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- PDB-5tun: Crystal structure of uninhibited human Cathepsin K at 1.62 Angstr... -

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Basic information

Entry
Database: PDB / ID: 5tun
TitleCrystal structure of uninhibited human Cathepsin K at 1.62 Angstrom resolution
ComponentsCathepsin K
KeywordsHYDROLASE / cathepsin K
Function / homology
Function and homology information


cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding ...cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / Collagen degradation / mitophagy / collagen catabolic process / extracellular matrix disassembly / bone resorption / cysteine-type peptidase activity / cellular response to transforming growth factor beta stimulus / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / 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 / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / nucleoplasm
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsAguda, A.H. / Kruglyak, N. / Nguyen, N.T. / Law, S. / Bromme, D. / Brayer, G.D.
Funding support Canada, 4items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 111082 Canada
Canadian Institutes of Health Research (CIHR)MOP-125866 Canada
Canadian Institutes of Health Research (CIHR)MOP-89974 Canada
Natural Sciences & Engineering Research CouncilRGPIN-326803-13 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
DepositionNov 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Structure summary
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin K


Theoretical massNumber of molelcules
Total (without water)23,5231
Polymers23,5231
Non-polymers00
Water6,972387
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.080, 66.640, 93.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cathepsin K / Cathepsin O / Cathepsin O2 / Cathepsin X


Mass: 23523.480 Da / Num. of mol.: 1 / Fragment: UNP residues 115-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Pichia (fungus) / References: UniProt: P43235, cathepsin K
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% polyethylene glycol (PEG) 8000, 0.1 M phosphate/citrate pH 4.2 and 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.62→38.24 Å / Num. obs: 26167 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.969 / Rmerge(I) obs: 0.196 / Net I/σ(I): 6.2
Reflection shellResolution: 1.62→1.71 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3744 / CC1/2: 0.72 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLM7.2.1data reduction
SCALA3.3.6data scaling
PHASER1.3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATK

1atk


Resolution: 1.62→27.121 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.43
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 1275 4.88 %4.88
Rwork0.1519 ---
obs0.1541 26108 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.62→27.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 0 387 2035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061709
X-RAY DIFFRACTIONf_angle_d0.9252308
X-RAY DIFFRACTIONf_dihedral_angle_d12.418630
X-RAY DIFFRACTIONf_chiral_restr0.041234
X-RAY DIFFRACTIONf_plane_restr0.004305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.68490.22871340.18222722X-RAY DIFFRACTION99
1.6849-1.76150.24181450.16442695X-RAY DIFFRACTION100
1.7615-1.85440.2371330.1582732X-RAY DIFFRACTION100
1.8544-1.97060.22811390.14812723X-RAY DIFFRACTION100
1.9706-2.12260.17641300.13422777X-RAY DIFFRACTION100
2.1226-2.33610.18511320.13992767X-RAY DIFFRACTION100
2.3361-2.67390.20321560.15192747X-RAY DIFFRACTION99
2.6739-3.36790.16051600.15262743X-RAY DIFFRACTION99
3.3679-27.12460.16721460.15122927X-RAY DIFFRACTION99

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