Research workbench
The crystal structure of the periplasmic domain of helicobacter pylori motb (residues 97-256, P3121).
Analyse The crystal structure of the periplasmic domain of helicobacter pylori motb… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S06
- Type
- protein
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Motility protein B
- UniProt
- P56427
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Motility protein B | protein | 162 | 40% helix, 23% strand | P56427 |
| B | Motility protein B | protein | 147 | 41% helix, 22% strand | P56427 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.54 | 0.80 | 40 | empty |
| 2 | 135 | 0.50 | 0.79 | 16 | empty |
| 3 | 59 | 0.42 | 0.82 | 13 | empty |
| 4 | 56 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1242 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3S06 · The crystal structure of the periplasmic domain of Helicobacter pylori MotB (residues… · the same entry in another collection · chain A against A, TM-score 1.00
- P56427 · AlphaFold monomer V2.0 prediction for motility protein B (P56427) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P56427
- Elsewhere: RCSB PDB 3S06 · PDBe 3S06 · UniProt P56427
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