+Open data
-Basic information
Entry | Database: PDB / ID: 3zqr | ||||||
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Title | NMePheB25 insulin analogue crystal structure | ||||||
Components |
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Keywords | HORMONE / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / DIABETES MELLITUS | ||||||
Function / homology | Function and homology information negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Antolikova, E. / Zakova, L. / Turkenburg, J.P. / Watson, C.J. / Hanclova, I. / Sanda, M. / Cooper, A. / Kraus, T. / Brzozowski, A.M. / Jiracek, J.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Non-Equivalent Role of Inter- and Intramolecular Hydrogen Bonds in the Insulin Dimer Interface. Authors: Antolikova, E. / Zakova, L. / Turkenburg, J.P. / Watson, C.J. / Hanclova, I. / Sanda, M. / Cooper, A. / Kraus, T. / Brzozowski, A.M. / Jiracek, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zqr.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zqr.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zqr ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zqr | HTTPS FTP |
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-Related structure data
Related structure data | 3zs2C 1ms0S 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
-Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 #2: Protein/peptide | Mass: 3447.980 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: THE N-PEPTIDE ATOM OF PHE 25 IS METHYLATED / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308 |
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-Non-polymers , 4 types, 116 molecules
#3: Chemical | ChemComp-IPH / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THIS IS A FULL LENGTH HUMAN INSULIN ANALOGUE WITH THE N-PEPTIDE ATOM OF BETA CHAIN RESIDUE 25 ...THIS IS A FULL LENGTH HUMAN INSULIN ANALOGUE WITH THE N-PEPTIDE ATOM OF BETA CHAIN RESIDUE 25 METHYLATED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE |
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Crystal grow | pH: 8.2 Details: 0.6 M NA2SO4, 0.3 M TRIS PH 8.2, 0.6 M ZN(AC)2, 0.06% PHENOL. |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5472 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 30, 2010 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5472 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 22062 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 2 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 10 / % possible all: 74.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MS0 Resolution: 1.9→54.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.313 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→54.29 Å
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