+Open data
-Basic information
Entry | Database: PDB / ID: 2qmk | |||||||||
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Title | Human pancreatic alpha-amylase complexed with nitrite | |||||||||
Components | Pancreatic alpha-amylase | |||||||||
Keywords | HYDROLASE / AMYLASE / PICHIA PASTORIS / DIABETES / CATALYSIS / PANCREATIC / ENZYME / HUMAN / ANION ACTIVATION / NITRITE / CHLORIDE / Carbohydrate metabolism / Glycoprotein / Glycosidase / Metal-binding / Pyrrolidone carboxylic acid / Secreted | |||||||||
Function / homology | Function and homology information polysaccharide digestion / Digestion of dietary carbohydrate / alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular exosome / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Williams, L.K. / Maurus, R. / Brayer, G.D. | |||||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Alternative catalytic anions differentially modulate human alpha-amylase activity and specificity Authors: Maurus, R. / Begum, A. / Williams, L.K. / Fredriksen, J.R. / Zhang, R. / Withers, S.G. / Brayer, G.D. | |||||||||
History |
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Remark 999 | SEQUENCE The authors state that the modification to glutamine 1 to form PCA happens in vivo. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qmk.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qmk.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 2qmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/2qmk ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qmk | HTTPS FTP |
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-Related structure data
Related structure data | 2qv4C 3baiC 3bajC 3bakC 3bawC 3baxC 3bayC 1hnyS 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
#1: Protein | Mass: 55931.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMY2A / Production host: Pichia pastoris (fungus) / References: UniProt: P04746, alpha-amylase |
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#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-NO2 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.12 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 60% 2-methylpentane-2,4-diol, 100 mM cacodylate, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 23, 2004 / Details: OSMIC MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→21.29 Å / Num. obs: 16454 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063 / Net I/σ(I): 0.195 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 8.6 / % possible all: 0.726 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HNY Resolution: 2.3→21.29 Å / σ(F): 0
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Displacement parameters | Biso mean: 27.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→21.29 Å
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Refine LS restraints |
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