Research workbench
Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal
Analyse Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YV8
- Type
- protein
- Length
- 216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cathepsin K; Lichostatinal
- EC
- 3.4.22.38
- UniProt
- P43235
- Ligands
- AG2, URE, SO4
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cathepsin K (EC 3.4.22.38) | protein | 213 | 26% helix, 23% strand | P43235 |
| B | Lichostatinal | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- AG2 · Agmatine · ligand · chains A, B
- URE · Urea · ligand · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 290 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 4YV8 · Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal · 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 4YV8 · PDBe 4YV8 · UniProt P43235
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