+Open data
-Basic information
Entry | Database: PDB / ID: 1ben | ||||||
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Title | INSULIN COMPLEXED WITH 4-HYDROXYBENZAMIDE | ||||||
Components | (HUMAN INSULIN) x 2 | ||||||
Keywords | HORMONE / INSULIN / GLUCOSE METABOLISM | ||||||
Function / homology | Function and homology information negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / vasodilation / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / glucose metabolic process / regulation of protein localization / glucose homeostasis / insulin receptor signaling pathway / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / Golgi membrane / endoplasmic reticulum lumen / 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 | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | ||||||
Authors | Smith, G.D. / Ciszak, E. / Pangborn, W. | ||||||
Citation | Journal: Protein Sci. / Year: 1996 Title: A novel complex of a phenolic derivative with insulin: structural features related to the T-->R transition. Authors: Smith, G.D. / Ciszak, E. / Pangborn, W. #1: Journal: Structure / Year: 1995 Title: Role of C-Terminal B-Chain Residues in Insulin Assembly: The Structure of Hexameric Lysb28Prob29-Human Insulin Authors: Ciszak, E. / Beals, J.M. / Frank, B.H. / Baker, J.C. / Carter, N.D. / Smith, G.D. #2: Journal: Biochemistry / Year: 1994 Title: Crystallographic Evidence for Dual Coordination Around Zinc in the T3R3 Human Insulin Hexamer Authors: Ciszak, E. / Smith, G.D. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: The Structure of a Complex of Hexameric Insulin and 4'-Hydroxyacetanilide Authors: Smith, G.D. / Ciszak, E. #4: Journal: Proteins / Year: 1992 Title: The Structure of a Rhombohedral R6 Insulin/Phenol Complex Authors: Smith, G.D. / Dodson, G.G. #5: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1988 Title: The Structure of 2Zn Pig Insulin Crystals at 1.5A Resolution Authors: Baker, E.N. / Blundell, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D.C. / Hubbard, R.E. / Isaacs, N.W. / Reynolds, C.D. / Sakabe, K. / Sakabe, N. / Vijayan, N.M. #6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984 Title: Structural Stability in the 4-Zinc Human Insulin Hexamer Authors: Smith, G.D. / Swenson, D.C. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ben.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ben.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ben.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ben_validation.pdf.gz | 400.9 KB | Display | wwPDB validaton report |
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Full document | 1ben_full_validation.pdf.gz | 404.1 KB | Display | |
Data in XML | 1ben_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 1ben_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/1ben ftp://data.pdbj.org/pub/pdb/validation_reports/be/1ben | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT OF INSULIN CONSISTS OF TWO INSULIN MONOMERS EACH CONSISTING OF TWO HETEROCHAINS. THE ENTRY PRESENTS COORDINATES FOR MONOMER I (CHAIN IDENTIFIERS A AND B) AND II (CHAIN IDENTIFIERS C AND D). APPLYING THE THREE-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS YIELDS A HEXAMER AROUND THE AXIS. THERE ARE TWO ZINC IONS AND ONE CHLORIDE ION PER INSULIN HEXAMER LOCATED ON THE THREE-FOLD AXIS AND HAVE OCCUPANCIES OF 0.33. WATERS HOH 18, HOH 54, AND HOH 59 ARE LOCATED ON THE THREE-FOLD AXIS. |
-Components
-Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GIFT OF LILLY RESEARCH LABORATORIES / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GIFT OF LILLY RESEARCH LABORATORIES / References: UniProt: P01308 |
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-Non-polymers , 4 types, 173 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | THE CONFORMATIONS OF THE TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A DIFFERENCE IN CONFORMATION ...THE CONFORMATI |
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Nonpolymer details | THE MODEL ALSO CONTAINS TWO ZINC IONS. THE FIRST ZINC ION (ZN B 31) IS COORDINATED BY THREE ...THE MODEL ALSO CONTAINS TWO ZINC IONS. THE FIRST ZINC ION (ZN B 31) IS COORDINATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 33 % Description: DATA WERE MEASURED FROM SIX CRYSTALS, GROWN IN MICROGRAVITY ON SHUTTLE FLIGHT, STS-60. THE R-AXIS-IIC SOFTWARE WAS USED TO INTEGRATE EACH IMAGE PLATE; SCALING AND MERGING WAS ...Description: DATA WERE MEASURED FROM SIX CRYSTALS, GROWN IN MICROGRAVITY ON SHUTTLE FLIGHT, STS-60. THE R-AXIS-IIC SOFTWARE WAS USED TO INTEGRATE EACH IMAGE PLATE; SCALING AND MERGING WAS ACCOMPLISHED WITH THE DREAM PROGRAM PACKAGE (R.H. BLESSING, CRYSTALLOGR. REV. 1, 3-58 (1987). | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: slow cooling / pH: 5.7 Details: 0.05M SODIUM CITRATE, 0.007M ZINC ACETATE, 0.06M 4-HYDROXYBENZAMIDE, 1.0M SODIUM CHLORIDE, PH=5.7. CRYSTALS GROWN BY SLOW COOLING., slow cooling | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 14, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→80 Å / Num. obs: 18002 / % possible obs: 76.6 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Rmerge(I) obs: 0.066 |
Reflection | *PLUS Num. measured all: 159339 |
-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.4→8 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 27.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→8 Å
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Refine LS restraints |
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Refinement | *PLUS σ(I): 17907 / Rfactor all: 0.176 / Rfactor obs: 0.154 / Rfactor Rwork: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |