MolNFT v1 · #41178 · protein
Crystal structure of staphylococcus aureus glutamate racemase in complex with D- glutamate
2JFQ: “Crystal structure of staphylococcus aureus glutamate racemase in complex with D- glutamate”. X-ray diffraction, 1 ligand (DGL), 8 pockets (best druggability 0.61). MolNFT v1 #41178 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2JFQ
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- Q6GHT5
- Ligands
- DGL
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate racemase (EC 5.1.1.3) | protein | 265 | 46% helix, 17% strand | Q6GHT5 |
Ligands and binding sites
- 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.61 | 0.75 | 48 | empty |
| 2 | 221 | 0.54 | 0.78 | 37 | empty |
| 3 | 92 | 0.54 | 0.84 | 18 | empty |
| 4 | 85 | 0.52 | 0.84 | 29 | DGL |
| 5 | 72 | 0.52 | 0.85 | 27 | DGL |
Interfaces
1 interface between chains.
- A–B · 1362 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2JFQ · Crystal structure of Staphylococcus aureus glutamate racemase in complex with D- Glutamate · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GHT5 · AlphaFold monomer V2.0 prediction for glutamate racemase (Q6GHT5) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q6GHT5
- Elsewhere: RCSB PDB 2JFQ · PDBe 2JFQ · UniProt Q6GHT5
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