Research workbench
Crystal structure of a pyridine nucleotide-disulfide family oxidoreductase from the enterococcus faecalis V583
Analyse Crystal structure of a pyridine nucleotide-disulfide family oxidoreductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OC4
- Type
- protein
- Length
- 843 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, pyridine nucleotide-disulfide family
- UniProt
- Q833L5
- Ligands
- FAD, NA
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase, pyridine nucleotide-disulfide family | protein | 422 | 24% helix, 31% strand | Q833L5 |
| B | Oxidoreductase, pyridine nucleotide-disulfide family | protein | 421 | 24% helix, 31% strand | Q833L5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.82 | 0.83 | 113 | FAD |
| 2 | 1122 | 0.80 | 0.81 | 95 | FAD |
| 3 | 281 | 0.68 | 0.83 | 39 | empty |
| 4 | 294 | 0.62 | 0.79 | 25 | empty |
| 5 | 376 | 0.61 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2516 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3OC4 · Crystal Structure of a pyridine nucleotide-disulfide family oxidoreductase from the… · 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 Q833L5
- Elsewhere: RCSB PDB 3OC4 · PDBe 3OC4 · UniProt Q833L5
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