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- PDB-1clv: YELLOW MEAL WORM ALPHA-AMYLASE IN COMPLEX WITH THE AMARANTH ALPHA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1clv | |||||||||
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Title | YELLOW MEAL WORM ALPHA-AMYLASE IN COMPLEX WITH THE AMARANTH ALPHA-AMYLASE INHIBITOR | |||||||||
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![]() | HYDROLASE / INSECT ALPHA-AMYLASE INHIBITOR / AMARANTHUS HYPOCHONDRIACUS / YELLOW MEAL WORM / KNOTTIN | |||||||||
Function / homology | ![]() alpha-amylase inhibitor activity / alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / endopeptidase inhibitor activity / calcium ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Pereira, P.J.B. / Lozanov, V. / Patthy, A. / Huber, R. / Bode, W. / Pongor, S. / Strobl, S. | |||||||||
![]() | ![]() Title: Specific inhibition of insect alpha-amylases: yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor at 2.0 A resolution. Authors: Pereira, P.J. / Lozanov, V. / Patthy, A. / Huber, R. / Bode, W. / Pongor, S. / Strobl, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.2 KB | Display | ![]() |
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PDB format | ![]() | 86.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 371.4 KB | Display | ![]() |
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Full document | ![]() | 372.4 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jaeS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 51263.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein/peptide | Mass: 3595.113 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN AMARANTHUS HYPOCHONDRIACUS (PRINCE'S FEATHER). References: UniProt: P80403 |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Sequence details | RESIDUE 1 IN THE PDB ENTRY IS A PYROGLUTAM |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.4 / Details: 12% PEG 1000, 12% PEG 8000, pH 5.4 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 33598 / % possible obs: 94.4 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.135 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.339 / % possible all: 68.3 |
Reflection | *PLUS Num. measured all: 279403 |
Reflection shell | *PLUS % possible obs: 68.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JAE Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 19.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Total num. of bins used: 20
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 32857 / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.161 / Rfactor Rfree: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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