MolNFT v1 · #122263 · protein
Glutamate racemase (muri) from mycobacterium smegmatis with bound D- glutamate, 1.8 ångström resolution, X-ray diffraction
5IJW: “Glutamate racemase (muri) from mycobacterium smegmatis with bound D- glutamate, 1.8 ångström resolution…”. X-ray diffraction, 2 ligands (DGL, IOD), 11 pockets (best druggability 0.85). MolNFT v1 #122263 on GenesisL1: 3D structure…
- PDB
- 5IJW
- Type
- protein
- Length
- 548 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- A0R1X0
- Ligands
- DGL, IOD
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate racemase (EC 5.1.1.3) | protein | 272 | 45% helix, 16% strand | A0R1X0 |
| B | Glutamate racemase (EC 5.1.1.3) | protein | 276 | 46% helix, 16% strand | A0R1X0 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.85 | 0.95 | 42 | empty |
| 2 | 68 | 0.54 | 0.87 | 12 | empty |
| 3 | 105 | 0.52 | 0.82 | 12 | empty |
| 4 | 101 | 0.51 | 0.82 | 29 | DGL |
| 5 | 118 | 0.50 | 0.81 | 31 | DGL, IOD |
Interfaces
1 interface between chains.
- A–B · 2276 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 5IJW · Glutamate Racemase (MurI) from Mycobacterium smegmatis with bound D-glutamate, 1.8… · the same entry in another collection · chain A against A, TM-score 1.00
- A0R1X0 · AlphaFold monomer V2.0 prediction for glutamate racemase (A0R1X0) · 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 A0R1X0
- Elsewhere: RCSB PDB 5IJW · PDBe 5IJW · UniProt A0R1X0
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