Research workbench
Crystal structure of glutamate dehydrogenase 3 from candida albicans in complex with alpha-ketoglutarate and NADPH
Analyse Crystal structure of glutamate dehydrogenase 3 from candida albicans in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7F79
- Type
- protein
- Length
- 2,723 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- UniProt
- A0A1D8PMH8
- Ligands
- NDP, AKG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate dehydrogenase | protein | 456 | 50% helix, 16% strand | A0A1D8PMH8 |
| B | Glutamate dehydrogenase | protein | 452 | 49% helix, 16% strand | A0A1D8PMH8 |
| C | Glutamate dehydrogenase | protein | 458 | 49% helix, 16% strand | A0A1D8PMH8 |
| D | Glutamate dehydrogenase | protein | 454 | 49% helix, 16% strand | A0A1D8PMH8 |
| E | Glutamate dehydrogenase | protein | 448 | 50% helix, 16% strand | A0A1D8PMH8 |
| F | Glutamate dehydrogenase | protein | 455 | 49% helix, 16% strand | A0A1D8PMH8 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 5 copies · chains A, B, D, F, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.88 | 0.95 | 40 | empty |
| 2 | 443 | 0.86 | 0.94 | 47 | empty |
| 3 | 472 | 0.86 | 0.93 | 39 | empty |
| 4 | 809 | 0.82 | 0.85 | 114 | GOL |
| 5 | 965 | 0.79 | 0.81 | 91 | NDP, AKG |
Interfaces
12 interfaces between chains.
- A–B · 1515 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1393 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1369 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 950 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 945 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7F79 · Crystal structure of glutamate dehydrogenase 3 from Candida albicans in complex 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 A0A1D8PMH8
- Elsewhere: RCSB PDB 7F79 · PDBe 7F79 · UniProt A0A1D8PMH8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.