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

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Basic information

Entry
Database: PDB / ID: 1bgo
TitleCRYSTAL STRUCTURE OF CYSTEINE PROTEASE HUMAN CATHEPSIN K IN COMPLEX WITH A COVALENT PEPTIDOMIMETIC INHIBITOR
ComponentsCATHEPSIN K
KeywordsHYDROLASE / SULFHYDRYL PROTEINASE / THIOL PROTEASE
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-I10 / Cathepsin K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.3 Å
AuthorsDesjarlais, R.L. / Yamashita, D.S. / Oh, H.-J. / Bondinell, W.E. / Uzinskas, I.N. / Erhard, K.F. / Allen, A.C. / Haltiwanger, R.C. / Zhao, B. / Smith, W.W. ...Desjarlais, R.L. / Yamashita, D.S. / Oh, H.-J. / Bondinell, W.E. / Uzinskas, I.N. / Erhard, K.F. / Allen, A.C. / Haltiwanger, R.C. / Zhao, B. / Smith, W.W. / Abdel-Meguid, S.S. / D'Alessio, K. / Janson, C.A. / Mcqueney, M.S. / Tomaszek, T.A. / Levy, M.A. / Veber, D.F.
Citation
Journal: J.Am.Chem.Soc. / Year: 1998
Title: Use of X-Ray Co-Crystal Structures and Molecular Modeling to Design Potent and Selective Non-Peptide Inhibitors of Cathepsin K
Authors: Desjarlais, R.L. / Yamashita, D.S. / Oh, H.J. / Uzinskas, I.N. / Erhard, K.F. / Allen, A.C. / Haltiwanger, R.C. / Zhao, B.G. / Smith, W.W. / Abdel-Meguid, S.S. / Dalessio, K. / Janson, C.A. ...Authors: Desjarlais, R.L. / Yamashita, D.S. / Oh, H.J. / Uzinskas, I.N. / Erhard, K.F. / Allen, A.C. / Haltiwanger, R.C. / Zhao, B.G. / Smith, W.W. / Abdel-Meguid, S.S. / Dalessio, K. / Janson, C.A. / Mcqueney, M.S. / Tomaszek, T.A. / Levy, M.A. / Veber, D.F.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal Structure of Human Osteoclast Cathepsin K Complex with E-64
Authors: Zhao, B. / Janson, C.A. / Amegadzie, B.Y. / D'Alessio, K. / Griffin, C. / Hanning, C.R. / Jones, C. / Kurdyla, J. / Mcqueney, M. / Qiu, X. / Smith, W.W. / Abdel-Meguid, S.S.
History
DepositionMay 29, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Aug 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 1.5Oct 23, 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)24,0052
Polymers23,5231
Non-polymers4821
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.550, 71.550, 55.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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-I10 / 1-[2-(3-BIPHENYL)-4-METHYLVALERYL)]AMINO-3-(2-PYRIDYLSULFONYL)AMINO-2-PROPANONE


Mass: 481.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H31N3O4S
#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: 2.95 Å3/Da / Density % sol: 58 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 %PEG80001reservoir
20.06 Msodium acetate1reservoir
30.12 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Sep 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→35 Å / Num. obs: 11258 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.27 / % possible all: 54
Reflection shell
*PLUS
% possible obs: 54 %

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Processing

Software
NameVersionClassification
XENGENdata collection
CCP4data reduction
X-PLOR3.851model building
X-PLOR3.851refinement
XENGENdata reduction
CCP4data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: molecular replacement
Starting model: 1ATK

1atk


Resolution: 2.3→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1016 10.5 %RANDOM
Rwork0.24 ---
obs0.24 9666 79.3 %-
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 error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 34 19 1751
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.82
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: 2.3→2.4 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.369 56 11 %
Rwork0.275 455 -
obs--33.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / 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_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.82

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