MolNFT v1 · #146443 · protein
Bovine glutamate dehydrogenase complexed with NADPH, glutamate, and GTP
6DHQ · Glutamate dehydrogenase 1, mitochondrial: “Bovine glutamate dehydrogenase complexed with NADPH, glutamate, and GTP”. X-ray diffraction, 3 ligands (GLU, NDP, GTP), 20 pockets (best druggability 0.87). MolNFT v1 #146443 on GenesisL1…
- PDB
- 6DHQ
- Type
- protein
- Length
- 3,006 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase 1, mitochondrial
- EC
- 1.4.1.2
- UniProt
- A0A140T871
- Ligands
- GLU, NDP, GTP
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate dehydrogenase 1, mitochondrial (EC 1.4.1.2) | protein | 501 | 49% helix, 14% strand | A0A140T871 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 6 copies · chains A, B, C, D, E, F
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.87 | 0.87 | 78 | empty |
| 2 | 1105 | 0.87 | 0.87 | 78 | empty |
| 3 | 1078 | 0.83 | 0.84 | 90 | empty |
| 4 | 1170 | 0.82 | 0.83 | 83 | empty |
| 5 | 725 | 0.81 | 0.85 | 57 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1979 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1972 Ų buried · 23 hydrogen bonds · protein-protein
- C–E · 1967 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 1956 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1941 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6DHQ · Bovine glutamate dehydrogenase complexed with NADPH, glutamate, and GTP · the same entry in another collection · chain C against C, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A140T871
- Elsewhere: RCSB PDB 6DHQ · PDBe 6DHQ · UniProt A0A140T871
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