MolNFT v1 · #58976 · protein
Crystal structure of a phage-related protein (BB3626) from bordetella bronchiseptica RB50 at 2.05 a resolution
3BJQ: “Crystal structure of a phage-related protein (BB3626) from bordetella bronchiseptica RB50 at 2.05 a resolution”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.75). MolNFT v1 #58976 on GenesisL1: 3D structure…
- PDB
- 3BJQ
- Type
- protein
- Length
- 2,975 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phage-related protein
- UniProt
- Q7WDF2
- Ligands
- CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 10 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phage-related protein | protein | 296 | 34% helix, 26% strand | Q7WDF2 |
| B | Phage-related protein | protein | 303 | 33% helix, 25% strand | Q7WDF2 |
| C | Phage-related protein | protein | 294 | 34% helix, 26% strand | Q7WDF2 |
| D | Phage-related protein | protein | 303 | 33% helix, 26% strand | Q7WDF2 |
| E | Phage-related protein | protein | 305 | 33% helix, 25% strand | Q7WDF2 |
| F | Phage-related protein | protein | 296 | 33% helix, 26% strand | Q7WDF2 |
| G | Phage-related protein | protein | 295 | 34% helix, 26% strand | Q7WDF2 |
| H | Phage-related protein | protein | 292 | 34% helix, 27% strand | Q7WDF2 |
| I | Phage-related protein | protein | 293 | 33% helix, 26% strand | Q7WDF2 |
| J | Phage-related protein | protein | 298 | 34% helix, 26% strand | Q7WDF2 |
Ligands and binding sites
- CL · Chloride ion · ion · chains D
- PG4 · Tetraethylene glycol · additive · 22 copies · chains A, B, E, C, D, F, J, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.75 | 0.78 | 119 | PG4 |
| 2 | 892 | 0.75 | 0.79 | 82 | PG4 |
| 3 | 842 | 0.75 | 0.79 | 72 | CL, PG4 |
| 4 | 635 | 0.73 | 0.80 | 54 | empty |
| 5 | 670 | 0.73 | 0.79 | 61 | PG4 |
Interfaces
21 interfaces between chains.
- B–E · 1970 Ų buried · 38 hydrogen bonds · protein-protein
- H–J · 1710 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1661 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 1602 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1599 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 modified (engineered).
Compared structures
- 3BJQ · Crystal structure of a phage-related protein (BB3626) from bordetella bronchiseptica RB50… · 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 Q7WDF2
- Elsewhere: RCSB PDB 3BJQ · PDBe 3BJQ · UniProt Q7WDF2
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