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Yorodumi- PDB-1pig: PIG PANCREATIC ALPHA-AMYLASE COMPLEXED WITH THE OLIGOSACCHARIDE V-1532 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pig | ||||||||||||
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Title | PIG PANCREATIC ALPHA-AMYLASE COMPLEXED WITH THE OLIGOSACCHARIDE V-1532 | ||||||||||||
Components | ALPHA-AMYLASE | ||||||||||||
Keywords | GLYCOSYLTRANSFERASE / ALPHA-AMYLASE ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE GLYCOSYLTRANSFERASE | ||||||||||||
Function / homology | Function and homology information alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) | ||||||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.2 Å | ||||||||||||
Authors | Machius, M. / Vertesy, L. / Huber, R. / Wiegand, G. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Carbohydrate and protein-based inhibitors of porcine pancreatic alpha-amylase: structure analysis and comparison of their binding characteristics. Authors: Machius, M. / Vertesy, L. / Huber, R. / Wiegand, G. #1: Journal: J.Mol.Biol. / Year: 1995 Title: The Crystal Structure of Porcine Pancreatic Alpha-Amylase in Complex with the Microbial Inhibitor Tendamistat Authors: Wiegand, G. / Epp, O. / Huber, R. #2: Journal: Protein Sci. / Year: 1995 Title: Carbohydrate Binding Sites in a Pancreatic Alpha-Amylase-Substrate Complex, Derived from X-Ray Structure Analysis at 2.1 Angstrom Resolution Authors: Qian, M. / Haser, R. / Payan, F. #3: Journal: J.Mol.Biol. / Year: 1994 Title: Refined Molecular Structure of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution Authors: Larson, S.B. / Greenwood, A. / Cascio, D. / Day, J. / McPherson, A. #4: Journal: Biochemistry / Year: 1994 Title: The Active Center of a Mammalian Alpha-Amylase. Structure of the Complex of a Pancreatic Alpha-Amylase with a Carbohydrate Inhibitor Refined to 2.2-A Resolution Authors: Qian, M. / Haser, R. / Buisson, G. / Duee, E. / Payan, F. #5: Journal: J.Mol.Biol. / Year: 1993 Title: Structure and Molecular Model Refinement of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution Authors: Qian, M. / Haser, R. / Payan, F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pig.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pig.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/1pig ftp://data.pdbj.org/pub/pdb/validation_reports/pi/1pig | HTTPS FTP |
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-Related structure data
Related structure data | 1pifSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55373.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00690, alpha-amylase |
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-Sugars , 5 types, 5 molecules
#2: Polysaccharide | 4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#5: Polysaccharide | beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-cellobiose |
#7: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 231 molecules
#6: Chemical | ChemComp-HMC / |
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#8: Chemical | ChemComp-CA / |
#9: Chemical | ChemComp-CL / |
#10: Water | ChemComp-HOH / |
-Details
Nonpolymer details | TRESTATIN LIKE COMPOUNDS HAVE BEEN ISOLATED FROM STREPTOMYCES GALBUS CULTURE MEDIUM AND TREATED ...TRESTATIN LIKE COMPOUNDS HAVE BEEN ISOLATED FROM STREPTOMYC |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.39 Å3/Da / Density % sol: 72 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6 Details: VAPOR DIFFUSION; 10 MICROLITER OF PROTEIN (15 MG/ML IN 0.1 M AMMONIUM CACODYLATE, PH 10.0 0.001 M V-1532) WERE STEPWISE CONCENTRATED OVER 0.1, 0.15, AND 0.25 M AMMONIUM CACODYLATE, PH 6.0., vapor diffusion PH range: 6.0-10.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 275 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 20, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20.5 Å / Num. obs: 47260 / % possible obs: 93.7 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.123 |
Reflection shell | Resolution: 2.2→2.3 Å / % possible all: 97.8 |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: 1PIF Resolution: 2.2→7 Å / σ(F): 2
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Displacement parameters | Biso mean: 28.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å
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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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