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Yorodumi- PDB-1epq: ENDOTHIA ASPARTIC PROTEINASE (ENDOTHIAPEPSIN) COMPLEXED WITH PD-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1epq | ||||||
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Title | ENDOTHIA ASPARTIC PROTEINASE (ENDOTHIAPEPSIN) COMPLEXED WITH PD-133,450 (SOT PHE GLY+SCC GCL) | ||||||
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: 1.9 Å | ||||||
Authors | Dealwis, C. / Cooper, J.B. / Blundell, T.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1993 Title: Analyses of ligand binding in five endothiapepsin crystal complexes and their use in the design and evaluation of novel renin inhibitors. Authors: Lunney, E.A. / Hamilton, H.W. / Hodges, J.C. / Kaltenbronn, J.S. / Repine, J.T. / Badasso, M. / Cooper, J.B. / Dealwis, C. / Wallace, B.A. / Lowther, W.T. #1: Journal: To be Published Title: A Structural Comparison of 21 Inhibitor Complexes of the Aspartic Proteinase from Endothia Parasitica Authors: Bailey, D. / Cooper, J.B. #2: 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 | 1epq.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1epq.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 1epq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/1epq ftp://data.pdbj.org/pub/pdb/validation_reports/ep/1epq | HTTPS FTP |
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-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: CIS PROLINE - PRO E 23 / 2: CIS PROLINE - PRO E 133 |
-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-0QF / Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 656.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H52N4O7S2 References: N-[(1S)-2-{[(2S,3R,4S)-1-cyclohexyl-3,4-dihydroxy-6-methylheptan-2-yl]amino}-1-(ethylsulfanyl)-2-oxoethyl]-Nalpha-(morpholin-4-ylsulfonyl)-L-phenylalaninamide | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR HAS A K(I) OF 6 NM FOR ENDOTHIAPE | 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: 2.02 Å3/Da / Density % sol: 39.07 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Method: unknown / PH range low: 6.3 / PH range high: 4.5 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 19853 / % possible obs: 94 % / Rmerge(I) obs: 0.051 |
-Processing
Software | Name: RESTRAIN / Classification: refinement | ||||||||||||
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Refinement | Resolution: 1.9→20 Å / σ(F): 0 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.
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: RESTRAIN / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor obs: 0.17 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |