Research workbench
Crystal structure of glutamate racemase from campylobacter jejuni subsp. jejuni
Analyse Crystal structure of glutamate racemase from campylobacter jejuni subsp. jejuni in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UHO
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate racemase
- EC
- 5.1.1.3
- UniProt
- Q9PM24
- Ligands
- DGL, CA, CL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate racemase (EC 5.1.1.3) | protein | 250 | 48% helix, 17% strand | Q9PM24 |
Ligands and binding sites
- DGL · D-glutamic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.78 | 0.82 | 88 | DGL |
| 2 | 62 | 0.33 | 0.77 | 17 | EDO, CL |
| 3 | 52 | 0.27 | 0.74 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 922 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3UHO · Crystal Structure of Glutamate Racemase from Campylobacter jejuni subsp. jejuni · the same entry in another collection · chain B against B, TM-score 1.00
- Q9PM24 · AlphaFold monomer V2.0 prediction for glutamate racemase (Q9PM24) · 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 Q9PM24
- Elsewhere: RCSB PDB 3UHO · PDBe 3UHO · UniProt Q9PM24
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