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
View more details
wwPDB Validation3D Report Full Report
This is version 1.5 of the entry. See complete history.
Literature
- 👁 Image
Download Mendeley
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
Asymmetric Unit
👁 ImageExplore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (E64)
Biological Assembly 1
Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (E64)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 assigned by authors.
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
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| CATHEPSIN K | 215 | Homo sapiens | Mutation(s): 0 EC: 3.4.22.38 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS: P43235 GTEx: ENSG00000143387 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P43235 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| E64 Download:Ideal Coordinates CCD File | B [auth A] | N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C15 H30 N5 O5 QPQNJAXBPHVASB-QWRGUYRKSA-O | 👁 Image | ||
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 Name | Purpose |
|---|---|
| XENGEN | data collection |
| XENGEN | data reduction |
| X-PLOR | model building |
| X-PLOR | refinement |
| XENGEN | data scaling |
| X-PLOR | phasing |
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 (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
