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- PDB-7w33: The crystal structure of human CtsL in complex with 14a -

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Basic information

Entry
Database: PDB / ID: 7w33
TitleThe crystal structure of human CtsL in complex with 14a
ComponentsProcathepsin L
KeywordsHYDROLASE / Human protease / CtsL / Antiviral inhibitor / 14a
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 / Trafficking and processing of endosomal TLR / proteoglycan binding / zymogen activation / Assembly of collagen fibrils and other multimeric structures / antigen processing and presentation / protein autoprocessing / Collagen degradation / collagen catabolic process / fibronectin binding / serpin family protein binding / collagen binding / Attachment and Entry / Degradation of the extracellular matrix / receptor-mediated endocytosis of virus by host cell / multivesicular body / endocytic vesicle lumen / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / : / histone binding / adaptive immune response / Attachment and Entry / lysosome / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-89B / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsZhao, Y. / Shao, M. / Zhao, J. / Yang, H. / Rao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200131 China
CitationJournal: Signal Transduct Target Ther / Year: 2024
Title: Structure-based design of pan-coronavirus inhibitors targeting host cathepsin L and calpain-1.
Authors: Xie, X. / Lan, Q. / Zhao, J. / Zhang, S. / Liu, L. / Zhang, Y. / Xu, W. / Shao, M. / Peng, J. / Xia, S. / Zhu, Y. / Zhang, K. / Zhang, X. / Zhang, R. / Li, J. / Dai, W. / Ge, Z. / Hu, S. / ...Authors: Xie, X. / Lan, Q. / Zhao, J. / Zhang, S. / Liu, L. / Zhang, Y. / Xu, W. / Shao, M. / Peng, J. / Xia, S. / Zhu, Y. / Zhang, K. / Zhang, X. / Zhang, R. / Li, J. / Dai, W. / Ge, Z. / Hu, S. / Yu, C. / Wang, J. / Ma, D. / Zheng, M. / Yang, H. / Xiao, G. / Rao, Z. / Lu, L. / Zhang, L. / Bai, F. / Zhao, Y. / Jiang, S. / Liu, H.
History
DepositionNov 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Oct 23, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Procathepsin L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2202
Polymers37,6051
Non-polymers6151
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.203, 109.203, 92.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Procathepsin L / Cathepsin L1 / Major excreted protein / MEP


Mass: 37605.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL, CTSL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07711, cathepsin L
#2: Chemical ChemComp-89B / N-[(2S)-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2R,3S)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide


Mass: 614.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H35FN4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.83 Å3/Da / Density % sol: 32.86 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 100mM sodium acetate (pH 4.1), 15% (w/v) PEG 2000, protein concentration 8 mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.39→34.53 Å / Num. obs: 11299 / % possible obs: 99.7 % / Redundancy: 25.631 % / Biso Wilson estimate: 49.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.33 / Rrim(I) all: 0.337 / Χ2: 0.763 / Net I/σ(I): 11.26 / Num. measured all: 289600 / Scaling rejects: 59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.39-2.4625.8644.5941.737940.7754.68796.6
2.46-2.5226.8253.8652.268000.8673.94100
2.52-2.626.4623.4322.557850.8933.499100
2.6-2.6826.1242.6493.227490.9412.70199.9
2.68-2.7624.4542.0463.937290.9622.08999.9
2.76-2.8625.4711.8184.517170.971.85599.7
2.86-2.9726.3871.3235.96920.9861.34899.9
2.97-3.0924.7610.9027.316640.990.921100
3.09-3.2327.5030.8288.876320.9940.843100
3.23-3.3927.3880.59211.586110.9970.603100
3.39-3.5727.0420.42314.155900.9980.43199.8
3.57-3.7926.3830.27217.365490.9970.277100
3.79-4.0525.8820.22719.775250.9980.231100
4.05-4.3725.1460.1822.364930.9970.183100
4.37-4.7923.9930.14823.974490.9960.152100
4.79-5.3522.4020.13925.074130.9980.143100
5.35-6.1823.6260.14124.553720.9970.144100
6.18-7.5724.3020.11128.043180.9950.113100
7.57-10.7124.1360.08433.042570.9980.086100
10.71-34.5319.9250.07930.831600.9940.08198.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F06

6f06


Resolution: 2.39→34.53 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 1127 10 %
Rwork0.2222 10143 -
obs0.226 11270 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.82 Å2 / Biso mean: 68.5029 Å2 / Biso min: 47.22 Å2
Refinement stepCycle: final / Resolution: 2.39→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 45 5 1747
Biso mean--67.47 67.24 -
Num. residues----220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.50.45891360.40851217135397
2.5-2.630.46531380.356912461384100
2.63-2.80.37031390.32491257139699
2.8-3.020.34091380.279412381376100
3.02-3.320.32321400.246712621402100
3.32-3.80.26911400.203712681408100
3.8-4.780.16991440.164712921436100
4.78-34.530.21021520.189613631515100

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