Research workbench
Bovine glutamate dehydrogenase complexed with zinc
Analyse Bovine glutamate dehydrogenase complexed with zinc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DHM
- Type
- protein
- Length
- 2,976 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, ZN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Glutamate dehydrogenase 1, mitochondrial (EC 1.4.1.2) | protein | 495 | 48% helix, 15% strand | A0A140T871 |
| F | Glutamate dehydrogenase 1, mitochondrial (EC 1.4.1.2) | protein | 501 | 49% helix, 13% 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
- ZN · Zinc ion · metal · 12 copies · chains A, D, B, E, C, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.88 | 0.89 | 75 | empty |
| 2 | 1034 | 0.88 | 0.89 | 93 | empty |
| 3 | 991 | 0.87 | 0.88 | 74 | empty |
| 4 | 714 | 0.86 | 0.89 | 82 | ZN |
| 5 | 906 | 0.86 | 0.87 | 90 | empty |
Interfaces
15 interfaces between chains.
- D–F · 1967 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1835 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1816 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1758 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1708 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 6DHM · Bovine glutamate dehydrogenase complexed with zinc · the same entry in another collection · chain A against A, 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 6DHM · PDBe 6DHM · UniProt A0A140T871
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