Research workbench
Crystal structure of an oxidoreductase from enterococcus faecalis
Analyse Crystal structure of an oxidoreductase from enterococcus faecalis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FD8
- Type
- protein
- Length
- 2,090 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, GFO/IDH/MOCA family
- UniProt
- Q835X4
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxidoreductase, GFO/IDH/MOCA family | protein | 348 | 34% helix, 24% strand | Q835X4 |
| C | Oxidoreductase, GFO/IDH/MOCA family | protein | 347 | 35% helix, 24% strand | Q835X4 |
| D, F | Oxidoreductase, GFO/IDH/MOCA family | protein | 349 | 35% helix, 24% strand | Q835X4 |
| E | Oxidoreductase, GFO/IDH/MOCA family | protein | 349 | 34% helix, 24% strand | Q835X4 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.86 | 0.88 | 100 | PGE |
| 2 | 626 | 0.84 | 0.88 | 93 | PGE |
| 3 | 815 | 0.81 | 0.84 | 85 | PGE |
| 4 | 93 | 0.68 | 0.92 | 25 | empty |
| 5 | 354 | 0.62 | 0.78 | 53 | empty |
Interfaces
12 interfaces between chains.
- E–F · 1662 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1661 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1637 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 654 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 646 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3FD8 · Crystal Structure of an oxidoreductase from Enterococcus faecalis · the same entry in another collection · chain C against C, 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 Q835X4
- Elsewhere: RCSB PDB 3FD8 · PDBe 3FD8 · UniProt Q835X4
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