Research workbench
Crystal structure of the traffic ATPase (HP0525) of the helicobacter pylori type IV secretion system bound by sulfate
Analyse Crystal structure of the traffic ATPase (HP0525) of the helicobacter pylori… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OPX
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VIRB11 homolog
- UniProt
- Q7BK04
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | VIRB11 homolog | protein | 323 | 39% helix, 22% strand | Q7BK04 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.82 | 0.83 | 89 | SO4 |
| 2 | 1164 | 0.76 | 0.78 | 95 | SO4 |
| 3 | 83 | 0.38 | 0.77 | 21 | empty |
| 4 | 121 | 0.38 | 0.74 | 23 | empty |
| 5 | 64 | 0.35 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1879 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1OPX · Crystal structure of the traffic ATPase (HP0525) of the Helicobacter pylori type IV… · 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 Q7BK04
- Elsewhere: RCSB PDB 1OPX · PDBe 1OPX · UniProt Q7BK04
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