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- PDB-2xyg: Caspase-3:CAS329306 -

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Basic information

Entry
Database: PDB / ID: 2xyg
TitleCaspase-3:CAS329306
Components
  • CASPASE-3 SUBUNIT P12Caspase 3
  • CASPASE-3 SUBUNIT P17Caspase 3
KeywordsHYDROLASE / IN SILICO SCREENING / DOCKING / APOPTOSIS
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 / luteolysis ...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 / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / Apoptotic cleavage of cell adhesion proteins / death receptor binding / SMAC, XIAP-regulated apoptotic response / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / 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 / pyroptotic inflammatory response / 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 / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / 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 / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / 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
Caspase-like / 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 ...Caspase-like / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TQ8 / Caspase-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.54 Å
AuthorsGanesan, R. / Jelakovic, S. / Grutter, M.G. / Mittl, P.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: In Silico Identification and Crystal Structure Validation of Caspase-3 Inhibitors without a P1 Aspartic Acid Moiety.
Authors: Ganesan, R. / Jelakovic, S. / Mittl, P.R. / Caflisch, A. / Grutter, M.G.
History
DepositionNov 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CASPASE-3 SUBUNIT P17
B: CASPASE-3 SUBUNIT P12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8933
Polymers27,5412
Non-polymers3521
Water7,674426
1
A: CASPASE-3 SUBUNIT P17
B: CASPASE-3 SUBUNIT P12
hetero molecules

A: CASPASE-3 SUBUNIT P17
B: CASPASE-3 SUBUNIT P12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7876
Polymers55,0834
Non-polymers7042
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area13030 Å2
ΔGint-73.7 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.799, 83.538, 96.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CASPASE-3 SUBUNIT P17 / Caspase 3 / CASPASE-3 / CASP-3 / APOPAIN / CYSTEINE PROTEASE CPP32 / CPP-32 / PROTEIN YAMA / SREBP CLEAVAGE ...CASPASE-3 / CASP-3 / APOPAIN / CYSTEINE PROTEASE CPP32 / CPP-32 / PROTEIN YAMA / SREBP CLEAVAGE ACTIVITY 1 / SCA-1


Mass: 16524.814 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P42574, caspase-3
#2: Protein CASPASE-3 SUBUNIT P12 / Caspase 3 / CASPASE-3 / CASP-3 / APOPAIN / CYSTEINE PROTEASE CPP32 / CPP-32 / PROTEIN YAMA / SREBP CLEAVAGE ...CASPASE-3 / CASP-3 / APOPAIN / CYSTEINE PROTEASE CPP32 / CPP-32 / PROTEIN YAMA / SREBP CLEAVAGE ACTIVITY 1 / SCA-1


Mass: 11016.662 Da / Num. of mol.: 1 / Fragment: RESIDUES 185-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P42574, caspase-3
#3: Chemical ChemComp-TQ8 / N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide / CAS329306 / Tosyl phenylalanyl chloromethyl ketone


Mass: 351.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18ClNO3S / Comment: protease inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCAS329306 (TQ8): THE CL ATOM OF CAS329306 IS REPLACED BY THE SG OF ACTIVE SITE CYSTEINE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.96 % / Description: NONE
Crystal growDetails: 15% PEG6000, 0.1M SODIUM CITRATE, PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→20 Å / Num. obs: 37129 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.1

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.54→10 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
Details: COVALENT BOND BETWEEN SG CYS A163 AND C22 TQ8 A1176
RfactorNum. reflection% reflection
Rfree0.1972 1491 3.6 %
Rwork0.1794 --
obs0.1794 37129 90.3 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.717 Å20 Å20 Å2
2--0.554 Å20 Å2
3---1.163 Å2
Refinement stepCycle: LAST / Resolution: 1.54→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 22 426 2377
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00498
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2873
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1AA
X-RAY DIFFRACTION2AA
X-RAY DIFFRACTION3AA
X-RAY DIFFRACTION4AA
X-RAY DIFFRACTION5INH.PARINH.TOP

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