Research workbench
Crystal structure of a DUF1185 family protein (BB2672) from bordetella bronchiseptica RB50 at 1.70 a resolution
Analyse Crystal structure of a DUF1185 family protein (BB2672) from bordetella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BYQ
- Type
- protein
- Length
- 574 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein DUF1185
- UniProt
- Q7WJ28
- Ligands
- CL
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Uncharacterized protein DUF1185 | protein | 191 | 25% helix, 31% strand | Q7WJ28 |
| B | Uncharacterized protein DUF1185 | protein | 192 | 24% helix, 32% strand | Q7WJ28 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 27 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.80 | 0.91 | 59 | EDO |
| 2 | 135 | 0.73 | 0.92 | 45 | CL |
| 3 | 152 | 0.52 | 0.79 | 24 | empty |
| 4 | 130 | 0.48 | 0.79 | 26 | EDO |
| 5 | 50 | 0.44 | 0.84 | 14 | CL, EDO |
Interfaces
3 interfaces between chains.
- B–C · 2063 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1023 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 292 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 3BYQ · Crystal structure of a duf1185 family protein (bb2672) from bordetella bronchiseptica… · 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 Q7WJ28
- Elsewhere: RCSB PDB 3BYQ · PDBe 3BYQ · UniProt Q7WJ28
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