | ASN387 | |
| C | GLN84 | |
| C | LYS90 | |
| C | LYS114 | |
| C | ASP119 | |
| C | HIS195 | |
| C | HIS209 | |
| C | SER213 | |
| A | LYS114 | |
| C | TYR262 | |
| C | ARG265 | |
| C | SER381 | |
| C | ASN387 | |
| D | GLN84 | |
| D | LYS90 | |
| D | LYS114 | |
| D | ASP119 | |
| D | HIS195 | |
| D | HIS209 | |
| A | ASP119 | |
| D | SER213 | |
| D | TYR262 | |
| D | ARG265 | |
| D | SER381 | |
| D | ASN387 | |
| E | GLN84 | |
| E | LYS90 | |
| E | LYS114 | |
| E | ASP119 | |
| E | HIS195 | |
| A | HIS195 | |
| E | HIS209 | |
| E | SER213 | |
| E | TYR262 | |
| E | ARG265 | |
| E | SER381 | |
| E | ASN387 | |
| F | GLN84 | |
| F | LYS90 | |
| F | LYS114 | |
| F | ASP119 | |
| A | HIS209 | |
| F | HIS195 | |
| F | HIS209 | |
| F | SER213 | |
| F | TYR262 | |
| F | ARG265 | |
| F | SER381 | |
| F | ASN387 | |
| A | SER213 | |
| A | TYR262 | |
| A | ARG265 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12653548 |
| Chain | Residue | Details |
| A | SER393 | |
| E | ARG459 | |
| F | SER393 | |
| F | ARG459 | |
| A | ARG459 | |
| B | SER393 | |
| B | ARG459 | |
| C | SER393 | |
| C | ARG459 | |
| D | SER393 | |
| D | ARG459 | |
| E | SER393 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P26443 |
| Chain | Residue | Details |
| A | LYS11 | |
| E | LYS143 | |
| F | LYS11 | |
| F | LYS143 | |
| A | LYS143 | |
| B | LYS11 | |
| B | LYS143 | |
| C | LYS11 | |
| C | LYS143 | |
| D | LYS11 | |
| D | LYS143 | |
| E | LYS11 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 12 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P26443 |
| Chain | Residue | Details |
| A | SER22 | |
| E | SER71 | |
| F | SER22 | |
| F | SER71 | |
| A | SER71 | |
| B | SER22 | |
| B | SER71 | |
| C | SER22 | |
| C | SER71 | |
| D | SER22 | |
| D | SER71 | |
| E | SER22 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 54 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22076378 |
| Chain | Residue | Details |
| A | LYS27 | |
| B | LYS27 | |
| B | LYS53 | |
| B | LYS105 | |
| B | LYS306 | |
| B | LYS358 | |
| B | LYS400 | |
| B | LYS446 | |
| B | LYS470 | |
| B | LYS488 | |
| C | LYS27 | |
| A | LYS53 | |
| C | LYS53 | |
| C | LYS105 | |
| C | LYS306 | |
| C | LYS358 | |
| C | LYS400 | |
| C | LYS446 | |
| C | LYS470 | |
| C | LYS488 | |
| D | LYS27 | |
| D | LYS53 | |
| A | LYS105 | |
| D | LYS105 | |
| D | LYS306 | |
| D | LYS358 | |
| D | LYS400 | |
| D | LYS446 | |
| D | LYS470 | |
| D | LYS488 | |
| E | LYS27 | |
| E | LYS53 | |
| E | LYS105 | |
| A | LYS306 | |
| E | LYS306 | |
| E | LYS358 | |
| E | LYS400 | |
| E | LYS446 | |
| E | LYS470 | |
| E | LYS488 | |
| F | LYS27 | |
| F | LYS53 | |
| F | LYS105 | |
| F | LYS306 | |
| A | LYS358 | |
| F | LYS358 | |
| F | LYS400 | |
| F | LYS446 | |
| F | LYS470 | |
| F | LYS488 | |
| A | LYS400 | |
| A | LYS446 | |
| A | LYS470 | |
| A | LYS488 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 18 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:22076378 |
| Chain | Residue | Details |
| A | LYS33 | |
| D | LYS33 | |
| D | LYS329 | |
| D | LYS342 | |
| E | LYS33 | |
| E | LYS329 | |
| E | LYS342 | |
| F | LYS33 | |
| F | LYS329 | |
| F | LYS342 | |
| A | LYS329 | |
| A | LYS342 | |
| B | LYS33 | |
| B | LYS329 | |
| B | LYS342 | |
| C | LYS33 | |
| C | LYS329 | |
| C | LYS342 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P26443 |
| Chain | Residue | Details |
| A | TYR78 | |
| B | TYR78 | |
| C | TYR78 | |
| D | TYR78 | |
| E | TYR78 | |
| F | TYR78 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P00367 |
| Chain | Residue | Details |
| A | LYS90 | |
| B | LYS90 | |
| C | LYS90 | |
| D | LYS90 | |
| E | LYS90 | |
| F | LYS90 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 24 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P26443 |
| Chain | Residue | Details |
| A | LYS114 | |
| C | LYS130 | |
| C | LYS154 | |
| C | LYS269 | |
| D | LYS114 | |
| D | LYS130 | |
| D | LYS154 | |
| D | LYS269 | |
| E | LYS114 | |
| E | LYS130 | |
| E | LYS154 | |
| A | LYS130 | |
| E | LYS269 | |
| F | LYS114 | |
| F | LYS130 | |
| F | LYS154 | |
| F | LYS269 | |
| A | LYS154 | |
| A | LYS269 | |
| B | LYS114 | |
| B | LYS130 | |
| B | LYS154 | |
| B | LYS269 | |
| C | LYS114 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 6 |
| Details | MOD_RES: ADP-ribosylcysteine => ECO:0000250|UniProtKB:P00367 |
| Chain | Residue | Details |
| A | CYS115 | |
| B | CYS115 | |
| C | CYS115 | |
| D | CYS115 | |
| E | CYS115 | |
| F | CYS115 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 48 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P26443 |
| Chain | Residue | Details |
| A | LYS126 | |
| B | LYS134 | |
| B | LYS289 | |
| B | LYS295 | |
| B | LYS308 | |
| B | LYS333 | |
| B | LYS420 | |
| B | LYS423 | |
| C | LYS126 | |
| C | LYS134 | |
| C | LYS289 | |
| A | LYS134 | |
| C | LYS295 | |
| C | LYS308 | |
| C | LYS333 | |
| C | LYS420 | |
| C | LYS423 | |
| D | LYS126 | |
| D | LYS134 | |
| D | LYS289 | |
| D | LYS295 | |
| D | LYS308 | |
| A | LYS289 | |
| D | LYS333 | |
| D | LYS420 | |
| D | LYS423 | |
| E | LYS126 | |
| E | LYS134 | |
| E | LYS289 | |
| E | LYS295 | |
| E | LYS308 | |
| E | LYS333 | |
| E | LYS420 | |
| A | LYS295 | |
| E | LYS423 | |
| F | LYS126 | |
| F | LYS134 | |
| F | LYS289 | |
| F | LYS295 | |
| F | LYS308 | |
| F | LYS333 | |
| F | LYS420 | |
| F | LYS423 | |
| A | LYS308 | |
| A | LYS333 | |
| A | LYS420 | |
| A | LYS423 | |
| B | LYS126 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 12 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P00367 |
| Chain | Residue | Details |
| A | SER170 | |
| E | SER327 | |
| F | SER170 | |
| F | SER327 | |
| A | SER327 | |
| B | SER170 | |
| B | SER327 | |
| C | SER170 | |
| C | SER327 | |
| D | SER170 | |
| D | SER327 | |
| E | SER170 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P10860 |
| Chain | Residue | Details |
| A | THR353 | |
| B | THR353 | |
| C | THR353 | |
| D | THR353 | |
| E | THR353 | |
| F | THR353 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P00367 |
| Chain | Residue | Details |
| A | TYR455 | |
| B | TYR455 | |
| C | TYR455 | |
| D | TYR455 | |
| E | TYR455 | |
| F | TYR455 |
