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- PDB-3pd1: Caspase-3 K242A -

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Basic information

Entry
Database: PDB / ID: 3pd1
TitleCaspase-3 K242A
Components
  • Caspase-3
  • Inhibitor Ac-DEVD-CMK
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Salt Bridge / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-3 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / 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 ...caspase-3 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / 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 / cyclin-dependent protein serine/threonine kinase inhibitor activity / death-inducing signaling complex / 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 / 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 / death receptor binding / fibroblast apoptotic process / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / response to anesthetic / execution phase of apoptosis / negative regulation of cytokine production / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / pyroptotic inflammatory response / neurotrophin TRK receptor signaling pathway / negative regulation of activated T cell proliferation / response to tumor necrosis factor / negative regulation of cell cycle / T cell homeostasis / B cell homeostasis / Pyroptosis / cell fate commitment / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to X-ray / response to amino acid / response to glucose / response to UV / keratinocyte differentiation / Degradation of the extracellular matrix / striated muscle cell differentiation / intrinsic apoptotic signaling pathway / response to glucocorticoid / protein maturation / erythrocyte differentiation / response to nicotine / hippocampus development / apoptotic signaling pathway / enzyme activator activity / response to hydrogen peroxide / protein catabolic process / sensory perception of sound / regulation of protein stability / protein processing / response to wounding / neuron differentiation / response to estradiol / peptidase activity / positive regulation of neuron apoptotic process / 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 / apoptotic process / DNA damage response / protein-containing complex binding / glutamatergic synapse / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Rossmann fold - #1460 / Peptidase C14 family / 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 ...Rossmann fold - #1460 / Peptidase C14 family / 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: 1.62 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 1.3Feb 27, 2013Group: Other
Revision 1.4Nov 20, 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
B: Inhibitor Ac-DEVD-CMK


Theoretical massNumber of molelcules
Total (without water)29,1482
Polymers29,1482
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-9 kcal/mol
Surface area11690 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)116,5908
Polymers116,5908
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 area16710 Å2
ΔGint-97 kcal/mol
Surface area35220 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)116,5908
Polymers116,5908
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 area16570 Å2
ΔGint-94 kcal/mol
Surface area35360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.670, 84.530, 96.170
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-377-

HOH

21A-501-

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: 28612.570 Da / Num. of mol.: 1 / Fragment: UNP residues 29-277 / Mutation: 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) LysS / 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


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 291 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 (pH 8.5), 10 mM DTT, 3 mM NaN3., VAPOR DIFFUSION, ...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 (pH 8.5), 10 mM DTT, 3 mM NaN3., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Feb 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. all: 34489 / Num. obs: 34489 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.62→1.68 Å / % possible all: 99

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 1.62→33.71 Å / Occupancy max: 1 / Occupancy min: 0.05 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2258 3071 6.8 %
Rwork0.2077 27785 -
obs-30856 68.4 %
Solvent computationBsol: 23.8611 Å2
Displacement parametersBiso max: 54.86 Å2 / Biso mean: 18.6835 Å2 / Biso min: 7.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.203 Å20 Å20 Å2
2---1.852 Å20 Å2
3---2.054 Å2
Refinement stepCycle: LAST / Resolution: 1.62→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 0 268 2223
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d1.506
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_mcangle_it1.6882
X-RAY DIFFRACTIONc_scangle_it2.8092.5

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