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- PDB-7w34: The crystal structure of human CtsL in complex with 14b -

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Basic information

Entry
Database: PDB / ID: 7w34
TitleThe crystal structure of human CtsL in complex with 14b
ComponentsProcathepsin L
KeywordsHYDROLASE / Human protease / CtsL / Antiviral inhibitor / 14b
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 / zymogen activation / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / antigen processing and presentation / Collagen degradation / protein autoprocessing / fibronectin binding / collagen catabolic process / serpin family protein binding / collagen binding / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / Degradation of the extracellular matrix / 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 / : / adaptive immune response / histone binding / Attachment and Entry / lysosome / apical plasma membrane / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-89K / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsZhao, Y. / Shao, M. / Zhao, J. / Yang, H. / Rao, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)813300237 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

Downloads & links

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Assembly

Deposited unit
A: Procathepsin L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2082
Polymers37,6051
Non-polymers6031
Water00
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)109.361, 109.361, 92.481
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-89K / N-[(2S)-3-cyclohexyl-1-oxidanylidene-1-[[(2S,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: 602.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H42N4O6 / Feature type: SUBJECT OF INVESTIGATION
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: 33.09 %
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 8mg/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: 2.89→39.69 Å / Num. obs: 6525 / % possible obs: 99.9 % / Redundancy: 26.002 % / Biso Wilson estimate: 61.79 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.57 / Rrim(I) all: 0.581 / Χ2: 0.731 / Net I/σ(I): 10.08 / Num. measured all: 169661 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.89-2.9725.3744.7411.5115454604550.524.83898.9
2.97-3.0524.8154.4831.59113904594590.7264.577100
3.05-3.1426.4493.2052.49119554524520.8683.267100
3.14-3.2327.8553.2612.56120894344340.8153.322100
3.23-3.3427.6432.4363.56117764264260.8822.482100
3.34-3.4627.4481.7694.88111444064060.9781.803100
3.46-3.5927.3281.4915.75109864024020.9671.519100
3.59-3.7427.3180.9168.47102993773770.9860.934100
3.74-3.926.9080.7319.999833713710.9920.745100
3.9-4.0926.7530.66410.6594173523520.9910.677100
4.09-4.3126.2330.45612.9487883353350.9950.465100
4.31-4.5725.6010.32115.4881413183180.9970.327100
4.57-4.8924.6250.28316.8773633002990.9950.28999.7
4.89-5.2823.0480.25316.8967532932930.9970.259100
5.28-5.7925.4980.28515.9166552612610.9960.291100
5.79-6.4723.410.23717.0855952392390.9970.242100
6.47-7.4726.5630.17921.6156582132130.9980.182100
7.47-9.1525.750.10829.2348411881880.9980.11100
9.15-12.9423.9610.07834.3636661531530.9980.08100
12.94-39.6917.5760.06831.39161795920.9990.0796.8

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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: 2.89→39.69 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3028 651 10 %
Rwork0.2482 5862 -
obs0.2535 6513 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.94 Å2 / Biso mean: 60.9398 Å2 / Biso min: 41.29 Å2
Refinement stepCycle: final / Resolution: 2.89→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 44 0 1741
Biso mean--60.65 --
Num. residues----220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-3.120.41231250.39761138126399
3.12-3.430.34871290.321411461275100
3.43-3.930.30311280.257911581286100
3.93-4.940.26811310.205711751306100
4.94-39.690.28031380.211212451383100

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