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- PDB-4fea: Crystal structure of CASPASE-7 in Complex with allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 4fea
TitleCrystal structure of CASPASE-7 in Complex with allosteric inhibitor
ComponentsCaspase-7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cysteine protease / apoptosis / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / cysteine-type endopeptidase activity involved in apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / cysteine-type peptidase activity / striated muscle cell differentiation / protein catabolic process / protein processing / positive regulation of neuron apoptotic process / peptidase activity / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / RNA binding / extracellular space / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0TE / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.79 Å
AuthorsKabaleeswaran, V.
CitationJournal: Mol.Cell / Year: 2012
Title: A class of allosteric caspase inhibitors identified by high-throughput screening.
Authors: Feldman, T. / Kabaleeswaran, V. / Jang, S.B. / Antczak, C. / Djaballah, H. / Wu, H. / Jiang, X.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Sep 13, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-7
B: Caspase-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9474
Polymers56,1742
Non-polymers7732
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-15 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.720, 88.720, 185.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Caspase-7 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 28086.920 Da / Num. of mol.: 2 / Fragment: P20/P10 catalytic domain (UNP residues 57-303)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#2: Chemical ChemComp-0TE / chloro{methyl hydrogenato(3-)-kappa~2~N,S [pyridin-2-yl(pyridin-2(1H)-ylidene-kappaN)methyl]carbonodithiohydrazonate}copper


Mass: 386.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11ClCuN4S2

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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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate, pH 5.0-5.7, 1.9 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.378 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.378 Å / Relative weight: 1
ReflectionResolution: 3.785→76.834 Å / Num. all: 8266 / Num. obs: 8266 / % possible obs: 94.1 % / Redundancy: 5.1 % / Rsym value: 0.108 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.785-3.885.10.71.131486190.796
3.88-3.995.10.5121.530485950.51295.6
3.99-4.150.3642.129045770.36495.3
4.1-4.235.10.3122.429015680.31295.6
4.23-4.375.10.2433.126905300.24395.2
4.37-4.525.20.1824.126985230.18294.4
4.52-4.695.20.1495.125945030.14994.4
4.69-4.885.10.124624684830.12493.8
4.88-5.15.10.1385.523884670.13894.5
5.1-5.355.10.1315.822844510.13194.3
5.35-5.645.10.1266.121764250.12693.7
5.64-5.985.20.1246.120674010.12493.4
5.98-6.45.20.108719763830.10893.5
6.4-6.915.10.0828.818143570.08293.4
6.91-7.5750.07110.316263230.07192.4
7.57-8.4650.0511314652910.05191.4
8.46-9.7750.0461413212640.04691.6
9.77-11.9750.03717.411082210.03790.8
11.97-16.924.80.03818.28451770.03889.9
16.92-76.8344.10.04113.24391080.04188.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IBF

3ibf


Resolution: 3.79→76.83 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.23 / σ(F): 0 / Phase error: 27.05
RfactorNum. reflection% reflection
Rfree0.286 383 4.64 %
Rwork0.236 7874 -
obs0.242 8257 92.5 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 111.54 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 200.62 Å2 / Biso mean: 120.6361 Å2 / Biso min: 69.73 Å2
Baniso -1Baniso -2Baniso -3
1-15.889 Å2-0 Å2-0 Å2
2--15.889 Å2-0 Å2
3----31.7779 Å2
Refinement stepCycle: LAST / Resolution: 3.79→76.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 42 0 2795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012842
X-RAY DIFFRACTIONf_angle_d1.3523839
X-RAY DIFFRACTIONf_chiral_restr0.054449
X-RAY DIFFRACTIONf_plane_restr0.003485
X-RAY DIFFRACTIONf_dihedral_angle_d14.33991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.79-4.33290.2841220.2382629275194
4.3329-5.45870.29161400.21312588272893
5.4587-76.84960.27411210.25382657277890

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