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- PDB-1znk: Strong Solute-Solute Dispersive Interactions in a Protein-Ligand ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1znk | |||||||||
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Title | Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex | |||||||||
![]() | Major Urinary Protein | |||||||||
![]() | TRANSPORT PROTEIN / LIPOCALIN / BETA-BARREL | |||||||||
Function / homology | ![]() positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / energy reserve metabolic process / odorant binding / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation ...positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / energy reserve metabolic process / odorant binding / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation / locomotor rhythm / negative regulation of lipid storage / small molecule binding / negative regulation of gluconeogenesis / aerobic respiration / mitochondrion organization / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Malham, R. / Johnstone, S. / Bingham, R.J. / Barratt, E. / Phillips, S.E. / Laughton, C.A. / Homans, S.W. | |||||||||
![]() | ![]() Title: Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex. Authors: Malham, R. / Johnstone, S. / Bingham, R.J. / Barratt, E. / Phillips, S.E. / Laughton, C.A. / Homans, S.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.2 KB | Display | ![]() |
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PDB format | ![]() | 36.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.2 KB | Display | ![]() |
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Full document | ![]() | 444.8 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zndC ![]() 1zneC ![]() 1zngC ![]() 1znhC ![]() 1znlC ![]() 1qy0S C: citing same article ( 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 on special symmetry positions |
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Components
#1: Protein | Mass: 20139.400 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-F09 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: CdCl, malate, HCl , pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2005 Details: mirror; vertical focusing, glancing angle 3.5 mrad, 7.0 Ang. cut off, 1.2m long silicon substrate, rhodium coated, distance from source 16m, distance to focus - variable, typically 5m. |
Radiation | Monochromator: si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→42.2 Å / Num. all: 27220 / Num. obs: 27220 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 17.9 Å2 / Rsym value: 0.092 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3878 / Rsym value: 0.278 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QY0 Resolution: 1.6→42.2 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→42.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.034
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