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- PDB-2f7d: A mutant rabbit cathepsin K with a nitrile inhibitor -

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Basic information

Entry
Database: PDB / ID: 2f7d
TitleA mutant rabbit cathepsin K with a nitrile inhibitor
ComponentsCathepsin K
KeywordsHYDROLASE / papain cysteine protease
Function / homology
Function and homology information


cathepsin K / negative regulation of cartilage development / thyroid hormone generation / collagen catabolic process / bone resorption / proteolysis involved in protein catabolic process / lysosome / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Peptidase C1A, cathepsin K / 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 ...Peptidase C1A, cathepsin K / 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
Chem-NOQ / Cathepsin K
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsSomoza, J.R.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Beta-substituted cyclohexanecarboxamide: a nonpeptidic framework for the design of potent inhibitors of cathepsin K.
Authors: Crane, S.N. / Black, W.C. / Palmer, J.T. / Davis, D.E. / Setti, E. / Robichaud, J. / Paquet, J. / Oballa, R.M. / Bayly, C.I. / McKay, D.J. / Somoza, J.R. / Chauret, N. / Seto, C. / ...Authors: Crane, S.N. / Black, W.C. / Palmer, J.T. / Davis, D.E. / Setti, E. / Robichaud, J. / Paquet, J. / Oballa, R.M. / Bayly, C.I. / McKay, D.J. / Somoza, J.R. / Chauret, N. / Seto, C. / Scheigetz, J. / Wesolowski, G. / Masse, F. / Desmarais, S. / Ouellet, M.
History
DepositionNov 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)23,9092
Polymers23,5541
Non-polymers3541
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.125, 51.150, 104.245
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe cathepsin K monomer is probably the biological unit.

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Components

#1: Protein Cathepsin K / / OC-2 protein


Mass: 23554.498 Da / Num. of mol.: 1 / Mutation: Y61D, V157L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CTSK / Production host: Pichia pastoris (fungus) / References: UniProt: P43236, cathepsin K
#2: Chemical ChemComp-NOQ / (1R,2R)-N-(2-AMINOETHYL)-2-{[(4-METHOXYPHENYL)SULFONYL]METHYL}CYCLOHEXANECARBOXAMIDE


Mass: 354.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H26N2O4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.9
Details: 0.18 M magnesium formate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNumber: 16445 / Rmerge(I) obs: 0.081 / Χ2: 1.133 / D res high: 1.9 Å / D res low: 100 Å / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.0910097.610.051.094
3.254.0910010.0671.203
2.843.2510010.0831.194
2.582.8499.910.1041.189
2.392.5899.810.1181.208
2.252.3999.910.1341.134
2.142.2599.610.1641.087
2.052.1499.710.1911.049
1.972.0599.510.2261.018
1.91.9784.510.2841.042
ReflectionResolution: 1.9→100 Å / Num. all: 16445 / Num. obs: 16445 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.081 / Χ2: 1.133
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.970.28413711.04284.5
1.97-2.050.22616341.01899.5
2.05-2.140.19116451.04999.7
2.14-2.250.16416391.08799.6
2.25-2.390.13416581.13499.9
2.39-2.580.11816471.20899.8
2.58-2.840.10416701.18999.9
2.84-3.250.08316841.194100
3.25-4.090.06717051.203100
4.09-1000.0517921.09497.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→36.51 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1614 9.7 %RANDOM
Rwork0.174 ---
all0.182 16224 --
obs0.182 16224 97.1 %-
Displacement parametersBiso mean: 22.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.356 Å20 Å20 Å2
2---0.984 Å20 Å2
3----0.372 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 24 97 1772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.193
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.237 230 -
Rwork0.203 --
obs-2383 87.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2non.param
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:ion.param

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