Research workbench
Crystal structure of the urea channel from the human gastric pathogen helicobacter pylori
Analyse Crystal structure of the urea channel from the human gastric pathogen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UX4
- Type
- protein
- Length
- 540 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid-activated urea channel
- UniProt
- P56874
- Ligands
- XP4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Acid-activated urea channel | protein | 180 | 73% helix, 0% strand | P56874 |
Ligands and binding sites
- XP4 · 1,2-dimyristoyl-sn-glycero-3-phosphate · ligand · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.70 | 0.83 | 29 | empty |
| 2 | 330 | 0.69 | 0.82 | 29 | empty |
| 3 | 320 | 0.69 | 0.83 | 28 | empty |
| 4 | 408 | 0.66 | 0.79 | 52 | empty |
| 5 | 422 | 0.65 | 0.78 | 48 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1376 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1374 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3UX4 · Crystal structure of the urea channel from the human gastric pathogen Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
- P56874 · AlphaFold monomer V2.0 prediction for acid-activated urea channel (P56874) · a predicted model of the same protein · chain A 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 P56874
- Elsewhere: RCSB PDB 3UX4 · PDBe 3UX4 · UniProt P56874
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.