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- PDB-3edr: The crystal structure of caspase-7 in complex with Acetyl-LDESD-CHO -

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Basic information

Entry
Database: PDB / ID: 3edr
TitleThe crystal structure of caspase-7 in complex with Acetyl-LDESD-CHO
Components
  • (Caspase-7) x 2
  • Inhibitor Ac-ldesd-cho peptide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CASPASE / PEPTIDE INHIBITOR / APOPTOSIS / THIOL PROTEASE / 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 / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / fibroblast apoptotic process / execution phase of apoptosis ...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 / 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 / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / striated muscle cell differentiation / cysteine-type peptidase activity / protein maturation / protein catabolic process / protein processing / fibrillar center / peptidase activity / positive regulation of neuron apoptotic process / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Inclusion body clearance protein Iml2/Tetratricopeptide repeat protein 39 / Iml2/Tetratricopeptide repeat protein 39 / 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. ...Inclusion body clearance protein Iml2/Tetratricopeptide repeat protein 39 / Iml2/Tetratricopeptide repeat protein 39 / 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 / Tetratricopeptide-like helical domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-L-leucyl-L-alpha-aspartyl-L-alpha-glutamyl-L-seryl-L-aspartic aldehyde / IML2-like protein YKR018C / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsAgniswamy, J.
CitationJournal: Apoptosis / Year: 2008
Title: Structural basis for executioner caspase recognition of P5 position in substrates.
Authors: Fu, G. / Chumanevich, A.A. / Agniswamy, J. / Fang, B. / Harrison, R.W. / Weber, I.T.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Aug 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
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
Revision 1.4Nov 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

Downloads & links

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Assembly

Deposited unit
A: Caspase-7
B: Caspase-7
C: Caspase-7
D: Caspase-7
E: Inhibitor Ac-ldesd-cho peptide
F: Inhibitor Ac-ldesd-cho peptide


Theoretical massNumber of molelcules
Total (without water)63,0146
Polymers63,0146
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16850 Å2
ΔGint-78 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.637, 88.637, 187.708
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 / ICE-like apoptotic protease 3 / ICE-LAP3 / Apoptotic protease Mch-3 / CMH-1 / Caspase-7 ...CASP-7 / ICE-like apoptotic protease 3 / ICE-LAP3 / Apoptotic protease Mch-3 / CMH-1 / Caspase-7 subunit p20 / Caspase-7 subunit p11


Mass: 19564.598 Da / Num. of mol.: 2 / Fragment: P20 subunit (UNP residues 24 to 196)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Plasmid: PET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P55210, caspase-7
#2: Protein Caspase-7 / CASP-7 / ICE-like apoptotic protease 3 / ICE-LAP3 / Apoptotic protease Mch-3 / CMH-1 / Caspase-7 ...CASP-7 / ICE-like apoptotic protease 3 / ICE-LAP3 / Apoptotic protease Mch-3 / CMH-1 / Caspase-7 subunit p20 / Caspase-7 subunit p11


Mass: 11352.862 Da / Num. of mol.: 2 / Fragment: P10 subunit (UNP residues 207 to 303)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Plasmid: PET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P55210, caspase-7
#3: Protein/peptide Inhibitor Ac-ldesd-cho peptide


Type: Peptide-like / Class: Inhibitor / Mass: 589.594 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was obtained from EMD chemicals, Inc., NJ.
Source: (synth.) Saccharomyces cerevisiae (Baker's yeast) (yeast)
References: N-acetyl-L-leucyl-L-alpha-aspartyl-L-alpha-glutamyl-L-seryl-L-aspartic aldehyde, UniProt: P36114*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.1M Sodium Formate,0.1M Sodium Citrate, pH 5.5, 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 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2006
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 31796 / Num. obs: 28712 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.52
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.89 / Num. unique all: 1761 / % possible all: 57.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F1J

1f1j


Resolution: 2.45→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1273 -Random
Rwork0.201 ---
all0.232 28712 --
obs0.231 25635 89.3 %-
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 0 82 3943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4

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