1ATK | pdb_00001atk

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.

Experimental Data Snapshot

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

Starting Model: experimental
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Validation slider image for 1ATK

This is version 1.5 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1038/nsb0297-109
Primary Citation Related Structures:
1ATK

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43235
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E64 Query on E64 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C₁₅ H₃₀ N₅ O₅ QPQNJAXBPHVASB-QWRGUYRKSA-O		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

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

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

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Entry History

Deposition Data

Released Date: 1998-02-04

Deposition Author(s):

Abdel-Meguid, S.S.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.