Research workbench
Glutamate racemase (muri) from E. faecalis in complex with a 9-benzyl purine inhibitor
Analyse Glutamate racemase (muri) from E. faecalis in complex with a 9-benzyl purine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VVT
- Type
- protein
- Length
- 535 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- Q836J0
- Ligands
- I24, DGL
- Pockets
- 8 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate racemase (EC 5.1.1.3) | protein | 269 | 46% helix, 16% strand | Q836J0 |
| B | Glutamate racemase (EC 5.1.1.3) | protein | 266 | 48% helix, 16% strand | Q836J0 |
Ligands and binding sites
- I24 · 2-butoxy-9-(2,6-difluorobenzyl)-N-(2-morpholin-4-ylethyl)-9H-purin-6-amine · ligand · 2 copies · chains A, B
- DGL · D-glutamic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.60 | 0.79 | 43 | empty |
| 2 | 376 | 0.56 | 0.75 | 39 | empty |
| 3 | 229 | 0.55 | 0.78 | 24 | empty |
| 4 | 55 | 0.54 | 0.88 | 22 | DGL |
| 5 | 157 | 0.53 | 0.79 | 24 | I24 |
Interfaces
1 interface between chains.
- A–B · 1401 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 2VVT · Glutamate Racemase (MurI) from E. faecalis in complex with a 9-Benzyl Purine inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q836J0 · AlphaFold monomer V2.0 prediction for glutamate racemase (Q836J0) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q836J0
- Elsewhere: RCSB PDB 2VVT · PDBe 2VVT · UniProt Q836J0
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