MolNFT v1 · #68560 · protein
Crystal structure of dipeptide epimerase from enterococcus faecalis V583 complexed with mg and dipeptide L-leu-L-tyr
3JZU: “Crystal structure of dipeptide epimerase from enterococcus faecalis V583 complexed with mg and dipeptide…”. X-ray diffraction, 1 ligand (MG), 20 pockets (best druggability 0.87). MolNFT v1 #68560 on GenesisL1: 3D structure, binding…
- PDB
- 3JZU
- Type
- protein
- Length
- 2,846 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 0.87
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Dipeptide epimerase | protein | 355 | 41% helix, 24% strand | Q834W6 |
| B, C, D, F, G, H | Dipeptide epimerase | protein | 356 | 39% helix, 24% strand | Q834W6 |
Ligands and binding sites
- MG · Magnesium ion · metal · 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 | 904 | 0.87 | 0.89 | 96 | empty |
| 2 | 891 | 0.87 | 0.89 | 112 | empty |
| 3 | 691 | 0.85 | 0.89 | 92 | empty |
| 4 | 236 | 0.85 | 0.97 | 32 | empty |
| 5 | 233 | 0.85 | 0.97 | 31 | empty |
Interfaces
16 interfaces between chains.
- C–D · 1358 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1357 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1350 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1301 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1054 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3JZU · Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with… · the same entry in another collection · chain E against E, TM-score 1.00
- Q834W6 · AlphaFold monomer V2.0 prediction for hydrophobic dipeptide epimerase (Q834W6) · a predicted model of the same protein · chain B 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 3JZU · PDBe 3JZU · UniProt Q834W6
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