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- PDB-2qlf: Crystal Structure of Caspase-7 with inhibitor AC-DNLD-CHO -

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Basic information

Entry
Database: PDB / ID: 2qlf
TitleCrystal Structure of Caspase-7 with inhibitor AC-DNLD-CHO
Components
  • (Caspase-7) x 2
  • Inhibitor AC-DNLD-CHO
  • Peptide QGHGE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CYSTEINE PROTEASE / APOPTOSIS / THIOL PROTEASE / ZYMOGEN / 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 / cytosol / cytoplasm
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
N-acetyl-L-alpha-aspartyl-L-asparaginyl-N-[(1R)-2-carboxy-1-formylethyl]-L-leucinamide / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAgniswamy, J. / Fang, B. / Weber, I.
CitationJournal: Febs J. / Year: 2007
Title: Plasticity of S2-S4 specificity pockets of executioner caspase-7 revealed by structural and kinetic analysis.
Authors: Agniswamy, J. / Fang, B. / Weber, I.T.
History
DepositionJul 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: 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 1.2Dec 12, 2012Group: 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-DNLD-CHO
F: Inhibitor AC-DNLD-CHO
G: Peptide QGHGE


Theoretical massNumber of molelcules
Total (without water)63,3377
Polymers63,3377
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.464, 87.464, 185.825
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


Mass: 19564.598 Da / Num. of mol.: 2 / Fragment: P20 subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Plasmid: PET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / 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


Mass: 11352.862 Da / Num. of mol.: 2 / Fragment: P10 subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Plasmid: PET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P55210, caspase-7
#3: Protein/peptide Inhibitor AC-DNLD-CHO


Type: Peptide-like / Class: Inhibitor / Mass: 487.505 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: N-acetyl-L-alpha-aspartyl-L-asparaginyl-N-[(1R)-2-carboxy-1-formylethyl]-L-leucinamide
#4: Protein/peptide Peptide QGHGE


Mass: 527.508 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.24 Å3/Da / Density % sol: 62.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 14.5% PEG 3350, 0.3M diammonium hydrogen citrate, 10mM DTT, pH 6.7, 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: 2.8→50 Å / Num. all: 18047 / Num. obs: 13827 / % possible obs: 76.62 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.55 / Num. unique all: 1776 / % possible all: 91

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Processing

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

1f1j


Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 799 -Random
Rwork0.196 ---
obs0.202 13827 76.62 %-
all-18047 --
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3828 0 0 59 3887

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