+Open data
-Basic information
Entry | Database: PDB / ID: 1dhk | ||||||||||||
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Title | STRUCTURE OF PORCINE PANCREATIC ALPHA-AMYLASE | ||||||||||||
Components |
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Keywords | COMPLEX (HYDROLASE/INHIBITOR) / PANCREATIC ALPHA-AMYLASE / PORCINE / LECTIN-LIKE INHIBITOR / COMPLEX (HYDROLASE-INHIBITOR) / COMPLEX (HYDROLASE-INHIBITOR) complex | ||||||||||||
Function / homology | Function and homology information alpha-amylase inhibitor activity / alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate binding / carbohydrate metabolic process / calcium ion binding / extracellular space Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) Phaseolus vulgaris (French bean) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||||||||
Authors | Bompard-Gilles, C. / Payan, F. | ||||||||||||
Citation | Journal: Structure / Year: 1996 Title: Substrate mimicry in the active center of a mammalian alpha-amylase: structural analysis of an enzyme-inhibitor complex. Authors: Bompard-Gilles, C. / Rousseau, P. / Rouge, P. / Payan, F. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and Preliminary X-Ray Analysis of Pig Pancreatic Alpha-Amylase in Complex with a Bean Lectin-Like Inhibitor Authors: Gilles, C. / Rousseau, P. / Rouge, P. / Payan, F. #2: 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. #3: 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 | 1dhk.cif.gz | 197.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dhk.ent.gz | 155.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dhk_validation.pdf.gz | 544.9 KB | Display | wwPDB validaton report |
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Full document | 1dhk_full_validation.pdf.gz | 554.1 KB | Display | |
Data in XML | 1dhk_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1dhk_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/1dhk ftp://data.pdbj.org/pub/pdb/validation_reports/dh/1dhk | 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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Details | ALPHA-AI IS A DIMERIC MOLECULE (I2) CONSISTING OF TWO IDENTICAL SUBUNITS. IT BINDS TWO AMYLASE MOLECULES (2E) TO FORM A DIMERIC COMPLEX E2I2. HOWEVER, THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CORRESPONDS TO HALF THE COMPLEX MOLECULE (EI). IN THIS ENTRY, COORDINATES FOR ALL ATOMS ARE PROVIDED FOR ONE CHAIN OF AMYLASE AND ONE CHAIN OF ALPHA-AI. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 55400.699 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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#2: Protein | Mass: 24813.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / Organ: SEED / References: UniProt: P02873 |
-Sugars , 2 types, 3 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 326 molecules
#4: Chemical | #5: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.928 |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Num. obs: 66769 / % possible obs: 96.7 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.85→1.92 Å / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2 / % possible all: 98.4 |
Reflection | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 35 Å |
Reflection shell | *PLUS % possible obs: 98.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PPA NATIVE AND LECTIN FROM SEEDS OF LATHYRUS OCHRUS Resolution: 1.85→8 Å / σ(F): 0
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Displacement parameters | Biso mean: 23.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→8 Å
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Refine LS restraints |
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