Research workbench
Crystal structure of aspergillus niger apo- glutamate dehydrogenase
Analyse Crystal structure of aspergillus niger apo- glutamate dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XVI
- Type
- protein
- Length
- 2,751 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate dehydrogenase
- UniProt
- B6V7E4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glutamate dehydrogenase | protein | 459 | 46% helix, 15% strand | B6V7E4 |
| D, E, F | Glutamate dehydrogenase | protein | 458 | 45% helix, 15% strand | B6V7E4 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, D, 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 | 509 | 0.88 | 0.95 | 62 | empty |
| 2 | 454 | 0.88 | 0.95 | 54 | empty |
| 3 | 481 | 0.87 | 0.94 | 51 | empty |
| 4 | 819 | 0.82 | 0.85 | 115 | empty |
| 5 | 946 | 0.76 | 0.79 | 79 | empty |
Interfaces
12 interfaces between chains.
- A–E · 1594 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1567 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 1567 Ų buried · 28 hydrogen bonds · protein-protein
- D–F · 1155 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1130 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5XVI · Crystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase · 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 5XVI · PDBe 5XVI · UniProt B6V7E4
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