Research workbench
Crystal structure of Entamoeba histolytica serine protease inhibitor, Histopin, in the cleaved conformation
Analyse Crystal structure of Entamoeba histolytica serine protease inhibitor, Histopin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VLJ
- Type
- protein
- Length
- 364 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.83
- Source
- Entamoeba histolytica
- Molecule
- Serine protease inhibitor, putative
- UniProt
- C4M4Y1
- Ligands
- K, SCN
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · resolution 1.83 · 2 distinct chains · 32% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease inhibitor, putative | protein | 330 | 35% helix, 33% strand | C4M4Y1 |
| B | Serine protease inhibitor, putative | protein | 34 | 0% helix, 44% strand | C4M4Y1 |
Ligands and binding sites
- K · Potassium ion · metal · chains A
- SCN · Thiocyanate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.64 | 0.90 | 21 | empty |
| 2 | 87 | 0.39 | 0.77 | 13 | empty |
| 3 | 81 | 0.38 | 0.77 | 14 | GOL |
| 4 | 62 | 0.36 | 0.78 | 18 | PEG |
Interfaces
1 interface between chains.
- A–B · 2583 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 7VLJ · Crystal structure of entamoeba histolytica serine protease inhibitor, histopin, in the… · 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 C4M4Y1
- Elsewhere: RCSB PDB 7VLJ · PDBe 7VLJ · UniProt C4M4Y1
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