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Crystal structure of a trap periplasmic solute binding protein from bordetella bronchispeptica (BB3421), target efi-510039, with density modeled as pantoate
Analyse Crystal structure of a trap periplasmic solute binding protein from bordetella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NQ8
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative periplasmic substrate-binding transport protein
- UniProt
- Q7WGZ0
- Ligands
- PAF, SO4, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative periplasmic substrate-binding transport protein | protein | 300 | 52% helix, 21% strand | Q7WGZ0 |
| B | Putative periplasmic substrate-binding transport protein | protein | 301 | 50% helix, 22% strand | Q7WGZ0 |
Ligands and binding sites
- PAF · Pantoate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.77 | 0.88 | 49 | empty |
| 2 | 61 | 0.72 | 0.98 | 20 | PAF |
| 3 | 59 | 0.71 | 0.97 | 19 | PAF |
| 4 | 69 | 0.33 | 0.76 | 22 | empty |
| 5 | 68 | 0.32 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 899 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4NQ8 · Crystal structure of a trap periplasmic solute binding protein from Bordetella… · 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 Q7WGZ0
- Elsewhere: RCSB PDB 4NQ8 · PDBe 4NQ8 · UniProt Q7WGZ0
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