Research workbench
Periplasmic portion of the helicobacter pylori chemoreceptor tlpb with formamide bound
Analyse Periplasmic portion of the helicobacter pylori chemoreceptor tlpb with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UB8
- Type
- protein
- Length
- 315 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chemoreceptor tlpb
- Ligands
- ARF, SO4
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chemoreceptor tlpb | protein | 157 | 48% helix, 22% strand | — |
| B | Chemoreceptor tlpb | protein | 158 | 47% helix, 23% strand | — |
Ligands and binding sites
- ARF · Formamide · ligand · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 53 | 0.69 | 0.97 | 19 | ARF, SO4 |
| 2 | 54 | 0.29 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1436 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3UB8 · Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with formamide bound · 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
- Elsewhere: RCSB PDB 3UB8 · PDBe 3UB8
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