Research workbench
X-ray diffraction analysis of the CsStefin-1
Analyse X-ray diffraction analysis of the CsStefin-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZC1
- Type
- protein
- Length
- 596 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.30271
- Source
- Clonorchis sinensis
- Molecule
- Cystatin-1
- UniProt
- A6YID9
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.30271 · 3 distinct chains · 21% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cystatin-1 | protein | 101 | 21% helix, 40% strand | A6YID9 |
| C | Cystatin-1 | protein | 100 | 19% helix, 37% strand | A6YID9 |
| D, E, F | Cystatin-1 | protein | 98 | 22% helix, 36% strand | A6YID9 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.75 | 0.80 | 79 | empty |
| 2 | 157 | 0.66 | 0.87 | 23 | empty |
| 3 | 95 | 0.33 | 0.73 | 21 | empty |
| 4 | 54 | 0.28 | 0.74 | 17 | empty |
Interfaces
11 interfaces between chains.
- A–E · 355 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 340 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 337 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 334 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 310 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5ZC1 · X-ray diffraction analysis of the csstefin-1 · 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 A6YID9
- Elsewhere: RCSB PDB 5ZC1 · PDBe 5ZC1 · UniProt A6YID9
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