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- PDB-9hjy: Cathepsin L3 from Ixodes ricinus (IrCL3) inhibited by E-64 -

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Basic information

Entry
Database: PDB / ID: 9hjy
TitleCathepsin L3 from Ixodes ricinus (IrCL3) inhibited by E-64
ComponentsLate digestive cathepsin L
KeywordsHYDROLASE / Cathepsin / Cysteine Protease / Hard tick
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis
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-E64 / Late digestive cathepsin L
Similarity search - Component
Biological speciesIxodes ricinus (castor bean tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchenkmayerova, A. / Orsaghova, K. / Benova, M. / Busa, M. / Mares, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation21-08826S Czech Republic
CitationJournal: To Be Published
Title: Cathepsin L3 from Ixodes ricinus (IrCL3) inhibited by E-64
Authors: Orsaghova, K. / Benova, M. / Busa, M. / Schenkmayerova, A. / Mares, M. / Horn, M.
History
DepositionDec 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Late digestive cathepsin L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0594
Polymers24,1791
Non-polymers8813
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint0 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.967, 76.911, 152.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Late digestive cathepsin L


Mass: 24178.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes ricinus (castor bean tick) / Gene: CL3 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A481Y5N4
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1:1 protein (5.3 mg/ml in 5 mM sodium acetate pH 5.0, 150 mM sodium chloride) to reservoir (0.1 M sodium cacodylate pH 6.5, 0.2 M sodium chloride, 2 M ammonium sulfate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.6→42.38 Å / Num. obs: 29970 / % possible obs: 99.7 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.048 / Rrim(I) all: 0.178 / Χ2: 1 / Net I/σ(I): 10.6 / Num. measured all: 394665
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 99.9 % / Redundancy: 12.7 % / Rmerge(I) obs: 2.529 / Num. measured all: 18661 / Num. unique obs: 1465 / CC1/2: 0.501 / Rpim(I) all: 0.728 / Rrim(I) all: 2.635 / Χ2: 0.94 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIXVersion 1.21_5207refinement
AimlessCCP4I VERSION CCP4Interface 7.1.018data scaling
XDSVERSION Feb 5, 2021 BUILT=20210323data reduction
PHASERVersion 2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.38 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 1542 5.15 %
Rwork0.1774 --
obs0.1782 29963 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→42.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 58 126 1832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061796
X-RAY DIFFRACTIONf_angle_d0.742437
X-RAY DIFFRACTIONf_dihedral_angle_d18.237682
X-RAY DIFFRACTIONf_chiral_restr0.053258
X-RAY DIFFRACTIONf_plane_restr0.005323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.32781210.28442584X-RAY DIFFRACTION100
1.65-1.710.28891480.25352475X-RAY DIFFRACTION98
1.71-1.780.24081450.21252534X-RAY DIFFRACTION100
1.78-1.860.20991390.19952563X-RAY DIFFRACTION100
1.86-1.960.23141260.18372560X-RAY DIFFRACTION100
1.96-2.080.19521520.14932578X-RAY DIFFRACTION100
2.08-2.240.16491440.152554X-RAY DIFFRACTION99
2.24-2.470.16991240.15492588X-RAY DIFFRACTION100
2.47-2.820.171310.16062621X-RAY DIFFRACTION100
2.82-3.560.17131510.16212622X-RAY DIFFRACTION100
3.56-42.380.19281610.18892742X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.1113 Å / Origin y: -20.2187 Å / Origin z: -20.5794 Å
111213212223313233
T0.1261 Å20.0057 Å20.0099 Å2-0.1215 Å20.0201 Å2--0.1428 Å2
L1.1254 °20.0985 °20.0113 °2-1.1358 °20.3811 °2--1.5484 °2
S-0.0276 Å °0.0397 Å °0.0196 Å °-0.0218 Å °0.0185 Å °0.0121 Å °-0.0129 Å °0.0281 Å °0.007 Å °
Refinement TLS groupSelection details: all

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