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Yorodumi- PDB-1znd: Strong Solute-Solute Dispersive Interactions in a Protein-Ligand ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1znd | ||||||
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Title | Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex | ||||||
Components | Major Urinary Protein | ||||||
Keywords | TRANSPORT PROTEIN / LIPOCALIN / BETA-BARREL | ||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Malham, R. / Johnstone, S. / Bingham, R.J. / Barratt, E. / Phillips, S.E. / Laughton, C.A. / Homans, S.W. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1znd.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1znd.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 1znd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1znd_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 1znd_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 1znd_validation.xml.gz | 11 KB | Display | |
Data in CIF | 1znd_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/1znd ftp://data.pdbj.org/pub/pdb/validation_reports/zn/1znd | HTTPS FTP |
-Related structure data
Related structure data | 1zneC 1zngC 1znhC 1znkC 1znlC 1qy0S C: citing same article (ref.) S: Starting model for refinement |
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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: 20139.400 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: MUP1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P11589 | ||||
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#2: Chemical | #3: Chemical | #4: 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: 2.72 Å3/Da / Density % sol: 54.44 % |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 2005 / Details: confocal max flux (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: 1.6→19.5 Å / Num. all: 26264 / Num. obs: 26264 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.052 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 3678 / Rsym value: 0.273 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QY0 Resolution: 1.6→19.5 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: 25.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.037
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