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- PDB-3bc3: Exploring inhibitor binding at the S subsites of cathepsin L -

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Basic information

Entry
Database: PDB / ID: 3bc3
TitleExploring inhibitor binding at the S subsites of cathepsin L
ComponentsCathepsin L heavy and light chains
KeywordsHYDROLASE / cathepsin L inhibitor binding at the S subsites / Glycoprotein / Lysosome / Protease / Thiol protease / Zymogen
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / protein autoprocessing / Collagen degradation / fibronectin binding / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / endocytic vesicle lumen / Attachment and Entry / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / adaptive immune response / receptor-mediated endocytosis of virus by host cell / lysosome / Attachment and Entry / immune response / symbiont entry into host cell / apical plasma membrane / cysteine-type endopeptidase activity / fusion of virus membrane with host plasma membrane / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
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-OPT / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsChowdhury, S.F. / Joseph, L. / Kumar, S. / Tulsidas, S.R. / Bhat, S. / Ziomek, E. / Nard, R.M. / Sivaraman, J. / Purisima, E.O.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Exploring inhibitor binding at the S' subsites of cathepsin L
Authors: Chowdhury, S.F. / Joseph, L. / Kumar, S. / Tulsidas, S.R. / Bhat, S. / Ziomek, E. / Menard, R. / Sivaraman, J. / Purisima, E.O.
History
DepositionNov 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_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

Downloads & links

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Assembly

Deposited unit
A: Cathepsin L heavy and light chains
B: Cathepsin L heavy and light chains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1074
Polymers48,4472
Non-polymers1,6602
Water7,620423
1
A: Cathepsin L heavy and light chains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0542
Polymers24,2241
Non-polymers8301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cathepsin L heavy and light chains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0542
Polymers24,2241
Non-polymers8301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.765, 90.929, 126.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cathepsin L heavy and light chains / (EC 3.4.22.15) (Major excreted protein) (MEP)


Mass: 24223.701 Da / Num. of mol.: 2 / Fragment: UNp residues 114-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL / Production host: Pichia pastoris (fungus) / References: UniProt: P07711, cathepsin L
#2: Chemical ChemComp-OPT / S-benzyl-N-(biphenyl-4-ylacetyl)-L-cysteinyl-N~5~-(diaminomethyl)-D-ornithyl-N-(2-phenylethyl)-L-tyrosinamide


Mass: 830.048 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H55N7O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 17%(w/v) Polyethylene glycol 8000, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 4.2 % / Av σ(I) over netI: 21.1 / Number: 87370 / Rmerge(I) obs: 0.048 / Χ2: 1.98 / D res high: 2.2 Å / D res low: 50 Å / Num. obs: 21015 / % possible obs: 94.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.745098.110.0321.5614.2
3.764.7410010.0341.8684.5
3.293.7610010.0391.8574.5
2.993.2999.910.0543.3864.5
2.772.9999.910.0692.0254.5
2.612.7710010.0911.9164.5
2.482.6199.910.112.0694.5
2.372.4896.910.1321.5133.9
2.282.3782.810.1541.3023
2.22.2867.110.1871.2892.6
ReflectionResolution: 2.2→50 Å / Num. obs: 20987 / Rsym value: 0.048 / Net I/σ(I): 21.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1mhw

1mhw


Resolution: 2.2→30 Å / σ(F): 761
RfactorNum. reflection% reflection
Rfree0.234 1558 7 %
Rwork0.183 --
obs-19891 89.7 %
Solvent computationBsol: 44.397 Å2
Displacement parametersBiso mean: 30.797 Å2
Baniso -1Baniso -2Baniso -3
1--0.684 Å20 Å20 Å2
2---4.834 Å20 Å2
3---5.518 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 120 423 3865
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.044
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3inh.par
X-RAY DIFFRACTION4csw.par

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