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Crystal structure of L-cycloserine-bound form of alanine racemase from D-cycloserine-producing streptomyces lavendulae
Analyse Crystal structure of L-cycloserine-bound form of alanine racemase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VFT
- Type
- protein
- Length
- 762 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- Q65YW7
- Ligands
- DCS, CL
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 382 | 35% helix, 24% strand | Q65YW7 |
| B | Alanine racemase (EC 5.1.1.1) | protein | 380 | 38% helix, 23% strand | Q65YW7 |
Ligands and binding sites
- DCS · D-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-N,O-cycloserylamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.78 | 0.88 | 49 | DCS |
| 2 | 280 | 0.76 | 0.88 | 45 | DCS |
| 3 | 311 | 0.61 | 0.79 | 41 | empty |
| 4 | 81 | 0.53 | 0.85 | 26 | empty |
| 5 | 95 | 0.53 | 0.83 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2915 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 1VFT · Crystal structure of L-cycloserine-bound form of alanine racemase from… · the same entry in another collection · chain A 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 Q65YW7
- Elsewhere: RCSB PDB 1VFT · PDBe 1VFT · UniProt Q65YW7
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