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Yorodumi- PDB-1oex: Atomic Resolution Structure of Endothiapepsin in Complex with a H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oex | |||||||||
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Title | Atomic Resolution Structure of Endothiapepsin in Complex with a Hydroxyethylene Transition State Analogue Inhibitor H261 | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / ASPARTIC PROTEINASE MECHANISM / ATOMIC RESOLUTION / SUCCINIMIDE / ANISOTROPIC REFINEMENT / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information 4-hydroxy-3-polyprenylbenzoate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | CRYPHONECTRIA PARASITICA (chestnut blight fungus) SYNTHETIC CONSTRUCT (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.1 Å | |||||||||
Authors | Coates, L. / Erskine, P.T. / Mall, S. / Gill, R.S. / Wood, S.P. / Myles, D.A.A. / Cooper, J.B. | |||||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: Atomic Resolution Analysis of the Catalytic Site of an Aspartic Proteinase and an Unexpected Mode of Binding by Short Peptides Authors: Erskine, P.T. / Coates, L. / Mall, S. / Gill, R.S. / Wood, S.P. / Myles, D.A.A. / Cooper, J.B. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oex.cif.gz | 160 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oex.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 1oex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oex_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 1oex_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 1oex_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 1oex_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/1oex ftp://data.pdbj.org/pub/pdb/validation_reports/oe/1oex | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33795.840 Da / Num. of mol.: 1 / Fragment: RESIDUES 90-419 / Source method: isolated from a natural source Details: HYDROXYETHYLENE TRANSITION STATE ANALOGUE INHIBITOR H261 BOUND AT ACTIVE SITE Source: (natural) CRYPHONECTRIA PARASITICA (chestnut blight fungus) References: UniProt: P11838, EC: 3.4.23.22 | ||||
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#2: Protein/peptide | | ||||
#3: Chemical | ChemComp-GOL / | ||||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Sequence details | ASP A54 AND GLY A55 HAVE CYCLISED TO FORM A SUCCINIMID | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38 % |
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Crystal grow | pH: 4.6 Details: BATCH METHOD WITH ENZYME AT A CONCENTRATION OF 2 MG/ML IN 100 MM SODIUM ACETATE BUFFER AT PH 4.6 (MOEWS AND BUNN, 1970). CRYSTALS LEFT TO GROW FOLLOWING SLOW ADDITION OF AMMONIUM SULPHATE TO ...Details: BATCH METHOD WITH ENZYME AT A CONCENTRATION OF 2 MG/ML IN 100 MM SODIUM ACETATE BUFFER AT PH 4.6 (MOEWS AND BUNN, 1970). CRYSTALS LEFT TO GROW FOLLOWING SLOW ADDITION OF AMMONIUM SULPHATE TO FINAL CONCENTRATION OF 0.35 G/ML (55% SATURATION). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.834 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.834 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→15.6 Å / Num. obs: 105807 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.8 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.1→100 Å / Num. parameters: 27154 / Num. restraintsaints: 33073 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS AND KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 25 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→100 Å
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Refine LS restraints |
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