MolNFT v1 · #120258 · protein
Glutamate dehydrogenase from corynebacterium glutamicum (alpha- IMINOGLUTARATE/NADP+ complex)
5GUD: “Glutamate dehydrogenase from corynebacterium glutamicum (alpha- IMINOGLUTARATE/NADP+ complex)”. X-ray diffraction, 3 ligands (NDP, 2IT, K), 20 pockets (best druggability 0.83). MolNFT v1 #120258 on GenesisL1: 3D structure, binding…
- PDB
- 5GUD
- Type
- protein
- Length
- 2,694 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- UniProt
- A0A0U4QBJ6
- Ligands
- NDP, 2IT, K
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F | Glutamate dehydrogenase | protein | 447 | 52% helix, 15% strand | A0A0U4QBJ6 |
| B | Glutamate dehydrogenase | protein | 446 | 52% helix, 15% strand | A0A0U4QBJ6 |
| E | Glutamate dehydrogenase | protein | 460 | 49% helix, 15% strand | A0A0U4QBJ6 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- 2IT · (2Z)-2-iminopentanedioic acid · ligand · 4 copies · chains A, B, C, F
- K · Potassium ion · metal · 14 copies · chains A, B, C, D, F, E
- CIT · Citric acid · additive · chains E
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 | 225 | 0.83 | 0.96 | 26 | empty |
| 2 | 200 | 0.83 | 0.97 | 24 | empty |
| 3 | 223 | 0.80 | 0.94 | 35 | empty |
| 4 | 946 | 0.79 | 0.81 | 135 | K |
| 5 | 752 | 0.79 | 0.83 | 113 | K |
Interfaces
12 interfaces between chains.
- E–F · 1577 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 1467 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1458 Ų buried · 40 hydrogen bonds · protein-protein
- A–E · 1141 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 1131 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5GUD · Glutamate dehydrogenase from Corynebacterium glutamicum (alpha-iminoglutarate/NADP+… · 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 A0A0U4QBJ6
- Elsewhere: RCSB PDB 5GUD · PDBe 5GUD · UniProt A0A0U4QBJ6
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