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- PDB-3gjs: Caspase-3 Binds Diverse P4 Residues in Peptides -

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Basic information

Entry
Database: PDB / ID: 3gjs
TitleCaspase-3 Binds Diverse P4 Residues in Peptides
Components
  • Ac-YVAD-Cho inhibitor
  • Caspase-3 subunit p12
  • Caspase-3 subunit p17
KeywordsAPOPTOSIS / Enzyme catalysis / Cysteine protease / Protein recognition / Hydrolase / Phosphoprotein / Protease / S-nitrosylation / Thiol protease / Zymogen
Function / homology
Function and homology information


caspase-3 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / glial cell apoptotic process / NADE modulates death signalling / positive regulation of pyroptotic inflammatory response / luteolysis / synapse pruning ...caspase-3 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / glial cell apoptotic process / NADE modulates death signalling / positive regulation of pyroptotic inflammatory response / luteolysis / synapse pruning / response to cobalt ion / platelet formation / cellular response to staurosporine / CASP5-mediated substrate cleavage / axonal fasciculation / cyclin-dependent protein serine/threonine kinase inhibitor activity / CASP4-mediated substrate cleavage / response to anesthetic / death-inducing signaling complex / Apoptotic cleavage of cell adhesion proteins / Apoptosis induced DNA fragmentation / 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 / death receptor binding / striated muscle cell differentiation / neurotrophin TRK receptor signaling pathway / regulation of synaptic vesicle cycle / negative regulation of cytokine production / execution phase of apoptosis / Other interleukin signaling / positive regulation of amyloid-beta formation / response to X-ray / Apoptotic cleavage of cellular proteins / keratinocyte differentiation / response to amino acid / response to glucose / response to tumor necrosis factor / Pyroptosis / pyroptotic inflammatory response / Caspase-mediated cleavage of cytoskeletal proteins / response to insulin-like growth factor stimulus / swimming behavior / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / regulation of macroautophagy / protein catabolic process / response to glucocorticoid / apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / response to hydrogen peroxide / protein processing / response to nicotine / protein maturation / regulation of protein stability / enzyme activator activity / positive regulation of neuron apoptotic process / response to estradiol / neuron differentiation / peptidase activity / response to lipopolysaccharide / protease binding / aspartic-type endopeptidase activity / response to hypoxia / response to ethanol / learning or memory / postsynaptic density / response to xenobiotic stimulus / cysteine-type endopeptidase activity / apoptotic process / neuronal cell body / protein-containing complex binding / glutamatergic synapse / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-like / 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-like / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFang, B. / Fu, G. / Agniswamy, J. / Harrison, R.W. / Weber, I.T.
CitationJournal: Apoptosis / Year: 2009
Title: Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling.
Authors: Fang, B. / Fu, G. / Agniswamy, J. / Harrison, R.W. / Weber, I.T.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 17, 2011Group: Structure summary
Revision 1.3Mar 26, 2025Group: 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 subunit p17
B: Caspase-3 subunit p12
C: Caspase-3 subunit p17
D: Caspase-3 subunit p12
E: Ac-YVAD-Cho inhibitor
F: Ac-YVAD-Cho inhibitor


Theoretical massNumber of molelcules
Total (without water)59,7166
Polymers59,7166
Non-polymers00
Water4,864270
1
A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
E: Ac-YVAD-Cho inhibitor


Theoretical massNumber of molelcules
Total (without water)29,8583
Polymers29,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-33 kcal/mol
Surface area11430 Å2
MethodPISA
2
C: Caspase-3 subunit p17
D: Caspase-3 subunit p12
F: Ac-YVAD-Cho inhibitor


Theoretical massNumber of molelcules
Total (without water)29,8583
Polymers29,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-32 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.4, 70.3, 93.4
Angle α, β, γ (deg.)90, 102.4, 90
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16639.902 Da / Num. of mol.: 2
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 Caspase-3 subunit p12 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Yama protein / SREBP cleavage activity 1 / ...CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Yama protein / SREBP cleavage activity 1 / SCA-1 / Caspase-3 subunit p17 / Caspase-3 subunit p12


Mass: 12739.485 Da / Num. of mol.: 2
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
#3: Protein/peptide Ac-YVAD-Cho inhibitor


Mass: 478.539 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol, 14-18% PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 42106

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 -random
Rwork0.216 --
obs-42106 -
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 0 270 4132

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