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- PDB-5t6u: Crystal structure of mouse cathepsin K at 2.9 Angstroms resolution. -

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Basic information

Entry
Database: PDB / ID: 5t6u
TitleCrystal structure of mouse cathepsin K at 2.9 Angstroms resolution.
ComponentsCathepsin K
KeywordsHYDROLASE / cathepsin K / N-ACETYL-D-GLUCOSAMINE
Function / homology
Function and homology information


RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / positive regulation of peptidase activity / Activation of Matrix Metalloproteinases / Collagen degradation / Trafficking and processing of endosomal TLR / cathepsin K / mononuclear cell differentiation / Degradation of the extracellular matrix / intramembranous ossification / negative regulation of cartilage development ...RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / positive regulation of peptidase activity / Activation of Matrix Metalloproteinases / Collagen degradation / Trafficking and processing of endosomal TLR / cathepsin K / mononuclear cell differentiation / Degradation of the extracellular matrix / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / MHC class II antigen presentation / thyroid hormone generation / proteoglycan binding / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / collagen catabolic process / bone resorption / cysteine-type peptidase activity / cellular response to transforming growth factor beta stimulus / collagen binding / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / response to insulin / response to organic cyclic compound / cellular response to tumor necrosis factor / response to ethanol / lysosome / immune response / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / proteolysis / extracellular space / nucleoplasm / cytoplasm
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLaw, S. / Aguda, A. / Nguyen, N. / Brayer, G. / Bromme, D.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP89974 Canada
Canadian Institutes of Health Research (CIHR)MOP201209 Canada
CitationJournal: Biochem. J. / Year: 2017
Title: Identification of mouse cathepsin K structural elements that regulate the potency of odanacatib.
Authors: Law, S. / Andrault, P.M. / Aguda, A.H. / Nguyen, N.T. / Kruglyak, N. / Brayer, G.D. / Bromme, D.
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9585
Polymers23,4481
Non-polymers5094
Water39622
1
A: Cathepsin K
hetero molecules

A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,91610
Polymers46,8972
Non-polymers1,0198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2780 Å2
ΔGint-80 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.920, 43.260, 133.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

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Components

#1: Protein Cathepsin K


Mass: 23448.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ctsk / Plasmid: ppic9k / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: P55097, cathepsin K
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M sodium phosphate pH 6.2 25% (v/v) 1,2-propanediol 10% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→43.26 Å / Num. obs: 5243 / % possible obs: 99.53 % / Redundancy: 5.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.122 / Net I/av σ(I): 10.6 / Net I/σ(I): 10.66
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.3 / CC1/2: 0.953 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
iMOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X6H

4x6h


Resolution: 2.9→43.26 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.45
RfactorNum. reflection% reflection
Rfree0.2206 261 4.98 %
Rwork0.205 --
obs0.2058 5241 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 29 22 1695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021709
X-RAY DIFFRACTIONf_angle_d0.6112307
X-RAY DIFFRACTIONf_dihedral_angle_d11.798618
X-RAY DIFFRACTIONf_chiral_restr0.045238
X-RAY DIFFRACTIONf_plane_restr0.002299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.65340.21251250.21732412X-RAY DIFFRACTION99
3.6534-43.26480.22581360.19772568X-RAY DIFFRACTION100

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