Research workbench
Crystal structure of alanine racemase from oenococcus oeni
Analyse Crystal structure of alanine racemase from oenococcus oeni in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CO8
- Type
- protein
- Length
- 705 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- Q04HB7
- Ligands
- PLP
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 360 | 33% helix, 26% strand | Q04HB7 |
| B | Alanine racemase (EC 5.1.1.1) | protein | 345 | 32% helix, 24% strand | Q04HB7 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.77 | 0.81 | 84 | PLP |
| 2 | 319 | 0.76 | 0.88 | 52 | PLP |
| 3 | 163 | 0.72 | 0.90 | 45 | empty |
| 4 | 173 | 0.63 | 0.84 | 31 | empty |
| 5 | 79 | 0.53 | 0.85 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2327 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 2 cofactor (engineered, pyridoxal phosphate Schiff base).
Compared structures
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 Q04HB7
- Elsewhere: RCSB PDB 3CO8 · PDBe 3CO8 · UniProt Q04HB7
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