[English] 日本語
![](img/lk-miru.gif)
- PDB-1apw: CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PEN... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1apw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTALLOGRAPHIC ANALYSIS OF TRANSITION STATE MIMICS BOUND TO PENICILLOPEPSIN: DIFLUOROSTATINE-AND DIFLUOROSTATONE-CONTAINING PEPTIDES | |||||||||
![]() |
| |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() penicillopepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Sielecki, A.R. / James, M.N.G. | |||||||||
![]() | ![]() Title: Crystallographic analysis of transition state mimics bound to penicillopepsin: difluorostatine- and difluorostatone-containing peptides. Authors: James, M.N. / Sielecki, A.R. / Hayakawa, K. / Gelb, M.H. #1: ![]() Title: Aspartic Proteinases and Their Catalytic Pathway Authors: James, M.N.G. / Sielecki, A.R. #2: ![]() Title: Stereochemical Analysis of Peptide Bond Hydrolysis Catalyzed by the Aspartic Proteinase Penicillopepsin Authors: James, M.N.G. / Sielecki, A.R. #3: ![]() Title: X-Ray Diffraction Studies on Penicillopepsin and its Complexes: The Hydrolytic Mechanism Authors: James, M.N.G. / Sielecki, A.R. / Hofmann, T. #4: ![]() Title: Effect of Ph on the Activities of Penicillopepsin and Rhizopus Pepsin and a Proposal for the Productive Substrate Binding Mode in Penicillopepsin Authors: Hofmann, T. / Hodges, R.S. / James, M.N.G. #5: ![]() Year: 1983 Title: Crystallographic Analysis of a Pepstatin Analogue Binding to the Aspartyl Proteinase Penicillopepsin at 1.8 Angstroms Resolution Authors: James, M.N.G. / Sielecki, A.R. / Moult, J. #6: ![]() Title: Structure and Refinement of Penicillopepsin at 1.8 Angstroms Resolution Authors: James, M.N.G. / Sielecki, A.R. #7: ![]() Title: Conformational Flexibility in the Active Sites of Aspartyl Proteinases Revealed by a Pepstatin Fragment Binding to Penicillopepsin Authors: James, M.N.G. / Sielecki, A. / Salituro, F. / Rich, D.H. / Hofmann, T. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 77.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 59.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 434.2 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Atom site foot note | 1: RESIDUES PRO E 134 AND PRO E 315 ARE CIS PROLINES. 2: THE REGION FROM SER E 277 TO SER E 281 IS POORLY ORDERED. 3: THE FOLLOWING WATER MOLECULES ARE SITTING ON A SPECIAL POSITION: HOH 563, HOH 584 AND HOH 585. | ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein / Protein/peptide , 2 types, 2 molecules EI
#1: Protein | Mass: 33468.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
---|---|
#2: Protein/peptide | Mass: 506.626 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TRANSITION STATE MIMIC |
-Sugars , 2 types, 2 molecules ![](data/chem/img/MAN.gif)
![](data/chem/img/HSY.gif)
![](data/chem/img/HSY.gif)
#3: Sugar | ChemComp-MAN / |
---|---|
#4: Sugar | ChemComp-HSY / |
-Non-polymers , 3 types, 297 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/DMF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMF.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / |
---|---|
#6: Chemical | ChemComp-DMF / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.37 % |
---|---|
Crystal grow | *PLUS Method: other / Details: NMR |
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 45 Å / Num. all: 27895 / Num. obs: 24987 / Rmerge(I) obs: 0.031 |
-
Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→8 Å / σ(I): 1 /
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 22464 / σ(I): 1 / Rfactor obs: 0.131 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 12.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|