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Yorodumi- PDB-2est: Crystallographic study of the binding of a trifluoroacetyl dipept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2est | ||||||
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Title | Crystallographic study of the binding of a trifluoroacetyl dipeptide anilide inhibitor with elastase | ||||||
Components | ELASTASE | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / SERINE PROTEINASE | ||||||
Function / homology | Function and homology information pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Sieker, L.C. / Hughes, D.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1982 Title: Crystallographic study of the binding of a trifluoroacetyl dipeptide anilide inhibitor with elastase. Authors: Hughes, D.L. / Sieker, L.C. / Bieth, J. / Dimicoli, J.L. #1: Journal: Eur.J.Biochem. / Year: 1980 Title: The Indirect Mechanism of Action of the Trifluoroacetyl Peptides on Elastase Authors: Dimicoli, J.-L. / Renaud, A. / Bieth, J. #2: Journal: J.Mol.Biol. / Year: 1978 Title: The Atomic Structure of Crystalline Porcine Pancreatic Elastase at 2.5 Angstroms Resolution. Comparisons with the Structure of Alpha-Chymotrypsin Authors: Sawyer, L. / Shotton, C.M. / Campbell, J.W. / Wendell, P.L. / Muirhead, H. / Watson, H.C. / Diamond, R. / Ladner, R.C. | ||||||
History |
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Remark 700 | SHEET THE TWO SEVEN STRANDED SHEETS IN THIS STRUCTURE ARE REALLY SIX STRANDED BETA BARRELS - THIS ...SHEET THE TWO SEVEN STRANDED SHEETS IN THIS STRUCTURE ARE REALLY SIX STRANDED BETA BARRELS - THIS IS DENOTED BY THE FIRST STRAND RECURRING AS THE LAST STRAND. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2est.cif.gz | 63.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2est.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 2est.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2est_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 2est_full_validation.pdf.gz | 504.7 KB | Display | |
Data in XML | 2est_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 2est_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/2est ftp://data.pdbj.org/pub/pdb/validation_reports/es/2est | HTTPS FTP |
-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: SEE REMARK 7. |
-Components
#1: Protein | Mass: 25928.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase |
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#2: Chemical | ChemComp-2Z5 / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | THE RESIDUE NUMBERING IS BASED ON THAT OF CHYMOTRYPSINOGEN A. THE ENZYME HAS BEEN ASSIGNED CHAIN ...THE RESIDUE NUMBERING IS BASED ON THAT OF CHYMOTRYPS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.85 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5 / Method: unknown / Details: Shotton, D.M., (1968) J.Mol.Biol., 32, 155. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 8481 / Num. measured all: 15401 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.21 / Highest resolution: 2.5 Å Details: NOTE THAT THE SG - SG DISTANCES FOR THE FOUR DISULFIDE BRIDGES ARE ALL ABOUT 3 ANGSTROMS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 7187 / σ(I): 2 / Rfactor obs: 0.21 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 4 |