MolNFT v1 · #9449 · protein
Bovine glutamate dehydrogenase complexed with NAD and 2-oxoglutarate
1HWY: “Bovine glutamate dehydrogenase complexed with NAD and 2-oxoglutarate”. X-ray diffraction, 3 ligands (NAD, AKG, PO4), 20 pockets (best druggability 0.87). MolNFT v1 #9449 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1HWY
- Type
- protein
- Length
- 3,006 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- EC
- 1.4.1.3
- UniProt
- P00366
- Ligands
- NAD, AKG, PO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate dehydrogenase (EC 1.4.1.3) | protein | 501 | 50% helix, 13% strand | P00366 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 12 copies · chains A, B, F, C, E, D
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 24 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 | 1164 | 0.87 | 0.87 | 78 | empty |
| 2 | 1126 | 0.86 | 0.87 | 79 | empty |
| 3 | 665 | 0.84 | 0.89 | 74 | NAD |
| 4 | 678 | 0.83 | 0.87 | 73 | NAD |
| 5 | 693 | 0.83 | 0.87 | 80 | NAD |
Interfaces
12 interfaces between chains.
- B–F · 2012 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 1996 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1987 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 1974 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1970 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 1HWY · Bovine glutamate dehydrogenase complexed with NAD and 2-oxoglutarate · the same entry in another collection · chain F against F, TM-score 1.00
- P00366 · AlphaFold monomer V2.0 prediction for glutamate dehydrogenase 1, mitochondrial (P00366) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P00366
- Elsewhere: RCSB PDB 1HWY · PDBe 1HWY · UniProt P00366
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.