MolNFT v1 · #111589 · protein

Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal

4YV8: “Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal”. X-ray diffraction, 3 ligands (AG2, URE, SO4). MolNFT v1 #111589 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

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 Å² 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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