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- PDB-2xyh: Caspase-3:CAS60254719 -

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Basic information

Entry
Database: PDB / ID: 2xyh
TitleCaspase-3:CAS60254719
Components
  • CASPASE-3 SUBUNIT P12
  • CASPASE-3 SUBUNIT P17
KeywordsHYDROLASE / IN SILICO SCREENING / DOCKING / APOPTOSIS
Function / homology
Function and homology information


Stimulation of the cell death response by PAK-2p34 / caspase-3 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / glial cell apoptotic process / positive regulation of pyroptotic inflammatory response / NADE modulates death signalling / luteolysis ...Stimulation of the cell death response by PAK-2p34 / caspase-3 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / glial cell apoptotic process / positive regulation of pyroptotic inflammatory response / 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 / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / fibroblast apoptotic process / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / : / epithelial cell apoptotic process / negative regulation of cytokine production / platelet formation / Other interleukin signaling / execution phase of apoptosis / positive regulation of amyloid-beta formation / pyroptotic inflammatory response / negative regulation of B cell proliferation / T cell homeostasis / Apoptotic cleavage of cellular proteins / B cell homeostasis / negative regulation of activated T cell proliferation / neurotrophin TRK receptor signaling pathway / protein maturation / negative regulation of cell cycle / response to X-ray / Pyroptosis / cell fate commitment / response to amino acid / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to tumor necrosis factor / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / enzyme activator activity / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / apoptotic signaling pathway / hippocampus development / response to nicotine / sensory perception of sound / regulation of protein stability / protein catabolic process / response to hydrogen peroxide / neuron differentiation / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / DNA damage response / protein-containing complex binding / apoptotic process / 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
5-CHLORO-4-OXOPENTANOIC ACID / Caspase-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.89 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
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6923
Polymers27,5412
Non-polymers1511
Water5,350297
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)55,3846
Polymers55,0834
Non-polymers3012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area13270 Å2
ΔGint-70.9 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.531, 83.522, 95.813
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 / 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 / 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-TQ9 / 5-CHLORO-4-OXOPENTANOIC ACID


Mass: 150.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7ClO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details5-CHLORO-4-OXOPENTANOIC ACID (TQ9): THE C5 ATOM OF 4-OXOPENTANOIC ACID IS COVALENTLY BOUND TO CYS163-SG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.58 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→20 Å / Num. obs: 21385 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.05

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.89→10 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2155 820 3.7 %
Rwork0.1773 --
obs0.1773 20901 94.1 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.291 Å20 Å20 Å2
2---0.058 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.89→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1931 0 8 297 2236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004764
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_deg1.23877
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

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