Research workbench
Structure of the urease accessory protein uref from helicobacter pylori
Analyse Structure of the urease accessory protein uref from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CXN
- Type
- protein
- Length
- 620 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease accessory protein uref
- UniProt
- Q09065
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urease accessory protein uref | protein | 207 | 74% helix, 0% strand | Q09065 |
| B | Urease accessory protein uref | protein | 209 | 73% helix, 0% strand | Q09065 |
| C | Urease accessory protein uref | protein | 204 | 74% helix, 0% strand | Q09065 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.77 | 0.81 | 84 | empty |
| 2 | 558 | 0.72 | 0.80 | 62 | empty |
| 3 | 177 | 0.68 | 0.87 | 35 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1734 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 442 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 3CXN · Structure of the Urease Accessory Protein UreF from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
- Q09065 · AlphaFold monomer V2.0 prediction for urease accessory protein uref (Q09065) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q09065
- Elsewhere: RCSB PDB 3CXN · PDBe 3CXN · UniProt Q09065
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