Research workbench
Crystal structure of helicobacter pylori urease accessory protein UREF/H/G complex
Analyse Crystal structure of helicobacter pylori urease accessory protein UREF/H/G… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HI0
- Type
- protein
- Length
- 1,356 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease accessory protein uref; Urease accessory protein ureh; Urease accessory protein…
- UniProt
- Q09065, Q09067, Q09066
- Ligands
- GDP
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Urease accessory protein uref | protein | 227 | 72% helix, 0% strand | Q09065 |
| B, D | Urease accessory protein ureh | protein | 255 | 10% helix, 49% strand | Q09067 |
| E, F | Urease accessory protein ureg | protein | 196 | 41% helix, 18% strand | Q09066 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 449 | 0.87 | 0.95 | 58 | empty |
| 2 | 480 | 0.73 | 0.82 | 45 | GDP |
| 3 | 51 | 0.71 | 0.99 | 17 | empty |
| 4 | 455 | 0.71 | 0.81 | 47 | GDP |
| 5 | 52 | 0.67 | 0.97 | 18 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1779 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1386 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1370 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1324 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 873 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4HI0 · Crystal Structure of Helicobacter pylori Urease Accessory Protein UreF/H/G complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q09067 · AlphaFold monomer V2.0 prediction for urease accessory protein ureh (Q09067) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q09065 · AlphaFold monomer V2.0 prediction for urease accessory protein uref (Q09065) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q09066 · AlphaFold monomer V2.0 prediction for urease accessory protein ureg (Q09066) · a predicted model of the same protein · chain E 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 Q09065
- Every structure of UniProt Q09067
- Every structure of UniProt Q09066
- Elsewhere: RCSB PDB 4HI0 · PDBe 4HI0 · UniProt Q09065 · UniProt Q09067 · UniProt Q09066
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