Research workbench
Cryoem structure of helicobacter pylori urea channel in open state.
Analyse Cryoem structure of helicobacter pylori urea channel in open state. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NSK
- Type
- protein
- Length
- 1,092 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid-activated urea channel
- UniProt
- P56874
- Ligands
- XP4
- Pockets
- 20 · best druggability 0.70
Structure
electron microscopy · 1 distinct chain · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Acid-activated urea channel | protein | 182 | 71% helix, 1% strand | P56874 |
Ligands and binding sites
- XP4 · 1,2-dimyristoyl-sn-glycero-3-phosphate · ligand · 18 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.70 | 0.79 | 48 | empty |
| 2 | 374 | 0.70 | 0.82 | 28 | empty |
| 3 | 574 | 0.70 | 0.78 | 47 | empty |
| 4 | 360 | 0.70 | 0.82 | 28 | empty |
| 5 | 548 | 0.70 | 0.78 | 49 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1467 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1461 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 1461 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1461 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1460 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6NSK · CryoEM structure of Helicobacter pylori urea channel in open state. · the same entry in another collection · chain C against C, 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 0.97
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 P56874
- Elsewhere: RCSB PDB 6NSK · PDBe 6NSK · UniProt P56874
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