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- PDB-6dev: Human caspase-6 E35K -

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Basic information

Entry
Database: PDB / ID: 6dev
TitleHuman caspase-6 E35K
ComponentsCaspase-6Caspase 6
KeywordsHYDROLASE
Function / homology
Function and homology information


caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptosis ...caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / pyroptosis / Apoptotic cleavage of cellular proteins / protein autoprocessing / intrinsic apoptotic signaling pathway by p53 class mediator / Caspase-mediated cleavage of cytoskeletal proteins / cysteine-type peptidase activity / epithelial cell differentiation / activation of innate immune response / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain ...Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.348 Å
AuthorsTubeleviciute-Aydin, A. / Beautrait, A. / Lynham, J. / Sharma, G. / Gorelik, A. / Deny, L.J. / Soya, N. / Lukacs, G.L. / Nagar, B. / Marinier, A. / LeBlanc, A.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-243413-BCA-CGAG-45097 Canada
CitationJournal: Sci Rep / Year: 2019
Title: Identification of Allosteric Inhibitors against Active Caspase-6.
Authors: Tubeleviciute-Aydin, A. / Beautrait, A. / Lynham, J. / Sharma, G. / Gorelik, A. / Deny, L.J. / Soya, N. / Lukacs, G.L. / Nagar, B. / Marinier, A. / LeBlanc, A.C.
History
DepositionMay 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-6
B: Caspase-6
C: Caspase-6
D: Caspase-6


Theoretical massNumber of molelcules
Total (without water)138,0054
Polymers138,0054
Non-polymers00
Water3,333185
1
A: Caspase-6
B: Caspase-6


Theoretical massNumber of molelcules
Total (without water)69,0032
Polymers69,0032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-21 kcal/mol
Surface area21170 Å2
MethodPISA
2
C: Caspase-6
D: Caspase-6


Theoretical massNumber of molelcules
Total (without water)69,0032
Polymers69,0032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-21 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.385, 91.326, 86.682
Angle α, β, γ (deg.)90.00, 91.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Caspase-6 / Caspase 6 / CASP-6 / Apoptotic protease Mch-2


Mass: 34501.301 Da / Num. of mol.: 4 / Mutation: E35K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6, MCH2 / Production host: Escherichia coli (E. coli) / References: UniProt: P55212, caspase-6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 100 mM sodium acetate pH 4.6, 2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 2.348→36.47 Å / Num. obs: 41219 / % possible obs: 98 % / Redundancy: 7.2 % / Net I/σ(I): 15.1
Reflection shellResolution: 2.348→2.43 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FXO

4fxo


Resolution: 2.348→36.47 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.48
RfactorNum. reflection% reflection
Rfree0.2485 2018 5.72 %
Rwork0.2053 --
obs0.2078 35269 83.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.348→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7240 0 0 185 7425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027409
X-RAY DIFFRACTIONf_angle_d0.4679954
X-RAY DIFFRACTIONf_dihedral_angle_d8.9414412
X-RAY DIFFRACTIONf_chiral_restr0.0391066
X-RAY DIFFRACTIONf_plane_restr0.0021262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3481-2.40680.4168160.2952194X-RAY DIFFRACTION7
2.4068-2.47190.3963520.2715884X-RAY DIFFRACTION32
2.4719-2.54460.27681130.2541689X-RAY DIFFRACTION60
2.5446-2.62670.30491500.24852258X-RAY DIFFRACTION82
2.6267-2.72060.29341630.2472768X-RAY DIFFRACTION98
2.7206-2.82950.31071690.24682798X-RAY DIFFRACTION100
2.8295-2.95820.28071810.22032825X-RAY DIFFRACTION100
2.9582-3.11410.25141670.21092819X-RAY DIFFRACTION100
3.1141-3.30910.26851680.212843X-RAY DIFFRACTION100
3.3091-3.56440.23031760.20572817X-RAY DIFFRACTION100
3.5644-3.92270.22991610.20482788X-RAY DIFFRACTION99
3.9227-4.48940.22091700.1712815X-RAY DIFFRACTION99
4.4894-5.65280.21391780.17862848X-RAY DIFFRACTION100
5.6528-36.47480.23771540.19932905X-RAY DIFFRACTION99

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