Research workbench
Crystal structure of uree from helicobacter pylori (metal of unknown identity bound)
Analyse Crystal structure of uree from helicobacter pylori (metal of unknown identity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LA0
- Type
- protein
- Length
- 592 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease accessory protein uree
- UniProt
- Q09064
- Ligands
- UNX
- Pockets
- 1 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Urease accessory protein uree | protein | 148 | 20% helix, 37% strand | Q09064 |
| B | Urease accessory protein uree | protein | 149 | 19% helix, 36% strand | Q09064 |
| C | Urease accessory protein uree | protein | 147 | 20% helix, 37% strand | Q09064 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.61 | 0.72 | 74 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1073 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1016 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 115 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 83 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LA0 · Crystal Structure of UreE from Helicobacter pylori (metal of unknown identity bound) · the same entry in another collection · chain A against A, TM-score 1.00
- Q09064 · AlphaFold monomer V2.0 prediction for urease accessory protein uree (Q09064) · 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 Q09064
- Elsewhere: RCSB PDB 3LA0 · PDBe 3LA0 · UniProt Q09064
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