Research workbench
Structure of Helicobacter pylori EgtU bound to EGT
Analyse Structure of Helicobacter pylori EgtU bound to EGT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DP7
- Type
- protein
- Length
- 1,325 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.35
- Source
- Helicobacter pylori (strain P12)
- Molecule
- Osmoprotection protein
- UniProt
- B6JM49
- Ligands
- LW8
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · resolution 3.35 · 1 distinct chain · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Osmoprotection protein | protein | 265 | 49% helix, 18% strand | B6JM49 |
Ligands and binding sites
- LW8 · trimethyl-[(2S)-1-oxidanyl-1-oxidanylidene-3-(2-sulfanylidene-1,3-dihydroimidazol-4-yl)propan-2-yl]azanium · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.77 | 0.89 | 36 | LW8 |
| 2 | 632 | 0.76 | 0.82 | 70 | LW8 |
| 3 | 231 | 0.75 | 0.89 | 34 | LW8 |
| 4 | 248 | 0.74 | 0.88 | 37 | LW8 |
| 5 | 865 | 0.73 | 0.78 | 76 | empty |
Interfaces
5 interfaces between chains.
- A–E · 590 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 590 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 520 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 438 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 390 Ų buried · 3 hydrogen bonds · protein-protein
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 B6JM49
- Elsewhere: RCSB PDB 8DP7 · PDBe 8DP7 · UniProt B6JM49
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.