Research workbench
The crystal structure of the cathepsin K Variant M5 in complex with chondroitin-4-sulfate
Analyse The crystal structure of the cathepsin K Variant M5 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H7D
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.242
- Source
- Homo sapiens
- Molecule
- Cathepsin K
- EC
- 3.4.22.38
- UniProt
- P43235
- Ligands
- E64, BDP, ASG, CA
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.242 · 1 distinct chain · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Cathepsin K (EC 3.4.22.38) | protein | 215 | 29% helix, 22% strand | P43235 |
Ligands and binding sites
- E64 · N-[N-[1-hydroxycarboxyethyl-carbonyl]leucylamino-butyl]-guanidine · ligand · 2 copies · chains A, E
- BDP · beta-D-glucopyranuronic acid · sugar · 3 copies · chains A
- ASG · 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.63 | 0.94 | 21 | empty |
| 2 | 50 | 0.36 | 0.80 | 17 | empty |
| 3 | 51 | 0.29 | 0.75 | 13 | E64 |
Interfaces
1 interface between chains.
- A–E · 367 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3H7D · The crystal structure of the cathepsin K variant M5 in complex with chondroitin-4-sulfate · the same entry in another collection · chain A against A, TM-score 1.00
- P43235 · AlphaFold monomer V2.0 prediction for cathepsin K (P43235) · a predicted model of the same protein · 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 P43235
- Elsewhere: RCSB PDB 3H7D · PDBe 3H7D · UniProt P43235
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