Research workbench
Structure of the charge-transfer intermediate of the transmembrane redox catalyst dsbb
Analyse Structure of the charge-transfer intermediate of the transmembrane redox… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E9J
- Type
- protein
- Length
- 644 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL/DISULFIDE oxidoreductase dsba; THIOL/DISULFIDE oxidoreductase dsbb
- EC
- 1.8.4.-, 1.8.5.-
- UniProt
- P0AEG4, P0A6M2
- Ligands
- UQ1
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | THIOL/DISULFIDE oxidoreductase dsba (EC 1.8.4.-) | protein | 188 | 50% helix, 4% strand | P0AEG4 |
| C, F | THIOL/DISULFIDE oxidoreductase dsbb (EC 1.8.5.-) | protein | 134 | 50% helix, 1% strand | P0A6M2 |
Ligands and binding sites
- UQ1 · Ubiquinone-1 · ligand · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.77 | 0.82 | 80 | UQ1 |
| 2 | 778 | 0.77 | 0.81 | 90 | UQ1 |
| 3 | 625 | 0.73 | 0.79 | 55 | empty |
| 4 | 193 | 0.57 | 0.80 | 38 | empty |
| 5 | 114 | 0.40 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- E–F · 674 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 673 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 586 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 52 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3E9J · Structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB · the same entry in another collection · chain F against F, TM-score 1.00
- P0AEG4 · AlphaFold monomer V2.0 prediction for THIOL:DISULFIDE interchange protein dsba (P0AEG4) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P0A6M2 · AlphaFold monomer V2.0 prediction for disulfide bond formation protein B (P0A6M2) · a predicted model of the same protein · chain C against A, TM-score 0.83
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 P0AEG4
- Every structure of UniProt P0A6M2
- Elsewhere: RCSB PDB 3E9J · PDBe 3E9J · UniProt P0AEG4 · UniProt P0A6M2
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