Research workbench
Crystal structure of glutamate dehydrogenase from peptoniphilus asaccharolyticus
Analyse Crystal structure of glutamate dehydrogenase from peptoniphilus asaccharolyticus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YFQ
- Type
- protein
- Length
- 792 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-specific glutamate dehydrogenase
- EC
- 1.4.1.2
- UniProt
- P28997
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 395 | 51% helix, 16% strand | P28997 |
| B | NAD-specific glutamate dehydrogenase (EC 1.4.1.2) | protein | 397 | 50% helix, 15% strand | P28997 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.70 | 0.77 | 80 | SO4 |
| 2 | 699 | 0.69 | 0.76 | 73 | SO4 |
| 3 | 314 | 0.60 | 0.78 | 34 | empty |
| 4 | 312 | 0.59 | 0.77 | 31 | empty |
| 5 | 101 | 0.44 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1167 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2YFQ · Crystal structure of Glutamate dehydrogenase from Peptoniphilus asaccharolyticus · the same entry in another collection · chain A against A, TM-score 1.00
- P28997 · AlphaFold monomer V2.0 prediction for NAD-specific glutamate dehydrogenase (P28997) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P28997
- Elsewhere: RCSB PDB 2YFQ · PDBe 2YFQ · UniProt P28997
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