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Yorodumi- PDB-5er2: High-resolution X-ray diffraction study of the complex between en... -
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-Basic information
Entry | Database: PDB / ID: 5er2 | ||||||
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Title | High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor. the analysis of the inhibitor binding and description of the rigid body shift in the enzyme | ||||||
Components | ENDOTHIAPEPSIN | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Sali, A. / Veerapandian, B. / Cooper, J.B. / Foundling, S.I. / Hoover, D.J. / Blundell, T.L. | ||||||
Citation | Journal: EMBO J. / Year: 1989 Title: High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme. Authors: Sali, A. / Veerapandian, B. / Cooper, J.B. / Foundling, S.I. / Hoover, D.J. / Blundell, T.L. #1: Journal: FEBS Lett. / Year: 1984 Title: The Active Site of Aspartic Proteinases Authors: Pearl, L. / Blundell, T. #2: Journal: Proc.FEBS Meet. / Year: 1979 Title: Active Site of Acid Proteinases Authors: Blundell, T.L. / Jones, H.B. / Khan, G. / Taylor, G. / Sewell, T.S. / Pearl, L.H. / Wood, S.P. #3: Journal: Proc.FEBS Meet. / Year: 1979 Title: The Three-Dimensional Structure of Acid Proteinases Authors: Blundell, T.L. / Jenkins, J.A. / Khan, G. / Roychowdhury, P. / Sewell, T. / Tickle, I.J. / Wood, E.A. #4: Journal: Biochim.Biophys.Acta / Year: 1979 Title: Four-Fold Structural Repeat in the Acid Proteases Authors: Blundell, T.L. / Sewell, B.T. / Mclachlan, A.D. #5: Journal: Nature / Year: 1978 Title: Structural Evidence for Gene Duplication in the Evolution of Acid Proteases Authors: Tang, J. / James, M.N.G. / Hsu, I.N. / Jenkins, J.A. / Blundell, T.L. #6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977 Title: Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica Authors: Subramanian, E. / Swan, I.D.A. / Liu, M. / Davies, D.R. / Jenkins, J.A. / Tickle, I.J. / Blundell, T.L. #7: Journal: Adv.Exp.Med.Biol. / Year: 1977 Title: X-Ray Analysis and Circular Dichroism of the Acid Protease from Endothia Parasitica and Chymosin Authors: Jenkins, J. / Tickle, I. / Sewell, T. / Ungaretti, L. / Wollmer, A. / Blundell, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5er2.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5er2.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 5er2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/5er2 ftp://data.pdbj.org/pub/pdb/validation_reports/er/5er2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO E 23 AND PRO E 133 ARE CIS PROLINES. 2: RESIDUE HIS I 3 HAS ATOMS WITH ALTERNATE POSITIONS DENOTED C AND N IN THE ATOM RECORDS. |
-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, EC: 3.4.23.6 |
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#2: Chemical | ChemComp-0EK / Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 948.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H77N9O9 References: 6-ammonio-N-{[(2R,3R)-3-{[N-(tert-butoxycarbonyl)-L-phenylalanyl-3-(1H-imidazol-3-ium-4-yl)-L-alanyl]amino}-4- cyclohexyl-2-hydroxybutyl](2-methylpropyl)carbamoyl}-L-norleucyl-L-phenylalanine |
#3: Water | ChemComp-HOH / |
Sequence details | THE COMPLETE SEQUENCE WAS DETERMINED BY V. PEDERSEN AS TRYPTIC FRAGMENTS WHICH WERE ALIGNED IN THE ...THE COMPLETE SEQUENCE WAS DETERMINED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.26 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4.5 / Method: batch method | |||||||||||||||||||||||||
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: 1.8 Å / Lowest resolution: 20 Å / Num. obs: 21985 / % possible obs: 89 % / Num. measured all: 26706 / Rmerge(I) obs: 0.05 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→20 Å 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: 1.8→20 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 2 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |