Research workbench
Bacillithiol disulfide reductase bdr (ypda) from bacillus cereus
Analyse Bacillithiol disulfide reductase bdr (ypda) from bacillus cereus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A76
- Type
- protein
- Length
- 1,301 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase
- EC
- 1.8.1.9
- UniProt
- Q81FS4
- Ligands
- FAD, NA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thioredoxin reductase (EC 1.8.1.9) | protein | 326 | 25% helix, 28% strand | Q81FS4 |
| C | Thioredoxin reductase (EC 1.8.1.9) | protein | 325 | 26% helix, 28% strand | Q81FS4 |
| D | Thioredoxin reductase (EC 1.8.1.9) | protein | 324 | 26% helix, 26% strand | Q81FS4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.85 | 0.91 | 67 | FAD |
| 2 | 528 | 0.85 | 0.91 | 69 | FAD |
| 3 | 429 | 0.83 | 0.91 | 58 | FAD |
| 4 | 441 | 0.83 | 0.90 | 62 | FAD |
| 5 | 71 | 0.65 | 0.93 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1406 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1405 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 614 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 614 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 578 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7A76 · Bacillithiol Disulfide Reductase Bdr (YpdA) from Bacillus cereus · 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 Q81FS4
- Elsewhere: RCSB PDB 7A76 · PDBe 7A76 · UniProt Q81FS4
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