Research workbench
Crystal structure of B.SUBTILIS glutamate racemase (race) with D-glu
Analyse Crystal structure of B.SUBTILIS glutamate racemase (race) with D-glu in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZUW
- Type
- protein
- Length
- 779 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase 1
- EC
- 5.1.1.3
- UniProt
- P94556
- Ligands
- DGL
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate racemase 1 (EC 5.1.1.3) | protein | 261 | 50% helix, 18% strand | P94556 |
| B | Glutamate racemase 1 (EC 5.1.1.3) | protein | 256 | 47% helix, 17% strand | P94556 |
| C | Glutamate racemase 1 (EC 5.1.1.3) | protein | 262 | 50% helix, 17% strand | P94556 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1063 | 0.77 | 0.79 | 96 | DGL |
| 2 | 244 | 0.54 | 0.77 | 38 | empty |
| 3 | 71 | 0.53 | 0.86 | 23 | DGL |
| 4 | 210 | 0.53 | 0.77 | 34 | empty |
| 5 | 264 | 0.49 | 0.74 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1365 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 557 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1ZUW · Crystal structure of B.subtilis glutamate racemase (RacE) with D-Glu · the same entry in another collection · chain A against A, TM-score 1.00
- P94556 · AlphaFold monomer V2.0 prediction for glutamate racemase 1 (P94556) · 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 P94556
- Elsewhere: RCSB PDB 1ZUW · PDBe 1ZUW · UniProt P94556
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