MolNFT v1 · #78642 · protein
Crystal structure of helicobacter pylori urease accessory protein UREF/H complex
3SF5: “Crystal structure of helicobacter pylori urease accessory protein UREF/H complex”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.73). MolNFT v1 #78642 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3SF5
- Type
- protein
- Length
- 980 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Urease accessory protein uref; Urease accessory protein ureh
- UniProt
- Q09065, Q09067
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Urease accessory protein uref | protein | 229 | 71% helix, 0% strand | Q09065 |
| B | Urease accessory protein ureh | protein | 261 | 11% helix, 47% strand | Q09067 |
| C | Urease accessory protein uref | protein | 230 | 72% helix, 0% strand | Q09065 |
| D | Urease accessory protein ureh | protein | 260 | 11% helix, 47% strand | Q09067 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains B, A, C, D
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.73 | 0.85 | 51 | PEG |
| 2 | 64 | 0.72 | 0.97 | 19 | empty |
| 3 | 72 | 0.72 | 0.96 | 19 | empty |
| 4 | 180 | 0.59 | 0.82 | 23 | empty |
| 5 | 193 | 0.56 | 0.80 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1844 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1422 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1407 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3SF5 · Crystal Structure of Helicobacter pylori Urease Accessory Protein UreF/H complex · the same entry in another collection · chain D against D, 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
- Q09067 · AlphaFold monomer V2.0 prediction for urease accessory protein ureh (Q09067) · a predicted model of the same protein · chain D against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 3SF5 · PDBe 3SF5 · UniProt Q09065 · UniProt Q09067
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