MolNFT v1 · #122265 · protein
Crystal structure of glutamate DEHYDROGENASE(GDH) from corynebacterium glutamicum
5IJZ · NADP-specific glutamate dehydrogenase: “Crystal structure of glutamate DEHYDROGENASE(GDH) from corynebacterium glutamicum”. X-ray diffraction, 2 ligands (NAP, AKG), 20 pockets (best druggability 0.83). MolNFT v1 #122265 on…
- PDB
- 5IJZ
- Type
- protein
- Length
- 5,221 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-specific glutamate dehydrogenase
- EC
- 1.4.1.4
- UniProt
- P31026
- Ligands
- NAP, AKG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, L | NADP-specific glutamate dehydrogenase (EC 1.4.1.4) | protein | 447 | 51% helix, 15% strand | P31026 |
| K | NADP-specific glutamate dehydrogenase (EC 1.4.1.4) | protein | 304 | 58% helix, 14% strand | P31026 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 9 copies · chains A, B, C, D, E, F, G, H, J
- AKG · 2-oxoglutaric acid · ligand · 9 copies · chains A, B, C, D, E, F, G, H, J
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 | 222 | 0.83 | 0.96 | 27 | empty |
| 2 | 203 | 0.83 | 0.96 | 27 | empty |
| 3 | 202 | 0.82 | 0.96 | 25 | empty |
| 4 | 252 | 0.82 | 0.94 | 34 | empty |
| 5 | 247 | 0.80 | 0.93 | 34 | empty |
Interfaces
27 interfaces between chains.
- D–F · 1486 Ų buried · 39 hydrogen bonds · protein-protein
- A–L · 1485 Ų buried · 40 hydrogen bonds · protein-protein
- C–I · 1476 Ų buried · 40 hydrogen bonds · protein-protein
- B–E · 1465 Ų buried · 38 hydrogen bonds · protein-protein
- G–K · 1459 Ų buried · 41 hydrogen bonds · protein-protein
Compared structures
- 5IJZ · Crystal structure of glutamate dehydrogenase(GDH) from Corynebacterium glutamicum · the same entry in another collection · chain L against L, 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 P31026
- Elsewhere: RCSB PDB 5IJZ · PDBe 5IJZ · UniProt P31026
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