[English] 日本語
![](img/lk-miru.gif)
- PDB-1zne: Strong Solute-Solute Dispersive Interactions in a Protein-Ligand ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1zne | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 51.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 35.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 451.8 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zndC ![]() 1zngC ![]() 1znhC ![]() 1znkC ![]() 1znlC ![]() 1qy0S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 20139.400 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-HE2 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 54.88 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 12, 2004 / Details: confocal max fluc (osmic) |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→26.6 Å / Num. all: 13860 / Num. obs: 13860 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 10.2 Å2 / Rsym value: 0.094 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2007 / Rsym value: 0.367 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1QY0 Resolution: 2→26.6 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→26.6 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.023
|