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Yorodumi- PDB-1bma: BENZYL METHYL AMINIMIDE INHIBITOR COMPLEXED TO PORCINE PANCREATIC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bma | ||||||
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Title | BENZYL METHYL AMINIMIDE INHIBITOR COMPLEXED TO PORCINE PANCREATIC ELASTASE | ||||||
Components | Chymotrypsin-like elastase family member 1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / Metal-binding / Protease / Secreted / Zymogen / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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: 1.8 Å | ||||||
Authors | Peisach, E. / Casebier, D. / Gallion, S.L. / Furth, P. / Petsko, G.A. / Hogan Jr., J.C. / Ringe, D. | ||||||
Citation | Journal: Science / Year: 1995 Title: Interaction of a peptidomimetic aminimide inhibitor with elastase. Authors: Peisach, E. / Casebier, D. / Gallion, S.L. / Furth, P. / Petsko, G.A. / Hogan Jr., J.C. / Ringe, D. #1: 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. #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 |
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Remark 700 | SHEET THE SHEETS PRESENTED AS *S1* AND *S2* IN SHEET RECORDS BELOW ARE ACTUALLY TWO SIX-STRANDED ...SHEET THE SHEETS PRESENTED AS *S1* AND *S2* IN SHEET RECORDS BELOW ARE ACTUALLY TWO SIX-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY TWO SEVEN-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS OF EACH SHEET ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bma.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bma.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/1bma ftp://data.pdbj.org/pub/pdb/validation_reports/bm/1bma | 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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-Components
#1: Protein | Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | ChemComp-0QH / ( Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 521.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36F3N4O3 References: (1R)-1-benzyl-1-methyl-1-(2-{[4-(1-methylethyl)phenyl]amino}-2-oxoethyl)-2-{(2S)-4-methyl-2-[(trifluoroacetyl) amino]pentanoyl}diazanium | ||
#5: Water | ChemComp-HOH / | ||
Nonpolymer details | NOTE THAT SUBCOMPONESequence details | THE RESIDUE NUMBERING SCHEME FOR THE PROTEIN IS SEQUENTIAL STARTING WITH VAL A 16 AND ENDING WITH ...THE RESIDUE NUMBERING SCHEME FOR THE PROTEIN IS SEQUENTIAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.84 % | ||||||||||||||||||||
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Crystal grow | Details: THE INHIBITOR WAS SOAKED INTO THE GROWN CRYSTALS USING A 4 MM STOCK SOLUTION OF THE INHIBITOR IN 10% ACETONITRILE. | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 2 ℃ / pH: 5 / Method: unknown / Details: or 20 degrees centigrade | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5148 Å |
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Detector | Type: SIEMENS / Date: May 20, 1994 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5148 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. obs: 39545 / % possible obs: 58.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063 |
Reflection | *PLUS Num. measured all: 44505 / Rmerge(I) obs: 0.063 |
-Processing
Software |
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Refinement | Resolution: 1.8→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 18.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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