MolNFT v1 · #65990 · protein
Crystal structure of a THIOL:DISULFIDE interchange protein dsba from bordetella parapertussis
3HD5: “Crystal structure of a THIOL:DISULFIDE interchange protein dsba from bordetella parapertussis”. X-ray diffraction, 2 pockets (best druggability 0.78). MolNFT v1 #65990 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HD5
- Type
- protein
- Length
- 542 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein dsba
- UniProt
- Q7W2Q0
- Pockets
- 2 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | THIOL:DISULFIDE interchange protein dsba | protein | 182 | 49% helix, 13% strand | Q7W2Q0 |
| B | THIOL:DISULFIDE interchange protein dsba | protein | 179 | 53% helix, 13% strand | Q7W2Q0 |
| C | THIOL:DISULFIDE interchange protein dsba | protein | 181 | 51% helix, 13% strand | Q7W2Q0 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 886 | 0.78 | 0.81 | 114 | empty |
| 2 | 50 | 0.28 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1438 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1191 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 979 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3HD5 · Crystal structure of a thiol:disulfide interchange protein dsbA from Bordetella… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7W2Q0 · AlphaFold monomer V2.0 prediction for THIOL:DISULFIDE interchange protein dsba (Q7W2Q0) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q7W2Q0
- Elsewhere: RCSB PDB 3HD5 · PDBe 3HD5 · UniProt Q7W2Q0
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