3C9E
Crystal structure of the cathepsin K : chondroitin sulfate complex.
- PDB DOI: https://doi.org/10.2210/pdb3C9E/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Komagataella pastoris
- Mutation(s): No 
- Deposited: 2008-02-15 Released: 2008-08-26 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.209 
- R-Value Work: 0.180 
- R-Value Observed: 0.180 
This is version 2.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Cathepsin K | 215 | Homo sapiens | Mutation(s): 0  Gene Names: CTSK, CTSO, CTSO2 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P43235 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid | B | 6 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G16831RV GlyCosmos:  G16831RV |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
E64 Query on E64 | D [auth A] | N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C15 H30 N5 O5 QPQNJAXBPHVASB-QWRGUYRKSA-O | |||
CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.209 
- R-Value Work: 0.180 
- R-Value Observed: 0.180 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 42 | α = 90 |
b = 143.9 | β = 90 |
c = 87.2 | γ = 90 |
Software Name | Purpose |
---|---|
MOSFLM | data reduction |
CNS | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
SCALA | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2008-08-26  Deposition Author(s): Kienetz, M., Cherney, M.M., James, M.N.G., Bromme, D.
Revision History (Full details and data files)
- Version 1.0: 2008-08-26
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2016-02-17
Changes: Derived calculations - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary