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- PDB-1re1: CRYSTAL STRUCTURE OF CASPASE-3 WITH A NICOTINIC ACID ALDEHYDE INH... -

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Basic information

Entry
Database: PDB / ID: 1re1
TitleCRYSTAL STRUCTURE OF CASPASE-3 WITH A NICOTINIC ACID ALDEHYDE INHIBITOR
Components(Caspase-3) x 2
KeywordsHYDROLASE / CYSTEINE PROTEASE / CASPASE-3 / APOPAIN / CPP32 / YAMA / COMPLEX (PROTEASE-INHIBITOR)
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 / cellular response to staurosporine / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to anesthetic / 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 / death receptor binding / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / axonal fasciculation / regulation of synaptic vesicle cycle / fibroblast apoptotic process / epithelial cell apoptotic process / Other interleukin signaling / platelet formation / negative regulation of cytokine production / positive regulation of amyloid-beta formation / execution phase of apoptosis / negative regulation of B cell proliferation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of activated T cell proliferation / T cell homeostasis / neurotrophin TRK receptor signaling pathway / B cell homeostasis / negative regulation of cell cycle / response to tumor necrosis factor / cell fate commitment / response to amino acid / response to X-ray / Pyroptosis / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to glucose / response to glucocorticoid / response to UV / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / protein maturation / enzyme activator activity / erythrocyte differentiation / hippocampus development / response to nicotine / apoptotic signaling pathway / sensory perception of sound / protein catabolic process / regulation of protein stability / protein processing / response to hydrogen peroxide / response to wounding / neuron differentiation / 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 / 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 / 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
Chem-NA3 / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBecker, J.W. / Rotonda, J. / Soisson, S.M.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Reducing the Peptidyl Features of Caspase-3 Inhibitors: A Structural Analysis
Authors: Becker, J.W. / Rotonda, J. / Soisson, S.M. / Aspiotis, R. / Bayly, C. / Francoeur, S. / Gallant, M. / Garcia-Calvo, M. / Giroux, A. / Grimm, E. / Han, Y. / Mckay, D. / Nicholson, D.W. / ...Authors: Becker, J.W. / Rotonda, J. / Soisson, S.M. / Aspiotis, R. / Bayly, C. / Francoeur, S. / Gallant, M. / Garcia-Calvo, M. / Giroux, A. / Grimm, E. / Han, Y. / Mckay, D. / Nicholson, D.W. / Peterson, E. / Renaud, J. / Roy, S. / Thornberry, N. / Zamboni, R.
History
DepositionNov 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)28,8523
Polymers28,5512
Non-polymers3011
Water46826
1
A: Caspase-3
B: Caspase-3
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)57,7036
Polymers57,1014
Non-polymers6022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area13840 Å2
ΔGint-63 kcal/mol
Surface area17270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.780, 83.760, 95.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe second part of the biological assemblyis generated by the two-fold axis: 1-x, y, -z

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Components

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


Mass: 16639.902 Da / Num. of mol.: 1 / Fragment: P17 subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P42574, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Caspase-3 / Cysteine protease CPP32 / Yama protein / CPP-32 / CASP-3 / SREBP cleavage activity 1 / SCA-1 / Apopain


Mass: 11910.604 Da / Num. of mol.: 1 / Fragment: P12 subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P42574, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Chemical ChemComp-NA3 / (3S)-3-{[(5-BROMOPYRIDIN-3-YL)CARBONYL]AMINO}-4-OXOBUTANOIC ACID


Mass: 301.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9BrN2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 12% PEG 5000, 100mM Citrate, 10mM DTT, 3mM NaN(3), pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 14, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 10056 / Num. obs: 9319 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.91 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 4.16
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.65 / % possible all: 48.2

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Processing

Software
NameVersionClassification
CNX2002refinement
SAINTV. 4.050data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PAU

1pau


Resolution: 2.5→19.89 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 43559.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USEDATOM 1 CB
RfactorNum. reflection% reflectionSelection details
Rfree0.261 896 10.5 %RANDOM
Rwork0.194 ---
obs-8560 85.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.86 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--3.07 Å20 Å2
3----3.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 17 26 1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 101 10.8 %
Rwork0.268 832 -
obs--57.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM.ICETOP_NA3.ICE

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