Research workbench
Crystal structure of dsba-dsbb-ubiquinone complex
Analyse Crystal structure of dsba-dsbb-ubiquinone complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HI7
- Type
- protein
- Length
- 322 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein dsba; Disulfide bond formation protein B
- EC
- 1.8.4.-, 1.8.5.-
- UniProt
- P0AEG4, P0A6M2
- Ligands
- UQ1, ZN
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | THIOL:DISULFIDE interchange protein dsba (EC 1.8.4.-) | protein | 188 | 50% helix, 11% strand | P0AEG4 |
| B | Disulfide bond formation protein B (EC 1.8.5.-) | protein | 134 | 62% helix, 0% strand | P0A6M2 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.77 | 0.79 | 99 | UQ1 |
| 2 | 50 | 0.30 | 0.76 | 15 | empty |
| 3 | 58 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 682 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2HI7 · Crystal structure of DsbA-DsbB-ubiqui complex · the same entry in another collection · chain A against A, 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 A 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 B against A, TM-score 0.82
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 2HI7 · PDBe 2HI7 · UniProt P0AEG4 · UniProt P0A6M2
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