[English] 日本語
Yorodumi- PDB-1eld: Structural analysis of the active site of porcine pancreatic elas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eld | ||||||
---|---|---|---|---|---|---|---|
Title | Structural analysis of the active site of porcine pancreatic elastase based on the x-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors | ||||||
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 Å | ||||||
Authors | Mattos, C. / Petsko, G.A. / Ringe, D. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Structural analysis of the active site of porcine pancreatic elastase based on the X-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors. Authors: Mattos, C. / Giammona, D.A. / Petsko, G.A. / Ringe, D. #1: Journal: Nat.Struct.Biol. / Year: 1994 Title: Analogous Inhibitors of Elastase Do not Always Bind Analogously Authors: Mattos, C. / Rasmussen, B. / Ding, X. / Petsko, G.A. / Ringe, D. #2: Journal: J.Mol.Recog. / Year: 1990 Title: Interaction of the Peptide Cf3-Leu-Ala-Nh-C6H4-Cf3(Tfla) with Porcine Pancreatic Elastase. X-Ray Studies at 1.8 Angstroms Authors: Li De La Sierra, I. / Papamichael, E. / Sakarelos, C. / Dimicoli, J.-L. / Prange, T. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1988 Title: Structure of Native Porcine Pancreatic Elastase at 1.65 Angstroms Resolution Authors: Meyer, E. / Cole, G. / Radhakrishnan, R. / Epp, O. #4: Journal: J.Mol.Biol. / Year: 1986 Title: Structure of the Product Complex of Acetyl-Ala-Pro-Ala with Porcine Pancreatic Elastase at 1.65 Angstroms Resolution Authors: Meyer, E. / Radhakrishnan, R. / Cole, G. / Presta, L.G. #5: Journal: J.Mol.Biol. / Year: 1982 Title: Crystallographic Study of the Binding of a Tri-Fluoroacetyl Dipeptide Anilide Inhibitor with Elastase Authors: Hughes, D.L. / Diecker, L.C. / Bieth, L.C. / Dimicoli, J.-L. #6: 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. #7: 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 |
| ||||||
Remark 700 | SHEET THE TWO SEVEN-STRANDED SHEETS IN THIS STRUCTURE ARE REALLY SIX-STRANDED BETA BARRELS. THIS IS ...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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1eld.cif.gz | 63.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1eld.ent.gz | 46.1 KB | Display | PDB format |
PDBx/mmJSON format | 1eld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eld_validation.pdf.gz | 460.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1eld_full_validation.pdf.gz | 468.6 KB | Display | |
Data in XML | 1eld_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1eld_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/1eld ftp://data.pdbj.org/pub/pdb/validation_reports/el/1eld | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-0Z0 / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-ACY / |
#5: Water | ChemComp-HOH / |
Sequence details | THE IDENTITY OF ASN A 81 AGREES WITH THE SEQUENCES OF SEVERAL OTHER ELASTASE STRUCTURES. THE ...THE IDENTITY OF ASN A 81 AGREES WITH THE SEQUENCES OF SEVERAL OTHER ELASTASE STRUCTURES |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.59 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Details: THE COMPLEX WAS CO-CRYSTALLIZED. THE CO-CRYSTALS WERE GROWN BY THE METHOD OF VAPOR DIFFUSION IN 40 MICROLITER DROPS CONTAINING 7MG/ML OF ELASTASE, 0.1 MILLIMOLAR TFA-PHE-ALA-TFM, 1.4 ...Details: THE COMPLEX WAS CO-CRYSTALLIZED. THE CO-CRYSTALS WERE GROWN BY THE METHOD OF VAPOR DIFFUSION IN 40 MICROLITER DROPS CONTAINING 7MG/ML OF ELASTASE, 0.1 MILLIMOLAR TFA-PHE-ALA-TFM, 1.4 MILLIMOLAR SODIUM SULFATE AND 100 MILLIMOLAR SODIUM ACETATE AT PH 5. THE RESERVOIR CONSISTED OF 100 MILLIMOLAR SODIUM SULFATE AND 100 MILLIMOLAR ACETATE BUFFER AT PH 5. | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 2 ℃ / pH: 5 / Method: unknown / Details: Sawyer, L., (1978) J. Mol. Biol., 118, 137. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 21511 / Observed criterion σ(I): 0 / Num. measured all: 58417 / Rmerge(I) obs: 0.089 |
-Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→10 Å / Rfactor Rwork: 0.196 / Rfactor obs: 0.196 / σ(F): 0 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
| ||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 / Num. reflection obs: 21511 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
|