1ATK

CRYSTAL STRUCTURE OF THE CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH THE COVALENT INHIBITOR E-64

• PDB DOI: https://doi.org/10.2210/pdb1ATK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 1996-12-19 Released: 1998-02-04 
• Deposition Author(s): Zhao, B., Smith, W.W., Janson, C.A., Abdel-Meguid, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.310 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 

Starting Model: experimental

Literature

Crystal structure of human osteoclast cathepsin K complex with E-64.

Zhao, B., Janson, C.A., Amegadzie, B.Y., D'Alessio, K., Griffin, C., Hanning, C.R., Jones, C., Kurdyla, J., McQueney, M., Qiu, X., Smith, W.W., Abdel-Meguid, S.S.

(1997) Nat Struct Biol 4: 109-111

• PubMed: 9033588 
• DOI: https://doi.org/10.1038/nsb0297-109
• Primary Citation of Related Structures:  
  1ATK

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.88 kDa 
• Atom Count: 1,702 
• Modelled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATHEPSIN K	A	215	Homo sapiens	Mutation(s): 0  EC: 3.4.22.38
UniProt & NIH Common Fund Data Resources
Find proteins for P43235 (Homo sapiens) Explore P43235  Go to UniProtKB:  P43235
PHAROS:  P43235 GTEx:  ENSG00000143387

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E64	B [auth A]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C15 H30 N5 O5 QPQNJAXBPHVASB-QWRGUYRKSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.310 
• R-Value Work: 0.215 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.4	α = 90
b = 50.7	β = 90
c = 104.9	γ = 90

Software Package:

Software Name	Purpose
XENGEN	data collection
XENGEN	data reduction
X-PLOR	model building
X-PLOR	refinement
XENGEN	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-02-04 
Deposition Author(s): Zhao, B., Smith, W.W., Janson, C.A., Abdel-Meguid, S.S.

Revision History  

• Version 1.0: 1998-02-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection, Other
• Version 1.4: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-09
  Changes: Data collection, Structure summary