MolNFT v1 · #78154 · protein
The crystal structure of the periplasmic domain of helicobacter pylori motb (residues 90-256).
3S0H · Motility protein B: “The crystal structure of the periplasmic domain of helicobacter pylori motb (residues 90-256).”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.72). MolNFT v1 #78154 on GenesisL1: 3D…
- PDB
- 3S0H
- Type
- protein
- Length
- 650 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Motility protein B
- UniProt
- P56427
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Motility protein B | protein | 162 | 36% helix, 20% strand | P56427 |
| B | Motility protein B | protein | 160 | 36% helix, 21% strand | P56427 |
| C | Motility protein B | protein | 169 | 33% helix, 20% strand | P56427 |
| D | Motility protein B | protein | 159 | 33% helix, 23% strand | P56427 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.72 | 0.84 | 52 | empty |
| 2 | 366 | 0.68 | 0.82 | 51 | empty |
| 3 | 107 | 0.62 | 0.88 | 23 | empty |
| 4 | 55 | 0.61 | 0.92 | 15 | empty |
| 5 | 219 | 0.60 | 0.81 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1675 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 1653 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1650 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1430 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 233 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3S0H · The crystal structure of the periplasmic domain of Helicobacter pylori MotB (residues… · the same entry in another collection · chain D against D, TM-score 1.00
- P56427 · AlphaFold monomer V2.0 prediction for motility protein B (P56427) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 3S0H · PDBe 3S0H · UniProt P56427
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