MolNFT v1 · #139971 · protein
Crystal structure of forward inhibited aspergillus niger glutamate dehydrogenase with both apo- and alpha ketoglutarate bound subunits
5XVV: “Crystal structure of forward inhibited aspergillus niger glutamate dehydrogenase with both apo- and alpha…”. X-ray diffraction, 1 ligand (AKG), 20 pockets (best druggability 0.89). MolNFT v1 #139971 on GenesisL1: 3D structure…
- PDB
- 5XVV
- Type
- protein
- Length
- 2,749 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- UniProt
- B6V7E4
- Ligands
- AKG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Glutamate dehydrogenase | protein | 458 | 47% helix, 16% strand | B6V7E4 |
| B, C | Glutamate dehydrogenase | protein | 459 | 46% helix, 17% strand | B6V7E4 |
| F | Glutamate dehydrogenase | protein | 457 | 47% helix, 16% strand | B6V7E4 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 22 copies · chains A, C, B, E, D, F
- BME · Beta-mercaptoethanol · additive · 6 copies · chains A, F, B, D, C, 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 | 592 | 0.89 | 0.95 | 68 | GOL |
| 2 | 549 | 0.88 | 0.94 | 60 | GOL |
| 3 | 546 | 0.88 | 0.94 | 63 | empty |
| 4 | 421 | 0.79 | 0.88 | 75 | GOL |
| 5 | 898 | 0.76 | 0.79 | 75 | AKG |
Interfaces
12 interfaces between chains.
- C–D · 1556 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 1541 Ų buried · 30 hydrogen bonds · protein-protein
- B–F · 1478 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1140 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 1127 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (additive adduct).
Compared structures
- 5XVV · Crystal Structure of Forward Inhibited Aspergillus niger Glutamate Dehydrogenase With… · 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 B6V7E4
- Elsewhere: RCSB PDB 5XVV · PDBe 5XVV · UniProt B6V7E4
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