Research workbench
The crystal structure of a protease from helicobacter pylori
Analyse The crystal structure of a protease from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EUF
- Type
- protein
- Length
- 829 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.-.-
- UniProt
- I9VHL9
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease (EC 3.4.-.-) | protein | 413 | 47% helix, 19% strand | I9VHL9 |
| B | Protease (EC 3.4.-.-) | protein | 416 | 45% helix, 19% strand | I9VHL9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.65 | 0.77 | 51 | ZN |
| 2 | 418 | 0.61 | 0.76 | 38 | ZN |
| 3 | 449 | 0.61 | 0.75 | 37 | empty |
| 4 | 120 | 0.51 | 0.81 | 19 | empty |
| 5 | 122 | 0.48 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1247 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 5EUF · The crystal structure of a protease from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
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 I9VHL9
- Elsewhere: RCSB PDB 5EUF · PDBe 5EUF · UniProt I9VHL9
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