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- PDB-3ai8: Cathepsin B in complex with the nitroxoline -

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Basic information

Entry
Database: PDB / ID: 3ai8
TitleCathepsin B in complex with the nitroxoline
ComponentsCathepsin B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cathepsin B / reversible inhibitor / Nitroxoline / 8-Hydroxy-5-nitroquinoline / HYDROLASE-HYDROLASE INHIBITOR complex
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 proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
5-nitroquinolin-8-ol / Cathepsin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsRenko, M. / Mirkovic, B. / Gobec, S. / Kos, J. / Turk, D.
CitationJournal: Chemmedchem / Year: 2011
Title: Novel mechanism of cathepsin B inhibition by antibiotic nitroxoline and related compounds
Authors: Mirkovic, B. / Renko, M. / Turk, S. / Sosic, I. / Jevnikar, Z. / Obermajer, N. / Turk, D. / Gobec, S. / Kos, J.
History
DepositionMay 11, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,5514
Polymers56,1712
Non-polymers3802
Water5,116284
1
B: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2752
Polymers28,0851
Non-polymers1901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2752
Polymers28,0851
Non-polymers1901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.682, 29.976, 119.198
Angle α, β, γ (deg.)90.000, 126.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cathepsin B / / Cathepsin B1 / APP secretase / APPS / Cathepsin B light chain / Cathepsin B heavy chain


Mass: 28085.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSB / Plasmid: PET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21de3 / References: UniProt: P07858, cathepsin B
#2: Chemical ChemComp-HNQ / 5-nitroquinolin-8-ol / NITROXOLINE / Nitroxoline


Mass: 190.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N2O3 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3
Details: 0.1M citric acid, 21% PEG6000, pH 3.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2010 / Details: Collimating and focusing, Pt-coated mirrors
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 25966 / Num. obs: 25966 / % possible obs: 92.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.2 / % possible all: 96.2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K9M

3k9m


Resolution: 2.11→29.1 Å / Cor.coef. Fo:Fc: 0.946 / WRfactor Rwork: 0.178 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.881 / SU R Cruickshank DPI: 0.36 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. The structure was refined also with MAIN
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1134 -random
Rwork0.183 ---
all0.198 22508 --
obs0.183 22508 86.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.93 Å2 / Biso mean: 22.877 Å2 / Biso min: 6.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.64 Å2
2---0.16 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.11→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 28 284 4250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0294081
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9295560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0495510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74223.989183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60715595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0541518
X-RAY DIFFRACTIONr_chiral_restr0.180.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0213236
X-RAY DIFFRACTIONr_mcbond_it2.7341.52528
X-RAY DIFFRACTIONr_mcangle_it4.45224052
X-RAY DIFFRACTIONr_scbond_it2.84831553
X-RAY DIFFRACTIONr_scangle_it4.5264.51508
LS refinement shellResolution: 2.107→2.162 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.22 1264 -
obs--65.59 %

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