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- PDB-1rhk: Crystal structure of the complex of caspase-3 with a phenyl-propy... -

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Basic information

Entry
Database: PDB / ID: 1rhk
TitleCrystal structure of the complex of caspase-3 with a phenyl-propyl-ketone inhibitor
Components
  • (Caspase-3) x 2
  • acetyl-asp-glu-val-fpr
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CYSTEINE PROTEASE / CASPASE-3 / APOPAIN / CPP32 / YAMA / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / 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 / platelet formation / negative regulation of cytokine production / Other interleukin signaling / 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 / response to X-ray / cell fate commitment / response to amino acid / Pyroptosis / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / protein maturation / response to glucose / response to glucocorticoid / response to UV / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / enzyme activator activity / intrinsic apoptotic signaling pathway / 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 / 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 / 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
N-acetyl-L-alpha-aspartyl-L-alpha-glutamyl-N-[(1S)-1-(carboxymethyl)-2-oxo-5-phenylpentyl]-L-valinamide / 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 14, 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: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.7Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.8Nov 20, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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
C: acetyl-asp-glu-val-fpr


Theoretical massNumber of molelcules
Total (without water)29,1553
Polymers29,1553
Non-polymers00
Water25214
1
A: Caspase-3
B: Caspase-3
C: acetyl-asp-glu-val-fpr

A: Caspase-3
B: Caspase-3
C: acetyl-asp-glu-val-fpr


Theoretical massNumber of molelcules
Total (without water)58,3106
Polymers58,3106
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
MethodPQS
2
A: Caspase-3
B: Caspase-3

A: Caspase-3
B: Caspase-3


Theoretical massNumber of molelcules
Total (without water)57,1014
Polymers57,1014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area12600 Å2
ΔGint-78 kcal/mol
Surface area18000 Å2
MethodPISA
3
A: Caspase-3
B: Caspase-3
C: acetyl-asp-glu-val-fpr

A: Caspase-3
B: Caspase-3
C: acetyl-asp-glu-val-fpr


Theoretical massNumber of molelcules
Total (without water)58,3106
Polymers58,3106
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area4770 Å2
ΔGint-13 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.940, 84.660, 96.820
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 assembly is 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 / Apopain / CASP-3 / SREBP cleavage activity 1 / SCA-1


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 / Apopain / CASP-3 / SREBP cleavage activity 1 / SCA-1


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: Protein/peptide acetyl-asp-glu-val-fpr


Type: Peptide-like / Class: Inhibitor / Mass: 604.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The inhibitor is chemically synthesized.
References: N-acetyl-L-alpha-aspartyl-L-alpha-glutamyl-N-[(1S)-1-(carboxymethyl)-2-oxo-5-phenylpentyl]-L-valinamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 12% PEG-5000, 100 mM Citrate, 10 mM DTT, 3 mM 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
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 29, 1996
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 10263 / Num. obs: 8371 / % possible obs: 81.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.93
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 1.38 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.3 / Num. unique all: 333 / % possible all: 33.3

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Processing

Software
NameVersionClassification
CNX2002refinement
X-GENdata reduction
SAINTV. 4.050data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Protein part of 1pau.pdb

1pau


Resolution: 2.5→19.98 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 26033.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.241 845 10.6 %RANDOM
Rwork0.19 ---
all-10270 --
obs-7965 77.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.987 Å2 / ksol: 0.299302 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å20 Å2
2--2.33 Å20 Å2
3----5.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 14 1928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 76 11.2 %
Rwork0.28 601 -
obs-889 40.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PARAM.ICETOP.ICE

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