Research workbench
Crystal structure of glutamate dehydrogenase from burkholderia thailandensis
Analyse Crystal structure of glutamate dehydrogenase from burkholderia thailandensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XGI
- Type
- protein
- Length
- 2,492 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- UniProt
- Q2SZ78
- Ligands
- NAD, AKG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glutamate dehydrogenase | protein | 416 | 51% helix, 17% strand | Q2SZ78 |
| B, D, E, F | Glutamate dehydrogenase | protein | 415 | 51% helix, 16% strand | Q2SZ78 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 6 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.76 | 0.78 | 109 | empty |
| 2 | 1049 | 0.75 | 0.78 | 97 | empty |
| 3 | 88 | 0.75 | 0.98 | 30 | empty |
| 4 | 78 | 0.73 | 0.97 | 28 | empty |
| 5 | 555 | 0.73 | 0.81 | 57 | NAD, AKG |
Interfaces
15 interfaces between chains.
- A–E · 2033 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 2028 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 2011 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 763 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 757 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4XGI · Crystal structure of Glutamate dehydrogenase from Burkholderia thailandensis · 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 Q2SZ78
- Elsewhere: RCSB PDB 4XGI · PDBe 4XGI · UniProt Q2SZ78
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