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- PDB-4qua: Caspase-3 Y195F -

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Basic information

Entry
Database: PDB / ID: 4qua
TitleCaspase-3 Y195F
Components
  • ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR
  • Caspase-3
Keywordshydrolase/hydrolase inhibitor / Allosteric Network / 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 pyroptotic inflammatory response / glial cell apoptotic process / : / NADE modulates death signalling ...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 pyroptotic inflammatory response / glial cell apoptotic process / : / NADE modulates death signalling / : / luteolysis / response to cobalt ion / : / cellular response to staurosporine / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / Caspase activation via Dependence Receptors in the absence of ligand / SMAC, XIAP-regulated apoptotic response / death receptor binding / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / axonal fasciculation / regulation of synaptic vesicle cycle / fibroblast apoptotic process / epithelial cell apoptotic process / platelet formation / negative regulation of cytokine production / Other interleukin signaling / positive regulation of amyloid-beta formation / execution phase of apoptosis / negative regulation of B cell proliferation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of activated T cell proliferation / T cell homeostasis / neurotrophin TRK receptor signaling pathway / B cell homeostasis / negative regulation of cell cycle / response to tumor necrosis factor / response to X-ray / cell fate commitment / response to amino acid / regulation of macroautophagy / Pyroptosis / Caspase-mediated cleavage of cytoskeletal proteins / protein maturation / response to glucose / response to glucocorticoid / response to UV / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / enzyme activator activity / intrinsic apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / response to nicotine / apoptotic signaling pathway / sensory perception of sound / protein catabolic process / regulation of protein stability / protein processing / response to hydrogen peroxide / neuron differentiation / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / peptidase activity / heart development / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / postsynaptic density / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / DNA damage response / apoptotic process / protein-containing complex binding / glutamatergic synapse / 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 / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsCade, C. / Swartz, P.D. / MacKenzie, S.H. / Clark, A.C.
CitationJournal: Biochemistry / Year: 2014
Title: Modifying caspase-3 activity by altering allosteric networks.
Authors: Cade, C. / Swartz, P. / MacKenzie, S.H. / Clark, A.C.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-3
D: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)32,2842
Polymers32,2842
Non-polymers00
Water3,837213
1
A: Caspase-3
D: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR

A: Caspase-3
D: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)64,5684
Polymers64,5684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x,y,-z+21
Buried area6540 Å2
ΔGint-17 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.320, 84.081, 96.164
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-331-

HOH

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Components

#1: Protein 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: 31749.094 Da / Num. of mol.: 1 / Mutation: Y195F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3
#2: Protein/peptide ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR


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


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ...Details: Proteins were dialyzed in a buffer of 10 mM Tris-HCl, pH 8.5, 1 mM DTT and concentrated to 10 mg/mL. Inhibitor, Ac-DEVD-CMK reconstituted in DMSO, was then added at a 5:1 inhibitor:peptide ratio (w/w). The protein was diluted to a concentration of 8 mg/mL by adding 10 mM Tris-HCl, pH 8.5, concentrated DTT, and concentrated NaN3 so that the final buffer consisted of 10 mM Tris-HCl, pH 8.5, 10 mM DTT, and 3 mM NaN3. Crystals were obtained at 291K by the hanging drop vapor diffusion method using 4 L drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL reservoir. The reservoir solutions for optimal crystal growth consisted of 100 mM sodium citrate, pH 5.0, 3 mM NaN3, 10 mM DTT, and 10% 16% PEG 6000 (w/v). Crystals appeared within 3.5 to 6 weeks for all mutants, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2012
RadiationMonochromator: Bending Magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.892→22.823 Å / Num. all: 21432 / Num. obs: 21432 / % possible obs: 95.31 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.09-2.141100
2.05-2.09199.8
2.01-2.051100
1.97-2.011100
1.93-1.97199.7
1.9-1.93199.5

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Processing

Software
NameVersionClassification
MAR345data collection
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.892→22.823 Å / SU ML: 0.33 / σ(F): 1.33 / Phase error: 28.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 1918 8.95 %Random
Rwork0.2087 ---
obs0.2128 21432 95.31 %-
all-21432 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.892→22.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 0 213 2180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072029
X-RAY DIFFRACTIONf_angle_d1.0942729
X-RAY DIFFRACTIONf_dihedral_angle_d14.709762
X-RAY DIFFRACTIONf_chiral_restr0.079295
X-RAY DIFFRACTIONf_plane_restr0.004350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8919-1.93920.52221070.52211108X-RAY DIFFRACTION77
1.9392-1.99160.39081270.3441301X-RAY DIFFRACTION90
1.9916-2.05010.29671310.29211298X-RAY DIFFRACTION90
2.0501-2.11630.32611370.26441407X-RAY DIFFRACTION97
2.1163-2.19190.31181420.22721443X-RAY DIFFRACTION100
2.1919-2.27950.41691260.33531252X-RAY DIFFRACTION87
2.2795-2.38320.26871330.20341367X-RAY DIFFRACTION96
2.3832-2.50870.23771430.18071463X-RAY DIFFRACTION100
2.5087-2.66560.23721430.17441448X-RAY DIFFRACTION99
2.6656-2.87110.25221420.17991451X-RAY DIFFRACTION99
2.8711-3.15930.21341440.18531469X-RAY DIFFRACTION100
3.1593-3.61490.18871450.15981473X-RAY DIFFRACTION100
3.6149-4.54850.1941450.14431482X-RAY DIFFRACTION99
4.5485-22.82430.18451530.15731552X-RAY DIFFRACTION100

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