Research workbench
Glutamate racemase mycobacterium tuberculosis (muri) with bound D- glutamate, 2.3 ångström resolution, X-ray diffraction
Analyse Glutamate racemase mycobacterium tuberculosis (muri) with bound D- glutamate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HJ7
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- P9WPW9
- Ligands
- DGL
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate racemase (EC 5.1.1.3) | protein | 254 | 49% helix, 17% strand | P9WPW9 |
| B | Glutamate racemase (EC 5.1.1.3) | protein | 260 | 48% helix, 16% strand | P9WPW9 |
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
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.85 | 0.95 | 42 | empty |
| 2 | 106 | 0.49 | 0.81 | 28 | DGL |
| 3 | 51 | 0.49 | 0.87 | 12 | empty |
| 4 | 107 | 0.48 | 0.80 | 30 | DGL |
| 5 | 50 | 0.44 | 0.84 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1841 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5HJ7 · Glutamate Racemase Mycobacterium tuberculosis (MurI) with bound D-glutamate, 2.3 Angstrom… · the same entry in another collection · chain B against B, TM-score 1.00
- P9WPW9 · AlphaFold monomer V2.0 prediction for glutamate racemase (P9WPW9) · 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 P9WPW9
- Elsewhere: RCSB PDB 5HJ7 · PDBe 5HJ7 · UniProt P9WPW9
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