Research workbench
Crystal structure of dipeptide epimerase from enterococcus faecalis V583
Analyse Crystal structure of dipeptide epimerase from enterococcus faecalis V583 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JVA
- Type
- protein
- Length
- 2,795 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptide epimerase
- UniProt
- Q834W6
- Ligands
- MG, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Dipeptide epimerase | protein | 353 | 39% helix, 24% strand | Q834W6 |
| B, F | Dipeptide epimerase | protein | 354 | 41% helix, 24% strand | Q834W6 |
| C | Dipeptide epimerase | protein | 344 | 42% helix, 21% strand | Q834W6 |
| D, H | Dipeptide epimerase | protein | 346 | 42% helix, 21% strand | Q834W6 |
| G | Dipeptide epimerase | protein | 345 | 42% helix, 21% strand | Q834W6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, G, E
- GOL · Glycerol · additive · 5 copies · chains A, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.85 | 0.86 | 131 | empty |
| 2 | 665 | 0.85 | 0.89 | 80 | empty |
| 3 | 636 | 0.84 | 0.89 | 82 | empty |
| 4 | 214 | 0.84 | 0.97 | 31 | empty |
| 5 | 201 | 0.84 | 0.97 | 30 | empty |
Interfaces
16 interfaces between chains.
- G–H · 1367 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1361 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1354 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1354 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1001 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3JVA · Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 · the same entry in another collection · chain H against H, TM-score 1.00
- Q834W6 · AlphaFold monomer V2.0 prediction for hydrophobic dipeptide epimerase (Q834W6) · a predicted model of the same protein · 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 Q834W6
- Elsewhere: RCSB PDB 3JVA · PDBe 3JVA · UniProt Q834W6
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