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Structure of the activation intermediate of cathepsin K in complex with the 3-cyano-3-aza-beta-amino acid inhibitor GU2602

Analyse Structure of the activation intermediate of cathepsin K in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7QBM
Type: protein
Length: 283 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cathepsin K
EC: 3.4.22.38
UniProt: P43235
Ligands: A0U, MG
Pockets: 1 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cathepsin K (EC 3.4.22.38)	protein	216	28% helix, 25% strand	P43235
P	Cathepsin K (EC 3.4.22.38)	protein	67	60% helix, 4% strand	P43235

Ligands and binding sites

A0U · ~{tert}-butyl ~{N}-[iminomethyl-[2-[methyl-(phenylmethyl)amino]-2-oxidanylidene-ethyl]amino]carbamate · ligand · chains A, P
MG · Magnesium ion · metal · chains A, P
ACT · Acetate ion · additive · chains P

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	235	0.55	0.78	35	A0U

Interfaces

1 interface between chains.

A–P · 906 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

7QBM · Structure of the activation intermediate of cathepsin K in complex with the… · 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 0.98

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 7QBM · PDBe 7QBM · UniProt P43235

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