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- PDB-1gfw: THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32... -

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Basic information

Entry
Database: PDB / ID: 1gfw
TitleTHE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32)IN COMPLEX WITH AN ISATIN SULFONAMIDE INHIBITOR.
Components
  • CASPASE-3 (APOPAIN, P10)
  • CASPASE-3 (APOPAIN, P20)
KeywordsHYDROLASE / CASPASE INHIBITOR / CASPASE-3 / APOPAIN / ISTIN SULFONAMIDE
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 / response to tumor necrosis factor / negative regulation of cell cycle / 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 / protein processing / regulation of protein stability / 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
Chem-MSI / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsConcha, N.O. / Janson, C.A.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Potent and selective nonpeptide inhibitors of caspases 3 and 7 inhibit apoptosis and maintain cell functionality.
Authors: Lee, D. / Long, S.A. / Adams, J.L. / Chan, G. / Vaidya, K.S. / Francis, T.A. / Kikly, K. / Winkler, J.D. / Sung, C.M. / Debouck, C. / Richardson, S. / Levy, M.A. / DeWolf Jr., W.E. / Keller, ...Authors: Lee, D. / Long, S.A. / Adams, J.L. / Chan, G. / Vaidya, K.S. / Francis, T.A. / Kikly, K. / Winkler, J.D. / Sung, C.M. / Debouck, C. / Richardson, S. / Levy, M.A. / DeWolf Jr., W.E. / Keller, P.M. / Tomaszek, T. / Head, M.S. / Ryan, M.D. / Haltiwanger, R.C. / Liang, P.H. / Janson, C.A. / McDevitt, P.J. / Johanson, K. / Concha, N.O. / Chan, W. / Abdel-Meguid, S.S. / Badger, A.M. / Lark, M.W. / Nadeau, D.P. / Suva, L.J. / Gowen, M. / Nuttall, M.E.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: CPP32, a novel human apoptotic protein with homology to Caenorhabditis elegans cell death protein ced-3 and mammalian interleukin-1-b-converting enzyme
Authors: Fernandes-Alnemri, T. / Litwack, G. / Alnemri, E.S.
History
DepositionJun 16, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionJun 23, 2000ID: 1QA8
Revision 1.0Jun 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 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 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4633
Polymers28,0632
Non-polymers4001
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-23 kcal/mol
Surface area11720 Å2
MethodPISA
2
A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules

A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules

A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules

A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,85412
Polymers112,2528
Non-polymers1,6024
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area33290 Å2
ΔGint-144 kcal/mol
Surface area33880 Å2
MethodPISA
3
A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules

A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules

A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules

A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,85412
Polymers112,2528
Non-polymers1,6024
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area32650 Å2
ΔGint-163 kcal/mol
Surface area34510 Å2
MethodPISA
4
A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules

A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9276
Polymers56,1264
Non-polymers8012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area14720 Å2
ΔGint-70 kcal/mol
Surface area18860 Å2
MethodPISA
5
A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules

A: CASPASE-3 (APOPAIN, P20)
B: CASPASE-3 (APOPAIN, P10)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9276
Polymers56,1264
Non-polymers8012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area11670 Å2
ΔGint-56 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.200, 83.300, 96.000
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 (APOPAIN, P20)


Mass: 16639.902 Da / Num. of mol.: 1
Fragment: ACTIVATED MATURE CASPASE-3 (P20) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 29-175)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HUMAN T-LYMPHOCYTE CELL LINE JURKAT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42574
#2: Protein CASPASE-3 (APOPAIN, P10)


Mass: 11423.142 Da / Num. of mol.: 1
Fragment: ACTIVATED MATURE CASPASE-3 (P10) WITHOUT PRO-DOMAIN OR LINKER (RESIDUES 181-277)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P42574
#3: Chemical ChemComp-MSI / 1-METHYL-5-(2-PHENOXYMETHYL-PYRROLIDINE-1-SULFONYL)-1H-INDOLE-2,3-DIONE


Mass: 400.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 4 ul hanging drops were prepared by mixing equal volumes of protein (10 mg/ml in 20 mM HEPES, pH 7.0) and reservoir solution. The drops equilibrated against 500 ul of 15-18% PEG6000, 0.1M ...Details: 4 ul hanging drops were prepared by mixing equal volumes of protein (10 mg/ml in 20 mM HEPES, pH 7.0) and reservoir solution. The drops equilibrated against 500 ul of 15-18% PEG6000, 0.1M sodium citrate, pH 5.9, 20 mM L-cysteine, and 5% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 7014 / Num. obs: 6775 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.174 / Net I/σ(I): 4.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.267 / Num. unique all: 692 / % possible all: 82.4
Reflection
*PLUS
Num. measured all: 113422
Reflection shell
*PLUS
% possible obs: 82.4 %

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851 & CNSrefinement
MAR345data collection
RefinementResolution: 2.8→40 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1413969.37 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: see Engh & Huber (1991) Acta Cryst A 47, 392-400.
Details: Data collection proceeded in the presence of "ice-rings"
RfactorNum. reflection% reflectionSelection details
Rfree0.285 687 10.8 %RANDOM
Rwork0.2 ---
all-7014 --
obs-6386 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 0.363132 Å2 / ksol: 33.276 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 28 45 1995
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 84 9.3 %
Rwork0.28 824 -
obs--80.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2protein_rep.param277.top
X-RAY DIFFRACTION3water_rep.paramwater.top
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.89
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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