MolNFT v1 · #144003 · protein
Helicobacter pylori ATPase, HP0525, in complex with 1G4 compound
6BGE · VIRB11-like protein: “Helicobacter pylori ATPase, HP0525, in complex with 1G4 compound”. X-ray diffraction, 2 ligands (DN7, SO4), 7 pockets (best druggability 0.69). MolNFT v1 #144003 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6BGE
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VIRB11-like protein
- UniProt
- Q6VRM0
- Ligands
- DN7, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | VIRB11-like protein | protein | 323 | 39% helix, 21% strand | Q6VRM0 |
Ligands and binding sites
- DN7 · 4-[(pyridin-2-yl)oxy]benzoic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.69 | 0.81 | 63 | SO4 |
| 2 | 401 | 0.67 | 0.80 | 59 | SO4 |
| 3 | 210 | 0.65 | 0.84 | 31 | DN7 |
| 4 | 138 | 0.42 | 0.75 | 29 | empty |
| 5 | 136 | 0.40 | 0.74 | 26 | GOL |
Interfaces
1 interface between chains.
- A–B · 437 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6BGE · Helicobacter pylori ATPase, HP0525, in complex with 1G2 compound · 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 Q6VRM0
- Elsewhere: RCSB PDB 6BGE · PDBe 6BGE · UniProt Q6VRM0
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