Research workbench
Crystal structure of glutamate racemase isoform RACE1 from bacillus anthracis
Analyse Crystal structure of glutamate racemase isoform RACE1 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
- 2DWU
- Type
- protein
- Length
- 797 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- Q81UL8
- Ligands
- DGL, K
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate racemase (EC 5.1.1.3) | protein | 265 | 49% helix, 18% strand | Q81UL8 |
| B, C | Glutamate racemase (EC 5.1.1.3) | protein | 266 | 49% helix, 18% strand | Q81UL8 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 3 copies · chains A, B, C
- K · Potassium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.79 | 0.81 | 115 | K, DGL |
| 2 | 367 | 0.59 | 0.76 | 53 | empty |
| 3 | 88 | 0.54 | 0.85 | 26 | DGL |
| 4 | 123 | 0.49 | 0.79 | 24 | empty |
| 5 | 135 | 0.48 | 0.78 | 22 | GOL |
Interfaces
2 interfaces between chains.
- A–B · 1451 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 695 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2DWU · Crystal Structure of Glutamate Racemase Isoform RacE1 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 Q81UL8
- Elsewhere: RCSB PDB 2DWU · PDBe 2DWU · UniProt Q81UL8
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