Research workbench
Double cache (dcache) sensing domain of tlpc chemoreceptor from helicobacter pylori
Analyse Double cache (dcache) sensing domain of tlpc chemoreceptor from helicobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WBF
- Type
- protein
- Length
- 773 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-accepting chemotaxis transducer (tlpc)
- UniProt
- O24911
- Ligands
- LAC
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl-accepting chemotaxis transducer (tlpc) | protein | 258 | 38% helix, 31% strand | O24911 |
| B | Methyl-accepting chemotaxis transducer (tlpc) | protein | 254 | 39% helix, 31% strand | O24911 |
| C | Methyl-accepting chemotaxis transducer (tlpc) | protein | 261 | 38% helix, 32% strand | O24911 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.70 | 0.78 | 67 | empty |
| 2 | 577 | 0.69 | 0.78 | 69 | empty |
| 3 | 317 | 0.55 | 0.75 | 28 | empty |
| 4 | 52 | 0.45 | 0.84 | 17 | empty |
| 5 | 51 | 0.42 | 0.83 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 555 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 553 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 242 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5WBF · Double CACHE (dCACHE) sensing domain of TlpC chemoreceptor from Helicobacter pylori · 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 O24911
- Elsewhere: RCSB PDB 5WBF · PDBe 5WBF · UniProt O24911
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