+Open data
-Basic information
Entry | Database: PDB / ID: 2ql9 | ||||||
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Title | Crystal Structure of Caspase-7 with inhibitor AC-DQMD-CHO | ||||||
Components |
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Keywords | HYDROLASE/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 / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Agniswamy, J. / Fang, B. / Weber, I. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ql9.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ql9.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ql9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ql9_validation.pdf.gz | 501.5 KB | Display | wwPDB validaton report |
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Full document | 2ql9_full_validation.pdf.gz | 510.8 KB | Display | |
Data in XML | 2ql9_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 2ql9_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/2ql9 ftp://data.pdbj.org/pub/pdb/validation_reports/ql/2ql9 | HTTPS FTP |
-Related structure data
Related structure data | 2ql5C 2ql7C 2qlbC 2qlfC 2qljC 1f1jS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | 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 | 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 |
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-Protein/peptide , 2 types, 3 molecules EFG
#3: Protein/peptide | #4: Protein/peptide | | Mass: 527.508 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 2 types, 297 molecules
#5: Chemical | ChemComp-CIT / |
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#6: Water | ChemComp-HOH / |
-Details
Compound details | THE INHIBITOR IS COVALENTLY |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.11 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2007 |
Radiation | Monochromator: si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→50 Å / Num. obs: 41654 / % possible obs: 90.94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 24.01 |
Reflection shell | Resolution: 2.14→2.22 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.23 / Num. unique all: 3638 / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1F1J Resolution: 2.14→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.14→50 Å
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