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- PDB-5v6u: Crystal structure of human caspase-7 soaked with allosteric inhib... -

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Basic information

Entry
Database: PDB / ID: 5v6u
TitleCrystal structure of human caspase-7 soaked with allosteric inhibitor 2-[(2-acetylphenyl)sulfanyl]benzoic acid
ComponentsCaspase-7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase / protease / inhibitor / allosteric / 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 / : / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / fibroblast 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 / : / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / fibroblast apoptotic process / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / : / 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 / heart development / peptidase activity / 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 / cytosol / cytoplasm
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
2-[(2-acetylphenyl)sulfanyl]benzoic acid / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVance, N.R. / Gakhar, L. / Spies, M.A.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Allosteric Tuning of Caspase-7: A Fragment-Based Drug Discovery Approach.
Authors: Vance, N.R. / Gakhar, L. / Spies, M.A.
History
DepositionMar 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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-7
B: Caspase-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9203
Polymers68,6482
Non-polymers2721
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, protein elutes as expected as a dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-11 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.393, 88.393, 185.358
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 34323.828 Da / Num. of mol.: 2 / Fragment: UNP residues 34-336
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-8YM / 2-[(2-acetylphenyl)sulfanyl]benzoic acid


Mass: 272.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 1.9 M sodium formate, 0.1 M sodium citrate, pH 5.7 / PH range: 5.0-5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.001374 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 15, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001374 Å / Relative weight: 1
ReflectionResolution: 2.8→48.08 Å / Num. obs: 21407 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.049 / Net I/av σ(I): 19.3 / Net I/σ(I): 19.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.024 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3099 / CC1/2: 0.846 / Rpim(I) all: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDS2016-01-11data reduction
SCALA3.3.22data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F1J

1f1j


Resolution: 2.8→48.079 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 1022 4.79 %
Rwork0.1911 --
obs0.1936 21338 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→48.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 19 76 3308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143300
X-RAY DIFFRACTIONf_angle_d1.4984449
X-RAY DIFFRACTIONf_dihedral_angle_d6.3052343
X-RAY DIFFRACTIONf_chiral_restr0.077498
X-RAY DIFFRACTIONf_plane_restr0.009572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94760.31721120.27682917X-RAY DIFFRACTION100
2.9476-3.13230.30721390.23392825X-RAY DIFFRACTION100
3.1323-3.3740.30591470.21242855X-RAY DIFFRACTION100
3.374-3.71350.23761370.18442887X-RAY DIFFRACTION100
3.7135-4.25050.24111750.16952863X-RAY DIFFRACTION100
4.2505-5.35410.2051500.16222906X-RAY DIFFRACTION100
5.3541-48.08620.24231620.19863063X-RAY DIFFRACTION100

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