Research workbench
Alanine racemase with bound inhibitor derived from D- cycloserine
Analyse Alanine racemase with bound inhibitor derived from D- cycloserine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EPV
- 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
- P10724
- Ligands
- DCS
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 382 | 32% helix, 27% strand | P10724 |
| B | Alanine racemase (EC 5.1.1.1) | protein | 380 | 33% helix, 27% strand | P10724 |
Ligands and binding sites
- DCS · D-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-N,O-cycloserylamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.75 | 0.90 | 51 | DCS |
| 2 | 222 | 0.74 | 0.89 | 49 | DCS |
| 3 | 379 | 0.71 | 0.83 | 75 | empty |
| 4 | 69 | 0.64 | 0.92 | 24 | empty |
| 5 | 112 | 0.53 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3356 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
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 P10724
- Elsewhere: RCSB PDB 1EPV · PDBe 1EPV · UniProt P10724
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