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- PDB-6hgy: CRYSTAL STRUCTURE OF CATHEPSIN K WITH N-DESMETHYL THALASSOSPIRAMIDE C -

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Basic information

Entry
Database: PDB / ID: 6hgy
TitleCRYSTAL STRUCTURE OF CATHEPSIN K WITH N-DESMETHYL THALASSOSPIRAMIDE C
ComponentsCathepsin K
KeywordsHYDROLASE / PROTEASE / CATHEPSIN K / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


cathepsin K / negative regulation of cartilage development / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / thyroid hormone generation / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process ...cathepsin K / negative regulation of cartilage development / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / thyroid hormone generation / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / fibronectin binding / extracellular matrix disassembly / bone resorption / mitophagy / collagen binding / Degradation of the extracellular matrix / cysteine-type peptidase activity / MHC class II antigen presentation / lysosomal lumen / proteolysis involved in protein catabolic process / lysosome / apical plasma membrane / serine-type endopeptidase activity / external side of plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / 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
THALASSOSPIRAMIDE C / Cathepsin K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZakarian, A. / Buckman, B.O. / Adler, M. / Griessner, A. / Blaesse, M.
CitationJournal: Org.Lett. / Year: 2019
Title: Total Synthesis of Covalent Cysteine Protease Inhibitor N-Desmethyl Thalassospiramide C and Crystallographic Evidence for Its Mode of Action.
Authors: Fournier, J. / Chen, K. / Mailyan, A.K. / Jackson, J.J. / Buckman, B.O. / Emayan, K. / Yuan, S. / Rajagopalan, R. / Misialek, S. / Adler, M. / Blaesse, M. / Griessner, A. / Zakarian, A.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3152
Polymers23,5231
Non-polymers7921
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.560, 44.884, 49.990
Angle α, β, γ (deg.)90.00, 115.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23523.480 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P43235, cathepsin K
#2: Chemical ChemComp-G4B / THALASSOSPIRAMIDE C


Mass: 791.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H61N5O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.05M MES pH 6.0, 0.1M Na-Oxalate, 0.1M CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 2.2→44.97 Å / Num. obs: 8527 / % possible obs: 86.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 7.69
Reflection shellResolution: 2.2→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.425 / % possible all: 77.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ATK

1atk


Resolution: 2.2→44.97 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.88 / SU B: 26.965 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 3.557 / ESU R Free: 0.378 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30996 782 10.3 %RANDOM
Rwork0.25006 ---
obs0.25627 6790 80.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.45 Å2
Baniso -1Baniso -2Baniso -3
1--3.81 Å2-0 Å2-1.11 Å2
2--3.24 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 57 19 1725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191708
X-RAY DIFFRACTIONr_bond_other_d0.0030.021542
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9692320
X-RAY DIFFRACTIONr_angle_other_deg1.23233542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1085216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45425.73375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07215258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.629154
X-RAY DIFFRACTIONr_chiral_restr0.1010.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022019
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02402
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1052.693864
X-RAY DIFFRACTIONr_mcbond_other1.1042.691863
X-RAY DIFFRACTIONr_mcangle_it1.7844.541080
X-RAY DIFFRACTIONr_mcangle_other1.7834.5431081
X-RAY DIFFRACTIONr_scbond_it1.3412.886844
X-RAY DIFFRACTIONr_scbond_other1.342.886845
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1944.8121241
X-RAY DIFFRACTIONr_long_range_B_refined3.20224.1291831
X-RAY DIFFRACTIONr_long_range_B_other3.20124.131832
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 14 -
Rwork0.569 170 -
obs--26.55 %
Refinement TLS params.Method: refined / Origin x: -3.434 Å / Origin y: 0.194 Å / Origin z: 11.756 Å
111213212223313233
T0.2654 Å20.0001 Å2-0.0132 Å2-0.0102 Å2-0.0049 Å2--0.0132 Å2
L4.5627 °2-0.0426 °21.0739 °2-1.9311 °20.2834 °2--3.2996 °2
S0.0818 Å °0.0187 Å °0.17 Å °0.0854 Å °-0.115 Å °0.0975 Å °0.0304 Å °-0.1114 Å °0.0333 Å °

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