Research workbench
Crystal structure of uree from helicobacter pylori (NI2+ bound form)
Analyse Crystal structure of uree from helicobacter pylori (NI2+ bound form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NY0
- Type
- protein
- Length
- 596 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease accessory protein uree
- UniProt
- Q09064
- Ligands
- NI
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urease accessory protein uree | protein | 147 | 21% helix, 35% strand | Q09064 |
| B | Urease accessory protein uree | protein | 153 | 19% helix, 32% strand | Q09064 |
| C, D | Urease accessory protein uree | protein | 148 | 19% helix, 29% strand | Q09064 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.74 | 0.91 | 37 | empty |
| 2 | 857 | 0.72 | 0.77 | 62 | empty |
| 3 | 244 | 0.70 | 0.85 | 42 | empty |
| 4 | 51 | 0.38 | 0.81 | 13 | empty |
| 5 | 65 | 0.31 | 0.74 | 10 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1236 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1095 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 202 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 98 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 53 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3NY0 · Crystal Structure of UreE from Helicobacter pylori (Ni2+ bound form) · 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 0.96
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 3NY0 · PDBe 3NY0 · UniProt Q09064
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