MolNFT v1 · #41177 · protein
Crystal structure of enterococcus faecalis glutamate racemase in complex with D- glutamate
2JFP: “Crystal structure of enterococcus faecalis glutamate racemase in complex with D- glutamate”. X-ray diffraction, 2 ligands (DGL, CA), 3 pockets (best druggability 0.63). MolNFT v1 #41177 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2JFP
- Type
- protein
- Length
- 534 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
- DGL, CA
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate racemase (EC 5.1.1.3) | protein | 267 | 47% helix, 16% strand | Q836J0 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.63 | 0.79 | 43 | empty |
| 2 | 356 | 0.62 | 0.78 | 44 | empty |
| 3 | 222 | 0.52 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 879 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2JFP · Crystal structure of Enterococcus faecalis glutamate racemase in complex with D- Glutamate · 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 0.96
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 2JFP · PDBe 2JFP · UniProt Q836J0
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