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- PDB-3kjf: Caspase 3 Bound to a covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 3kjf
TitleCaspase 3 Bound to a covalent inhibitor
Components(Caspase-3) x 2
KeywordsHYDROLASE / caspase 3 / Apoptosis / kinetics / Peptidomimetic Inhibitor / urazole / Phosphoprotein / Protease / S-nitrosylation / Thiol protease / Zymogen
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 / Activation of caspases through apoptosome-mediated cleavage / axonal fasciculation / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / : / fibroblast apoptotic process / epithelial cell apoptotic process / negative regulation of cytokine production / platelet formation / Other interleukin signaling / execution phase of apoptosis / positive regulation of amyloid-beta formation / negative regulation of B cell proliferation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of activated T cell proliferation / T cell homeostasis / B cell homeostasis / neurotrophin TRK receptor signaling pathway / negative regulation of cell cycle / protein maturation / response to X-ray / response to amino acid / cell fate commitment / Pyroptosis / 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 / protein processing / 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 / 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
Chem-B92 / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKamtekar, S. / Watt, W. / Finzel, B.C. / Harris, M.S. / Blinn, J. / Wang, Z. / Tomasselli, A.G.
CitationJournal: Biochim.Biophys.Acta / Year: 2010
Title: Kinetic and structural characterization of caspase-3 and caspase-8 inhibition by a novel class of irreversible inhibitors.
Authors: Wang, Z. / Watt, W. / Brooks, N.A. / Harris, M.S. / Urban, J. / Boatman, D. / McMillan, M. / Kahn, M. / Heinrikson, R.L. / Finzel, B.C. / Wittwer, A.J. / Blinn, J. / Kamtekar, S. / Tomasselli, A.G.
History
DepositionNov 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
B: Caspase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1013
Polymers29,5042
Non-polymers5981
Water2,738152
1
A: Caspase-3
B: Caspase-3
hetero molecules

A: Caspase-3
B: Caspase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2026
Polymers59,0074
Non-polymers1,1952
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14500 Å2
ΔGint-77 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.690, 68.160, 44.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Caspase-3 / 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.: 1
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 / 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: 12863.606 Da / Num. of mol.: 1
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: Chemical ChemComp-B92 / (3S)-3-({[(5S,10aS)-2-{(2S)-4-carboxy-2-[(phenylacetyl)amino]butyl}-1,3-dioxo-2,3,5,7,8,9,10,10a-octahydro-1H-[1,2,4]triazolo[1,2-a]cinnolin-5-yl]carbonyl}amino)-4-oxopentanoic acid


Mass: 597.616 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H35N5O9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUE AT POSITION 190 CHAIN B, IS A NATURAL VARIANT, AS LISTED IN UNP ENTRY P42574

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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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.8
Details: Inhibitor (2 microliters of a 100 mM DMSO stock) added to 100 microliters of protein (6.5 mg/mL) in 20 mM Tris, 10 mM DTT pH 8.0. Drops contained equal volumes of protein and well solution ...Details: Inhibitor (2 microliters of a 100 mM DMSO stock) added to 100 microliters of protein (6.5 mg/mL) in 20 mM Tris, 10 mM DTT pH 8.0. Drops contained equal volumes of protein and well solution (16% ethanol, 0.1 M Tris pH 7.8), VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 20643 / Num. obs: 16700 / % possible obs: 89.2 % / Biso Wilson estimate: 15.4 Å2
Reflection shellResolution: 2→2.05 Å / % possible all: 60.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→18.71 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.26 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20649 1822 9.8 %RANDOM
Rwork0.18068 ---
all0.18322 20643 --
obs0.18322 16700 89.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.373 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å20 Å20 Å2
2---0.85 Å20 Å2
3---3.6 Å2
Refinement stepCycle: LAST / Resolution: 2→18.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 43 152 2135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222035
X-RAY DIFFRACTIONr_bond_other_d0.0010.021390
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9752739
X-RAY DIFFRACTIONr_angle_other_deg0.8413.0013363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98123.50597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21615361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5731515
X-RAY DIFFRACTIONr_chiral_restr0.080.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
X-RAY DIFFRACTIONr_mcbond_it0.4261.51203
X-RAY DIFFRACTIONr_mcbond_other0.0941.5492
X-RAY DIFFRACTIONr_mcangle_it0.79921939
X-RAY DIFFRACTIONr_scbond_it1.3513832
X-RAY DIFFRACTIONr_scangle_it2.1174.5799
LS refinement shellResolution: 2→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 78 -
Rwork0.238 822 -
obs--60.24 %
Refinement TLS params.Method: refined / Origin x: 10.1825 Å / Origin y: 6.8699 Å / Origin z: 2.3314 Å
111213212223313233
T0.0229 Å2-0.0108 Å20.0043 Å2-0.0293 Å2-0.0235 Å2--0.0257 Å2
L2.573 °2-0.3809 °20.2099 °2-2.1403 °2-0.2385 °2--1.2235 °2
S-0.1033 Å °-0.1067 Å °0.1867 Å °0.105 Å °0.0891 Å °-0.0378 Å °-0.0698 Å °0.0372 Å °0.0142 Å °

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