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Crystal structure of alanine racemase from E.faecalis
Analyse Crystal structure of alanine racemase from E.faecalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E5P
- Type
- protein
- Length
- 1,112 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Enterococcus faecalis
- Molecule
- Alanine racemase
- EC
- 5.1.1.1
- UniProt
- Q837J0
- Ligands
- PLP
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alanine racemase (EC 5.1.1.1) | protein | 370 | 31% helix, 24% strand | Q837J0 |
| B, C | Alanine racemase (EC 5.1.1.1) | protein | 371 | 30% helix, 25% strand | Q837J0 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, C, B
- PPI · Propanoic acid · additive · 3 copies · chains A, C, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, C
- 2PE · Nonaethylene glycol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.79 | 0.86 | 83 | PPI, PLP |
| 2 | 170 | 0.77 | 0.93 | 44 | empty |
| 3 | 343 | 0.76 | 0.87 | 48 | PLP, PPI |
| 4 | 82 | 0.61 | 0.89 | 23 | empty |
| 5 | 397 | 0.58 | 0.75 | 62 | empty |
Interfaces
2 interfaces between chains.
- A–C · 3038 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 649 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3E5P · Crystal structure of alanine racemase from E.FAECALIS · 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 Q837J0
- Elsewhere: RCSB PDB 3E5P · PDBe 3E5P · UniProt Q837J0
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