[English] 日本語
Yorodumi- PDB-6apr: STRUCTURES OF COMPLEXES OF RHIZOPUSPEPSIN WITH PEPSTATIN AND OTHE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6apr | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURES OF COMPLEXES OF RHIZOPUSPEPSIN WITH PEPSTATIN AND OTHER STATINE-CONTAINING INHIBITORS | ||||||
Components |
| ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhizopus chinensis (fungus) Streptomyces argenteolus subsp. toyonakensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Suguna, K. / Davies, D.R. | ||||||
Citation | Journal: Proteins / Year: 1992 Title: Structures of complexes of rhizopuspepsin with pepstatin and other statine-containing inhibitors. Authors: Suguna, K. / Padlan, E.A. / Bott, R. / Boger, J. / Parris, K.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: Peptides: Structure and Function, Proceedings of the of the Eighth American Peptide Symposium Year: 1983 Title: Pepstatin Binding to Rhizopus Chinensis Aspartyl Proteinase Authors: Bott, R.R. / Davies, D.R. #4: 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. #5: 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 |
| ||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6apr.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6apr.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 6apr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6apr_validation.pdf.gz | 420.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6apr_full_validation.pdf.gz | 425 KB | Display | |
Data in XML | 6apr_validation.xml.gz | 17 KB | Display | |
Data in CIF | 6apr_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/6apr ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6apr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUES PRO E 26 AND PRO E 316 ARE CIS PROLINES. |
-Components
#1: Protein | Mass: 34068.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizopus chinensis (fungus) / References: UniProt: P06026, EC: 3.4.23.6 |
---|---|
#2: Protein/peptide | |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.32 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 6 / Method: other / Details: grown in the cold from a filtered | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. all: 18623 / Num. obs: 13024 / Rmerge(I) obs: 0.085 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→8 Å / σ(F): 0 Details: THERE IS DISORDER AT SER E 116, ARG E 151, ARG E 192 AND SER E 211.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection obs: 11696 / σ(F): 1 / Rfactor obs: 0.149 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |