Research workbench
Crystal structure of the glutamate racemase from bacillus anthracis
Analyse Crystal structure of the glutamate racemase from bacillus anthracis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GZM
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- Q81LA8
- Ligands
- DGL
- Pockets
- 15 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Glutamate racemase (EC 5.1.1.3) | protein | 266 | 47% helix, 17% strand | Q81LA8 |
| B | Glutamate racemase (EC 5.1.1.3) | protein | 265 | 47% helix, 17% strand | Q81LA8 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.62 | 0.80 | 36 | empty |
| 2 | 53 | 0.54 | 0.89 | 23 | DGL |
| 3 | 245 | 0.50 | 0.74 | 33 | empty |
| 4 | 69 | 0.49 | 0.84 | 24 | DGL |
| 5 | 177 | 0.48 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1652 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1636 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 435 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GZM · Crystal Structure of the Glutamate Racemase from Bacillus anthracis · the same entry in another collection · chain B against B, TM-score 1.00
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 Q81LA8
- Elsewhere: RCSB PDB 2GZM · PDBe 2GZM · UniProt Q81LA8
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