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- PDB-2h5i: Crystal structure of caspase-3 with inhibitor Ac-DEVD-Cho -

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Basic information

Entry
Database: PDB / ID: 2h5i
TitleCrystal structure of caspase-3 with inhibitor Ac-DEVD-Cho
Components
  • Ac-DEV(ASJ)
  • caspase-3, p12 subunit
  • caspase-3, p17 subunit
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ENZYME CATALYSIS / CYSTEINE PROTEASE / APOPTOSIS / INDUCED FIT / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


caspase-3 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / 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 / phospholipase A2 activator activity / Stimulation of the cell death response by PAK-2p34 / 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 / cyclin-dependent protein serine/threonine kinase inhibitor activity / death-inducing signaling complex / 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 / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / axonal fasciculation / regulation of synaptic vesicle cycle / death receptor binding / fibroblast apoptotic process / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / response to anesthetic / execution phase of apoptosis / negative regulation of cytokine production / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / pyroptotic inflammatory response / neurotrophin TRK receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of cell cycle / response to tumor necrosis factor / T cell homeostasis / B cell homeostasis / Pyroptosis / cell fate commitment / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to X-ray / response to amino acid / response to glucose / response to UV / keratinocyte differentiation / Degradation of the extracellular matrix / striated muscle cell differentiation / intrinsic apoptotic signaling pathway / response to glucocorticoid / protein maturation / erythrocyte differentiation / response to nicotine / hippocampus development / apoptotic signaling pathway / enzyme activator activity / protein catabolic process / response to hydrogen peroxide / sensory perception of sound / regulation of protein stability / protein processing / response to wounding / neuron differentiation / response to estradiol / peptidase activity / positive regulation of neuron apoptotic process / 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 / cytoplasm / cytosol
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
Ac-Asp-Glu-Val-Asp-Aldehyde / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsFang, B. / Boross, P.I. / Tozser, J. / Weber, I.T.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural and kinetic analysis of caspase-3 reveals role for s5 binding site in substrate recognition
Authors: Fang, B. / Boross, P.I. / Tozser, J. / Weber, I.T.
History
DepositionMay 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: caspase-3, p17 subunit
B: caspase-3, p12 subunit
C: Ac-DEV(ASJ)


Theoretical massNumber of molelcules
Total (without water)28,2713
Polymers28,2713
Non-polymers00
Water4,035224
1
A: caspase-3, p17 subunit
B: caspase-3, p12 subunit
C: Ac-DEV(ASJ)

A: caspase-3, p17 subunit
B: caspase-3, p12 subunit
C: Ac-DEV(ASJ)


Theoretical massNumber of molelcules
Total (without water)56,5436
Polymers56,5436
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Unit cell
Length a, b, c (Å)69.920, 86.050, 97.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

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Components

#1: Protein caspase-3, p17 subunit / E.C.3.4.22.- / CASP-3 / Apopain / Cysteine protease CPP32 / Yama protein / CPP-32 / 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) / Gene: CASP3, CPP32 / Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P42574, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein caspase-3, p12 subunit / E.C.3.4.22.-


Mass: 11257.953 Da / Num. of mol.: 1 / Fragment: residues 184-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P42574, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Protein/peptide Ac-DEV(ASJ)


Type: Peptide-like / Class: Inhibitor / Mass: 488.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: Ac-Asp-Glu-Val-Asp-Aldehyde
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE INHIBITOR IS COVALENTLY CONNECTED TO CYS OF THE ENZYME TO FORM A HEMITHIOKETAL

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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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium citrate, 5% glycerol, 10 mM dithiothreitol and 14-18% PEG 6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2004
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. all: 32669 / Num. obs: 32669 / % possible obs: 99.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 14
Reflection shellResolution: 1.69→1.74 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 4 / % possible all: 95.6

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Processing

Software
NameClassification
MADCCDdata collection
HKL-2000data reduction
AMoREphasing
SHELXL-97refinement
MADCCDdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NME

1nme


Resolution: 1.69→10 Å / Num. parameters: 8881 / Num. restraintsaints: 8132 / Isotropic thermal model: Isotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1651 5.1 %RANDOM
Rwork0.1842 ---
all0.1865 32669 --
obs0.1786 30041 99.9 %-
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2197.5
Refinement stepCycle: LAST / Resolution: 1.69→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 0 224 2198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0261
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.051
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.047
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.69→1.77 Å /
RfactorNum. reflection
Rwork0.234 -
Rfree-177
obs-3528

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