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Yorodumi- PDB-1epr: ENDOTHIA ASPARTIC PROTEINASE (ENDOTHIAPEPSIN) COMPLEXED WITH PD-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1epr | ||||||
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Title | ENDOTHIA ASPARTIC PROTEINASE (ENDOTHIAPEPSIN) COMPLEXED WITH PD-135,040 | ||||||
Components | ENDOTHIAPEPSIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / ACID PROTEINASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Badasso, M. / Crawford, M. / Cooper, J.B. / Blundell, T.L. | ||||||
Citation | Journal: Protein Sci. / Year: 1994 Title: A structural comparison of 21 inhibitor complexes of the aspartic proteinase from Endothia parasitica. Authors: Bailey, D. / Cooper, J.B. #1: Journal: J.Mol.Biol. / Year: 1990 Title: The 3D Structure at 2 Angstroms Resolution of Endothiapepsin Authors: Blundell, T.L. / Jenkins, J. / Sewell, B.T. / Pearl, L.H. / Cooper, J.B. / Tickle, I.J. / Veerapandian, B. / Wood, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1epr.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1epr.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 1epr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1epr_validation.pdf.gz | 479.1 KB | Display | wwPDB validaton report |
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Full document | 1epr_full_validation.pdf.gz | 494.8 KB | Display | |
Data in XML | 1epr_validation.xml.gz | 11 KB | Display | |
Data in CIF | 1epr_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/1epr ftp://data.pdbj.org/pub/pdb/validation_reports/ep/1epr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: THR E 22 - PRO E 23 OMEGA = 293.30 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: SER E 132 - PRO E 133 OMEGA = 30.48 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: GLN E 134A - GLN E 135 OMEGA = 80.17 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 33813.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, endothiapepsin |
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#2: Chemical | ChemComp-0QS / |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUES 63A, 80A, 134A, 184A, 203A, 204A, 238A, 282A, 282B, AND 319A IN CHAIN E ARE INSERTIONS ...RESIDUES 63A, 80A, 134A, 184A, 203A, 204A, 238A, 282A, 282B, AND 319A IN CHAIN E ARE INSERTIONS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.3 % |
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Crystal grow | *PLUS Method: unknown |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.3 Å |
-Processing
Software | Name: RESTRAIN / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.3→12 Å / σ(F): 3 Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE ...Details: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE FOLLOWING RELATION: B = 8 * (PI)**2 * U**2. THERE ARE ARE LARGE NUMBER OF CLOSE ATOMIC INTERACTIONS, SOME AMONG ATOMS WITHIN THE ENTRY AND OTHERS BETWEEN ATOMS WITHIN THE ENTRY AND SYMMETRY-RELATED ENTRIES.
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Refinement step | Cycle: LAST / Resolution: 2.3→12 Å
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Refine LS restraints |
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Software | *PLUS Name: RESTRAIN / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor obs: 0.181 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |