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- PDB-8b4t: Human cathepsin B in complex with the carbamate inhibitor 7 -

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Basic information

Entry
Database: PDB / ID: 8b4t
TitleHuman cathepsin B in complex with the carbamate inhibitor 7
ComponentsCathepsin B
KeywordsHYDROLASE / Cathepsin B Cysteine cathepsin Inhibitor Carbamate Peptidomimetic Cysteine proteinases
Function / homology
Function and homology information


cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization ...cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization / collagen catabolic process / cysteine-type peptidase activity / collagen binding / epithelial cell differentiation / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / collagen-containing extracellular matrix / regulation of apoptotic process / ficolin-1-rich granule lumen / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / 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-P9F / Cathepsin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsRubesova, P. / Guetschow, M. / Mares, M.
Funding support Czech Republic, European Union, 2items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic Czech Republic
European Regional Development FundEuropean Union
CitationJournal: To Be Published
Title: Human cathepsin B in complex with the carbamate inhibitor 7
Authors: Rubesova, P. / Guetschow, M. / Mares, M.
History
DepositionSep 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4292
Polymers27,9561
Non-polymers4731
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.750, 81.550, 93.460
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 B / APP secretase / APPS / Cathepsin B1


Mass: 27956.156 Da / Num. of mol.: 1 / Mutation: S115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSB, CPSB / Plasmid: pPICZ(alpha) A / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P07858, cathepsin B
#2: Chemical ChemComp-P9F / (2S)-2-[[(2S)-2-[(4-chloranylphenoxy)carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid / (2~{S})-2-[[(2~{S})-2-[(4-chloranylphenoxy)carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid


Mass: 472.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H29ClN2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Sodium Acetate pH 5.5, 20% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.45→46.73 Å / Num. obs: 42360 / % possible obs: 98.8 % / Redundancy: 12.968 % / Biso Wilson estimate: 24.852 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.176 / Rrim(I) all: 0.183 / Χ2: 0.702 / Net I/σ(I): 11.36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.5412.5443.120.7866310.3973.2596.9
1.54-1.6413.3121.8131.563240.6561.88498.7
1.64-1.7713.541.1162.6959310.8571.1699.2
1.77-1.9412.7560.6614.5854700.9410.68998.7
1.94-2.1713.660.339.650180.9860.34399.8
2.17-2.513.3360.18616.5644550.9950.19499.9
2.5-3.0712.1920.11224.5237830.9970.11799
3.07-4.3312.6260.05842.1630030.9990.0699.7
4.33-46.7311.3920.04848.1617450.9980.0598.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation30.98 Å4 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDS3.1.5data reduction
XSCALEdata scaling
MOLREP11.7.03phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IPP

2ipp


Resolution: 1.45→46.73 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.998 / SU ML: 0.068 / SU R Cruickshank DPI: 0.0723 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 2101 5 %RANDOM
Rwork0.1773 ---
obs0.1788 40259 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.5 Å2 / Biso mean: 19.795 Å2 / Biso min: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---1.37 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: final / Resolution: 1.45→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 25 232 2209
Biso mean--26.73 31.28 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132196
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181861
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.6573004
X-RAY DIFFRACTIONr_angle_other_deg1.5561.5954361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0455284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.37422.768112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5315330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1961511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022600
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02486
LS refinement shellResolution: 1.45→1.49 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.404 148 -
Rwork0.387 2825 -
obs--95.63 %

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