Research workbench
The crystal structure of alpha-amino-epsilon-caprolactam racemase from achromobacter obae complexed with epsilon caprolactam
Analyse The crystal structure of alpha-amino-epsilon-caprolactam racemase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DXW
- Type
- protein
- Length
- 848 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-amino-epsilon-caprolactam racemase
- EC
- 5.1.-.-
- UniProt
- Q7M181
- Ligands
- PLP, ICC
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-amino-epsilon-caprolactam racemase (EC 5.1.-.-) | protein | 422 | 38% helix, 20% strand | Q7M181 |
| B | Alpha-amino-epsilon-caprolactam racemase (EC 5.1.-.-) | protein | 426 | 39% helix, 19% strand | Q7M181 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- ICC · azepan-2-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.71 | 0.85 | 50 | PLP, ICC |
| 2 | 229 | 0.70 | 0.86 | 52 | PLP, ICC |
| 3 | 82 | 0.41 | 0.79 | 20 | empty |
| 4 | 82 | 0.39 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3956 Ų buried · 68 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3DXW · The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7M181 · AlphaFold monomer V2.0 prediction for 2-aminohexano-6-lactam racemase (Q7M181) · a predicted model of the same protein · chain B against A, 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 Q7M181
- Elsewhere: RCSB PDB 3DXW · PDBe 3DXW · UniProt Q7M181
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