Research workbench
Thiol-disulfide oxidoreductase from bacteroides fragilis nctc 9343
Analyse Thiol-disulfide oxidoreductase from bacteroides fragilis nctc 9343 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FKF
- Type
- protein
- Length
- 559 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiol-disulfide oxidoreductase
- EC
- 1.8.4.7
- UniProt
- Q5L7K1
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thiol-disulfide oxidoreductase (EC 1.8.4.7) | protein | 141 | 32% helix, 23% strand | Q5L7K1 |
| C | Thiol-disulfide oxidoreductase (EC 1.8.4.7) | protein | 140 | 30% helix, 24% strand | Q5L7K1 |
| D | Thiol-disulfide oxidoreductase (EC 1.8.4.7) | protein | 137 | 31% helix, 25% strand | Q5L7K1 |
Ligands and binding sites
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.80 | 0.81 | 126 | empty |
| 2 | 126 | 0.50 | 0.80 | 33 | empty |
| 3 | 66 | 0.48 | 0.84 | 22 | empty |
| 4 | 65 | 0.44 | 0.82 | 24 | empty |
| 5 | 92 | 0.38 | 0.76 | 15 | empty |
Interfaces
6 interfaces between chains.
- B–D · 683 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 673 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 493 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 325 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 3FKF · thiol-disulfide oxidoreductase from Bacteroides fragilis NCTC 9343 · 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 Q5L7K1
- Elsewhere: RCSB PDB 3FKF · PDBe 3FKF · UniProt Q5L7K1
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