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Crystal structure of dipeptide epimerase from enterococcus faecalis V583 complexed with mg and dipeptide L-ile-L-tyr
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
- 3JW7
- Type
- protein
- Length
- 2,840 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptide epimerase
- UniProt
- Q834W6
- Ligands
- MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Dipeptide epimerase | protein | 355 | 41% helix, 24% strand | Q834W6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F, G, H
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 | 1014 | 0.86 | 0.87 | 89 | empty |
| 2 | 740 | 0.86 | 0.89 | 71 | empty |
| 3 | 673 | 0.85 | 0.89 | 73 | empty |
| 4 | 281 | 0.84 | 0.95 | 36 | empty |
| 5 | 254 | 0.84 | 0.95 | 36 | empty |
Interfaces
16 interfaces between chains.
- C–D · 1373 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1366 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1295 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1275 Ų buried · 19 hydrogen bonds · protein-protein
- B–H · 1019 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3JW7 · Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with… · 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 0.99
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 3JW7 · PDBe 3JW7 · UniProt Q834W6
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