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- PDB-4pep: THE MOLECULAR AND CRYSTAL STRUCTURES OF MONOCLINIC PORCINE PEPSIN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pep | |||||||||
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Title | THE MOLECULAR AND CRYSTAL STRUCTURES OF MONOCLINIC PORCINE PEPSIN REFINED AT 1.8 ANGSTROMS RESOLUTION | |||||||||
![]() | PEPSIN | |||||||||
![]() | HYDROLASE (ACID PROTEINASE) | |||||||||
Function / homology | ![]() Surfactant metabolism / pepsin A / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular exosome Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Andreeva, N. / Fedorov, A.A. / Sielecki, A. / James, M. | |||||||||
![]() | ![]() Title: Molecular and crystal structures of monoclinic porcine pepsin refined at 1.8 A resolution. Authors: Sielecki, A.R. / Fedorov, A.A. / Boodhoo, A. / Andreeva, N.S. / James, M.N. | |||||||||
History |
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Remark 700 | SHEET THE SHEET IDENTIFIED AS *I* BY THE DEPOSITORS CONTAINS A BIFURCATED STRAND. THIS IS ...SHEET THE SHEET IDENTIFIED AS *I* BY THE DEPOSITORS CONTAINS A BIFURCATED STRAND. THIS IS REPRESENTED BY DEFINING THE SHEET TWICE ON *SHEET* RECORDS BELOW. THUS SHEETS *IA* *IB* DIFFER ONLY IN STRAND 6. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.6 KB | Display | ![]() |
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PDB format | ![]() | 58 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 370.3 KB | Display | ![]() |
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Full document | ![]() | 385.1 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: RESIDUE PRO 23 IS A CIS PROLINE. 2: AS DETAILED IN THE REFERENCE CITED ON THE *JRNL* RECORDS ABOVE, THE FOLLOWING LOOPS ARE POORLY DETERMINED IN THE STRUCTURE PRESENTED IN THIS ENTRY (B FACTORS .GT. 40A**2) -ASP 200 - THR 203 SER ...2: AS DETAILED IN THE REFERENCE CITED ON THE *JRNL* RECORDS ABOVE, THE FOLLOWING LOOPS ARE POORLY DETERMINED IN THE STRUCTURE PRESENTED IN THIS ENTRY (B FACTORS .GT. 40A**2) -ASP 200 - THR 203 SER 241 - GLY 243 SER 250 - ASP 253 GLN 277 - SER 281 ASP 290 - GLU 297 IN ADDITION, THE SIDE CHAINS OF RESIDUES LEU 166 AND GLU 244 - ILE 247 HAVE POORLY DEFINED ELECTRON DENSITY AND/OR COULD HAVE MORE THAN ONE POSSIBLE CONFORMATION. |
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Components
#1: Protein | Mass: 34594.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.47 % | |||||||||||||||
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Crystal grow | *PLUS pH: 2 / Method: other / Details: pH is adjusted to 2.0 with 1M H2SO4 | |||||||||||||||
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: 23897 / Num. measured all: 90730 / Rmerge(I) obs: 0.062 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→8 Å / σ(F): 3 Details: 187 SOLVENTS ARE INCLUDED IN THIS ENTRY (HOH 328 TO 514). THOSE WITH LOWER RESIDUE NUMBERS (LOWER B FACTORS, HIGHER OCCUPANCIES) ARE MORE RELIABLE THAN THOSE LOCATED TOWARDS THE END OF THE ...Details: 187 SOLVENTS ARE INCLUDED IN THIS ENTRY (HOH 328 TO 514). THOSE WITH LOWER RESIDUE NUMBERS (LOWER B FACTORS, HIGHER OCCUPANCIES) ARE MORE RELIABLE THAN THOSE LOCATED TOWARDS THE END OF THE LIST (HIGHER B FACTORS, LOWER OCCUPANCIES).
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 3 / Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Num. reflection obs: 20519 / Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |