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Yorodumi- PDB-1psa: STRUCTURE OF A PEPSIN(SLASH)RENIN INHIBITOR COMPLEX REVEALS A NOV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1psa | ||||||
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Title | STRUCTURE OF A PEPSIN(SLASH)RENIN INHIBITOR COMPLEX REVEALS A NOVEL CRYSTAL PACKING INDUCED BY MINOR CHEMICAL ALTERATIONS IN THE INHIBITOR | ||||||
Components | PEPSIN APepsin | ||||||
Keywords | HYDROLASE/hydrolase inhibitor / ACID PROTEINASE / HYDROLASE-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information Surfactant metabolism / pepsin A / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.9 Å | ||||||
Authors | Chen, L. / Abad-Zapatero, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.B / Year: 1992 Title: Structure of a pepsin/renin inhibitor complex reveals a novel crystal packing induced by minor chemical alterations in the inhibitor. Authors: Chen, L. / Erickson, J.W. / Rydel, T.J. / Park, C.H. / Neidhart, D. / Luly, J. / Abad-Zapatero, C. #1: Journal: Adv.Exp.Med.Biol. / Year: 1991 Title: Inhibitor Binding Induces Structural Changes in Porcine Pepsin Authors: Abad-Zapatero, C. / Rydel, T.J. / Neidhart, D.J. / Luly, J. / Erickson, J.W. #2: Journal: Proteins / Year: 1990 Title: Revised 2.3 Angstroms Structure of Porcine Pepsin: Evidence for a Flexible Subdomain Authors: Abad-Zapatero, C. / Rydel, T.J. / Erickson, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1psa.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1psa.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 1psa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/1psa ftp://data.pdbj.org/pub/pdb/validation_reports/ps/1psa | 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 A 23 AND PRO B 23 ARE CIS PROLINES. 2: RESIDUES 239 - 242 AND 278 - 281 OF CHAINS *A* AND *B* HAD THE WEAKEST ELECTRON DENSITY. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.786, 0.036, 0.617), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
-Components
#1: Protein | Mass: 34513.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P00791, pepsin A #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THE INHIBITOR A-62095 IS A TETRAPEPTIDE ANALOGUE WITH A T-BOC BLOCKING GROUP AND CONTAINING ...THE INHIBITOR A-62095 IS A TETRAPEPTI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.98 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 2 / Method: unknownDetails: taken from Andreeva, N.S. et al (1984). J. Biol. Chem., 259, 11353-11365. | ||||||||||||||||||||
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: 2.9 Å / Lowest resolution: 3 Å / Num. all: 13736 / Num. obs: 11951 / % possible obs: 87 % / Num. measured all: 24379 / Rmerge(I) obs: 0.044 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.9→8 Å / Rfactor Rwork: 0.139 Details: THE SPACE GROUP OF THIS STRUCTURE IS MONOCLINIC P21, WITH C AXIS UNIQUE. THE ASYMMETRIC UNIT CONTAINS TWO PEPSIN/ INHIBITOR COMPLEXES. RESIDUES 239 - 242 AND 278 - 281 OF CHAINS *A* AND *B* ...Details: THE SPACE GROUP OF THIS STRUCTURE IS MONOCLINIC P21, WITH C AXIS UNIQUE. THE ASYMMETRIC UNIT CONTAINS TWO PEPSIN/ INHIBITOR COMPLEXES. RESIDUES 239 - 242 AND 278 - 281 OF CHAINS *A* AND *B* HAD THE WEAKEST ELECTRON DENSITY. | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Num. reflection all: 11284 / Rfactor obs: 0.139 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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