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- PDB-1ayw: CRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 1ayw
TitleCRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT BENZYLOXYBENZOYLCARBOHYDRAZIDE INHIBITOR
ComponentsCATHEPSIN K
KeywordsHYDROLASE / SULFHYDRYL PROTEINASE
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 / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / lysosome / apical plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / 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
Chem-IN3 / Cathepsin K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.4 Å
AuthorsZhao, B. / Smith, W.W. / Janson, C.A. / Abdel-Meguid, S.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Design of potent and selective human cathepsin K inhibitors that span the active site.
Authors: Thompson, S.K. / Halbert, S.M. / Bossard, M.J. / Tomaszek, T.A. / Levy, M.A. / Zhao, B. / Smith, W.W. / Abdel-Meguid, S.S. / Janson, C.A. / D'Alessio, K.J. / McQueney, M.S. / Amegadzie, B.Y. ...Authors: Thompson, S.K. / Halbert, S.M. / Bossard, M.J. / Tomaszek, T.A. / Levy, M.A. / Zhao, B. / Smith, W.W. / Abdel-Meguid, S.S. / Janson, C.A. / D'Alessio, K.J. / McQueney, M.S. / Amegadzie, B.Y. / Hanning, C.R. / DesJarlais, R.L. / Briand, J. / Sarkar, S.K. / Huddleston, M.J. / Ijames, C.F. / Carr, S.A. / Garnes, K.T. / Shu, A. / Heys, J.R. / Bradbeer, J. / Zembryki, D. / Lee-Rykaczewski, L. / James, I.E. / Lark, M.W. / Drake, F.H. / Gowen, M. / Gleason, J.G. / Veber, D.F.
History
DepositionNov 10, 1997Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.5Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)24,0712
Polymers23,5231
Non-polymers5481
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.680, 57.680, 131.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CATHEPSIN K


Mass: 23523.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: INHIBITOR COVALENTLY BOUND TO ACTIVE SITE CYS 25 / Source: (gene. exp.) Homo sapiens (human) / Cell: OSTEOCLAST / Cell line: SF21 / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43235, cathepsin K
#2: Chemical ChemComp-IN3 / 1-(N-BENZYLOXYCARBONYL-L-LEUCINYL)-5-(3-BENZYLOXY BENZOYL)CARBOHYDRAZIDE


Mass: 547.602 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H33N5O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.3 Å3/Da / Density % sol: 46.2 %
Crystal growpH: 4.5
Details: 22.5% PEG 8000, 0.075M SODIUM ACETATE, 0.15M LITHIUM ACETATE, PH4.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122.5 %PEG80001reservoir
20.075 Msodium acetate1reservoir
30.15 Mlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 8365 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 19.6
Reflection shellResolution: 2.4→2.56 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3 / Rsym value: 0.23 / % possible all: 61
Reflection shell
*PLUS
% possible obs: 61 %

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Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: molecular replacement
Starting model: 1ATK

1atk


Resolution: 2.4→8 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.379 769 10.5 %RANDOM
Rwork0.237 ---
obs0.237 7323 82.1 %-
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 40 62 1751
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.102 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.557 30 9 %
Rwork0.325 302 -
obs--30.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor obs: 0.325

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