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- PDB-3pcx: Caspase-3 E246A, K242A Double Mutant -

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Basic information

Entry
Database: PDB / ID: 3pcx
TitleCaspase-3 E246A, K242A Double Mutant
Components
  • Caspase-3Caspase 3
  • Inhibitor Ac-DEVD-CMK
KeywordsHydrolase/Hydrolase Inhibitor / Salt Bridge / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptosis / glial cell apoptotic process / NADE modulates death signalling / response to cobalt ion ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptosis / glial cell apoptotic process / NADE modulates death signalling / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / luteolysis / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / death receptor binding / SMAC, XIAP-regulated apoptotic response / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / positive regulation of amyloid-beta formation / pyroptosis / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / T cell homeostasis / negative regulation of activated T cell proliferation / neurotrophin TRK receptor signaling pathway / B cell homeostasis / protein maturation / negative regulation of cell cycle / response to X-ray / Caspase-mediated cleavage of cytoskeletal proteins / regulation of macroautophagy / response to amino acid / cell fate commitment / Pyroptosis / response to tumor necrosis factor / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / response to nicotine / apoptotic signaling pathway / hippocampus development / sensory perception of sound / protein catabolic process / regulation of protein stability / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / neuron apoptotic process / protease binding / response to lipopolysaccharide / response to hypoxia / aspartic-type endopeptidase activity / learning or memory / response to xenobiotic stimulus / positive regulation of apoptotic process / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / 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
Ac-Asp-Glu-Val-Asp-CMK / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsWalters, J. / Swartz, P. / Mattos, C. / Clark, A.C.
CitationJournal: Arch.Biochem.Biophys. / Year: 2011
Title: Thermodynamic, enzymatic and structural effects of removing a salt bridge at the base of loop 4 in (pro)caspase-3.
Authors: Walters, J. / Swartz, P. / Mattos, C. / Clark, A.C.
History
DepositionOct 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Dec 12, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-3
B: Inhibitor Ac-DEVD-CMK


Theoretical massNumber of molelcules
Total (without water)29,0892
Polymers29,0892
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-10 kcal/mol
Surface area12640 Å2
MethodPISA
2
A: Caspase-3
B: Inhibitor Ac-DEVD-CMK

A: Caspase-3
B: Inhibitor Ac-DEVD-CMK

A: Caspase-3
B: Inhibitor Ac-DEVD-CMK

A: Caspase-3
B: Inhibitor Ac-DEVD-CMK


Theoretical massNumber of molelcules
Total (without water)116,3588
Polymers116,3588
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area17920 Å2
ΔGint-96 kcal/mol
Surface area37920 Å2
MethodPISA
3
A: Caspase-3
B: Inhibitor Ac-DEVD-CMK

A: Caspase-3
B: Inhibitor Ac-DEVD-CMK

A: Caspase-3
B: Inhibitor Ac-DEVD-CMK

A: Caspase-3
B: Inhibitor Ac-DEVD-CMK


Theoretical massNumber of molelcules
Total (without water)116,3588
Polymers116,3588
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area17440 Å2
ΔGint-88 kcal/mol
Surface area38390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.936, 84.695, 96.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-453-

HOH

21A-558-

HOH

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Components

#1: Protein Caspase-3 / Caspase 3 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / ...CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1 / Caspase-3 subunit p17 / Caspase-3 subunit p12


Mass: 28554.535 Da / Num. of mol.: 1 / Fragment: UNP residues 29-277 / Mutation: E246A, K242A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Lys / References: UniProt: P42574, caspase-3
#2: Protein/peptide Inhibitor Ac-DEVD-CMK


Type: Peptide-like / Class: Inhibitor / Mass: 534.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: Ac-Asp-Glu-Val-Asp-CMK
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING ...Details: Inhibitor, Ac-DEVD-CMK, reconstituted in DMSO, was added at a 5:1 inhibitor:protein ratio (w/w). Final buffer consisted of 10 mM Tris-HCl, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, pH 8.5, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 16, 2006
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 48708 / Num. obs: 47295 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.45→1.5 Å / % possible all: 76

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 1.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2128 4299 9.5 %
Rwork0.1956 38238 -
obs-42537 93.7 %
Solvent computationBsol: 28.8039 Å2
Displacement parametersBiso max: 59.25 Å2 / Biso mean: 22.2194 Å2 / Biso min: 11.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.587 Å20 Å20 Å2
2---4.94 Å20 Å2
3---5.527 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 0 317 2305
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.46
X-RAY DIFFRACTIONc_mcbond_it0.9811.5
X-RAY DIFFRACTIONc_scbond_it1.9212
X-RAY DIFFRACTIONc_mcangle_it1.4772
X-RAY DIFFRACTIONc_scangle_it2.8412.5

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