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Yorodumi- PDB-3apr: BINDING OF A REDUCED PEPTIDE INHIBITOR TO THE ASPARTIC PROTEINASE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3apr | |||||||||
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Title | BINDING OF A REDUCED PEPTIDE INHIBITOR TO THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS. IMPLICATIONS FOR A MECHANISM OF ACTION | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / ASPARTIC PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Rhizopus microsporus var. chinensis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | |||||||||
Authors | Suguna, K. / Davies, D.R. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1987 Title: Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action. Authors: Suguna, K. / Padlan, E.A. / Smith, C.W. / Carlson, W.D. / Davies, D.R. #1: Journal: J.Mol.Biol. / Year: 1987 Title: Structure and Refinement at 1.8 Angstroms Resolution of the Aspartic Proteinase from Rhizopus Chinensis Authors: Suguna, K. / Bott, R.R. / Padlan, E.A. / Subramanian, E. / Sheriff, S. / Cohen, G.H. / Davies, D.R. #2: Journal: Biochemistry / Year: 1982 Title: Three-Dimensional Structure of the Complex of the Rhizopus Chinensis Carboxyl Proteinase and Pepstatin at 2.5 Angstroms Resolution Authors: Bott, R.R. / Subramanian, E. / Davies, D.R. #3: Journal: Adv.Exp.Med.Biol. / Year: 1977 Title: The Crystal Structure of an Acid Protease from Rhizopus Chinensis at 2.5 Angstroms Resolution Authors: Subramanian, E. / Liu, M. / Swan, I.D.A. / Davies, D.R. #4: 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. | |||||||||
History |
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Remark 700 | SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS ...SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *S2A* AND *S2B* REPRESENT ONE BIFURCATED SHEET. SHEETS *S3A* AND *S3B* REPRESENT ONE BIFURCATED SHEET. SHEETS *S4A* AND *S4B* REPRESENT ONE BIFURCATED SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3apr.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3apr.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 3apr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/3apr ftp://data.pdbj.org/pub/pdb/validation_reports/ap/3apr | 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 26 AND PRO E 316 ARE CIS PROLINES. / 2: SEE REMARK 5. / 3: SEE REMARK 6. |
-Components
#1: Protein | Mass: 34068.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizopus microsporus var. chinensis (fungus) References: UniProt: P06026, EC: 3.4.23.6 |
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#2: Protein/peptide | |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THERE IS A REDUCED PEPTIDE BOND BETWEEN PHE I 5 AND PHE I 6. IN THIS ENTRY IT IS IDENTIFIED AS PUK ...THERE IS A REDUCED PEPTIDE BOND BETWEEN PHE I 5 AND PHE I 6. IN THIS ENTRY IT IS IDENTIFIED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.74 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: unknown / Details: referred to J.Mol.Biol. 196.877-900 1987 | |||||||||||||||
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 / Num. obs: 36590 / Num. measured all: 118370 / Rmerge(I) obs: 0.045 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.147 / Highest resolution: 1.8 Å Details: THERE IS DISORDER AT SER E 116, ARG E 151, ARG E 192, AND SER E 211. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.16 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Rfactor obs: 0.147 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |