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- PDB-8b5f: Human cathepsin B in complex with the carbamate inhibitor 31 -

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Basic information

Entry
Database: PDB / ID: 8b5f
TitleHuman cathepsin B in complex with the carbamate inhibitor 31
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 / epithelial cell differentiation / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / regulation of apoptotic process / collagen-containing extracellular matrix / 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-P9U / Cathepsin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 31
Authors: Rubesova, P. / Guetschow, M. / Mares, M.
History
DepositionSep 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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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)28,7283
Polymers27,9561
Non-polymers7722
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint2 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.573, 81.565, 93.520
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-P9U / (2S)-2-[[(2S)-2-[[3-chloranyl-4-[[3-phenyl-2-(phenylmethyl)propanoyl]amino]phenoxy]carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid / (2~{S})-2-[[(2~{S})-2-[[3-chloranyl-4-[[3-phenyl-2-(phenylmethyl)propanoyl]amino]phenoxy]carbonylamino]-3-cyclohexyl-propanoyl]amino]-3-phenyl-propanoic acid


Mass: 710.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H44ClN3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Sodium Acetate pH 5.5, 30% PEG 5000 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: 1.7→46.76 Å / Num. obs: 26540 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 28.907 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.247 / Rrim(I) all: 0.257 / Χ2: 0.717 / Net I/σ(I): 9.34 / Num. measured all: 342373
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
1.7-1.812.8513.160.8353806419841870.333.29199.7
1.8-1.9312.5732.0041.3649989397839760.5462.08999.9
1.93-2.0813.431.0722.7249462368436830.8241.115100
2.08-2.2813.260.6314.745283341934150.9240.65799.9
2.28-2.5512.6960.3817.3140030315331530.9680.397100
2.55-2.9413.5090.23411.8837110275027470.9890.24399.9
2.94-3.612.3160.12520.6729214237723720.9960.1399.8
3.6-5.0713.10.06735.3424824189618950.9990.0799.9
5.07-46.7611.380.05437.0712655111511120.9990.05799.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.342
Highest resolutionLowest resolution
Rotation40.78 Å1.91 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDS1.12data reduction
XSCALE20220220data scaling
MOLREP11.7.02phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B4T

8b4t


Resolution: 1.7→46.76 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1778 / WRfactor Rwork: 0.1461 / FOM work R set: 0.7954 / SU B: 3.155 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1117 / SU Rfree: 0.1054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 1328 5 %RANDOM
Rwork0.1747 ---
obs0.1762 25215 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.77 Å2 / Biso mean: 23.241 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0 Å2
2---0.74 Å2-0 Å2
3---0.97 Å2
Refinement stepCycle: final / Resolution: 1.7→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 29 186 2175
Biso mean--32.82 32.39 -
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132114
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181799
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.6572880
X-RAY DIFFRACTIONr_angle_other_deg1.4661.5944208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0385266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.87222.804107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44515313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0031510
X-RAY DIFFRACTIONr_chiral_restr0.0830.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022456
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02463
LS refinement shellResolution: 1.7→1.74 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.321 94 -
Rwork0.352 1769 -
obs--99.52 %

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