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- PDB-8uac: CATHEPSIN L IN COMPLEX WITH AC1115 -

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Basic information

Entry
Database: PDB / ID: 8uac
TitleCATHEPSIN L IN COMPLEX WITH AC1115
ComponentsCathepsin L
KeywordsHYDROLASE/INHIBITOR / Viral Entry / Cysteine Protease / Protein Catabolism / Inflammation / Covid-19 / HYDROLASE / HYDROLASE-INHIBITOR complex
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 / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / protein autoprocessing / Collagen degradation / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / Attachment and Entry / endocytic vesicle lumen / 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 / Attachment and Entry / lysosome / symbiont entry into host cell / immune response / 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 / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChao, A. / DuPrez, K.T. / Han, F.Q.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To be Published
Title: CATHEPSIN L IN COMPLEX WITH AC1115
Authors: Chao, A. / DuPrez, K.T. / Han, F.Q.
History
DepositionSep 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin L
B: Cathepsin L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2124
Polymers48,3832
Non-polymers8292
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.880, 76.460, 102.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cathepsin L


Mass: 24191.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07711
#2: Chemical ChemComp-W28 / N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-1H-indole-2-carboxamide


Mass: 414.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C22H30N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.86 Å3/Da / Density % sol: 33.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M NaAc, pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.4→61.32 Å / Num. obs: 71556 / % possible obs: 99.6 % / Redundancy: 11.8 % / CC1/2: 0.997 / Net I/σ(I): 6.6
Reflection shellResolution: 1.4→1.42 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3493 / CC1/2: 0.614 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Blu-Icedata collection
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→51.418 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 3472 4.851 %RANDOM
Rwork0.2069 68094 --
all0.208 ---
obs-68094 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.232 Å2
Baniso -1Baniso -2Baniso -3
1--0.092 Å2-0 Å2-0 Å2
2---0.741 Å20 Å2
3---0.833 Å2
Refinement stepCycle: LAST / Resolution: 1.4→51.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 60 301 3673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123484
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163112
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.6654728
X-RAY DIFFRACTIONr_angle_other_deg1.841.5827200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.4958.7516
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg6.83654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53710535
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg10.173102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.32310158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024169
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02807
X-RAY DIFFRACTIONr_nbd_refined0.2330.2725
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.22997
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21728
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21730
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2218
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.223
X-RAY DIFFRACTIONr_nbd_other0.2230.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.233
X-RAY DIFFRACTIONr_mcbond_it1.7221.7631724
X-RAY DIFFRACTIONr_mcbond_other1.7191.7631724
X-RAY DIFFRACTIONr_mcangle_it2.5183.1572151
X-RAY DIFFRACTIONr_mcangle_other2.5183.1582152
X-RAY DIFFRACTIONr_scbond_it2.4582.0551760
X-RAY DIFFRACTIONr_scbond_other2.4582.0541760
X-RAY DIFFRACTIONr_scangle_it3.7783.6472571
X-RAY DIFFRACTIONr_scangle_other3.7773.6472572
X-RAY DIFFRACTIONr_lrange_it5.1323.084099
X-RAY DIFFRACTIONr_lrange_other5.13321.0864034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.2572580.27550010.27452870.9580.95299.47040.259
1.436-1.4760.2632490.25648080.25750810.9580.9699.52760.235
1.476-1.5180.3052080.24347290.24549690.9440.96399.3560.219
1.518-1.5650.282330.25246040.25348750.9480.96399.22050.223
1.565-1.6160.2882210.23644260.23946650.9540.96599.61420.206
1.616-1.6730.2572360.20843000.21145490.9590.97399.71420.183
1.673-1.7360.2681920.21841960.2244070.9550.96999.56890.19
1.736-1.8070.2541970.20940130.21142320.9610.97299.48010.18
1.807-1.8870.2772070.21438340.21740700.9560.97399.28750.189
1.887-1.9790.2751620.22137230.22339160.9540.9799.20840.196
1.979-2.0860.251830.21335190.21537090.9620.97399.81130.197
2.086-2.2120.231740.20733100.20834980.9690.97599.59980.195
2.212-2.3650.2531800.19731010.20133020.9620.97799.3640.189
2.365-2.5540.2391740.19329270.19631360.9650.97798.88390.19
2.554-2.7970.2061360.19326660.19328430.9750.97898.55790.195
2.797-3.1260.2541370.18724670.19126130.9660.97899.65560.201
3.126-3.6070.1921010.18422110.18423130.9790.97899.95680.206
3.607-4.4120.1961040.17718730.17819870.9730.9899.49670.209
4.412-6.2170.23780.21814660.21915610.9690.97398.91090.254
6.217-51.4180.271420.2579010.2579430.950.9571000.3

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