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- PDB-4p65: Crystal structure of an cyclohexylalanine substituted insulin analog. -

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Basic information

Entry
Database: PDB / ID: 4p65
TitleCrystal structure of an cyclohexylalanine substituted insulin analog.
Components(Insulin) x 2
KeywordsHORMONE / protein hormone / non-standard mutagenesis
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of protein metabolic process => GO:0051247 / negative regulation of acute inflammatory response / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / COPI-mediated anterograde transport / positive regulation of glycogen biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Signal attenuation / negative regulation of protein secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of nitric oxide mediated signal transduction / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / Regulation of insulin secretion / positive regulation of insulin receptor signaling pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / transport vesicle / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of brown fat cell differentiation / positive regulation of mitotic nuclear division / positive regulation of cell differentiation / regulation of transmembrane transporter activity / positive regulation of long-term synaptic potentiation / regulation of synaptic plasticity / cognition / activation of protein kinase B activity / positive regulation of cytokine production / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of nitric-oxide synthase activity / acute-phase response / negative regulation of proteolysis / hormone activity / vasodilation / insulin receptor binding / insulin receptor signaling pathway / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / wound healing / Golgi lumen / glucose metabolic process / regulation of protein localization / cell-cell signaling / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / positive regulation of protein kinase B signaling / protease binding / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / endoplasmic reticulum lumen / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of transcription, DNA-templated / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin-like / Insulin family signature. / Insulin-like superfamily / Insulin, conserved site
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPandyarajan, V. / Wan, Z. / Weiss, M.A.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Aromatic Anchor at an Invariant Hormone-Receptor Interface: FUNCTION OF INSULIN RESIDUE B24 WITH APPLICATION TO PROTEIN DESIGN.
Authors: Pandyarajan, V. / Smith, B.J. / Phillips, N.B. / Whittaker, L. / Cox, G.P. / Wickramasinghe, N. / Menting, J.G. / Wan, Z.L. / Whittaker, J. / Ismail-Beigi, F. / Lawrence, M.C. / Weiss, M.A.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin
B: Insulin
C: Insulin
D: Insulin
E: Insulin
F: Insulin
G: Insulin
H: Insulin
I: Insulin
J: Insulin
K: Insulin
L: Insulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,61822
Polymers34,85212
Non-polymers76610
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18580 Å2
ΔGint-233 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.040, 60.900, 59.300
Angle α, β, γ (deg.)90.00, 112.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
Insulin /


Mass: 2383.698 Da / Num. of mol.: 6 / Fragment: UNP residues 90-110 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide
Insulin /


Mass: 3424.967 Da / Num. of mol.: 6 / Fragment: UNP residues 25-54 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 4 types, 217 molecules

#3: Chemical
ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: sodium citrate, phenol, sodium chloride, zinc acetate, tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9871
20.9871
ReflectionResolution: 1.5→42.3 Å / Num. obs: 54128 / % possible obs: 95.8 % / Redundancy: 1.9 % / Net I/σ(I): 13.9
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZNJ
Resolution: 1.5→42.3 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 4823 10.01 %random selection
Rwork0.1598 ---
obs0.1641 48189 99.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 46 207 2574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012620
X-RAY DIFFRACTIONf_angle_d1.3513522
X-RAY DIFFRACTIONf_dihedral_angle_d14.777980
X-RAY DIFFRACTIONf_chiral_restr0.065383
X-RAY DIFFRACTIONf_plane_restr0.006445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.36171660.33191447X-RAY DIFFRACTION99
1.5171-1.53490.34971600.30431471X-RAY DIFFRACTION100
1.5349-1.55360.2911580.27341420X-RAY DIFFRACTION99
1.5536-1.57330.31111600.26441445X-RAY DIFFRACTION99
1.5733-1.5940.29981660.24371436X-RAY DIFFRACTION100
1.594-1.61580.27211560.22971446X-RAY DIFFRACTION100
1.6158-1.63890.25411590.2161465X-RAY DIFFRACTION100
1.6389-1.66340.23831610.20061417X-RAY DIFFRACTION100
1.6634-1.68940.23991620.17671456X-RAY DIFFRACTION100
1.6894-1.71710.21561700.17991435X-RAY DIFFRACTION100
1.7171-1.74670.22541880.17281423X-RAY DIFFRACTION100
1.7467-1.77840.24551630.1681487X-RAY DIFFRACTION100
1.7784-1.81270.2151540.16831435X-RAY DIFFRACTION100
1.8127-1.84970.22821550.1581466X-RAY DIFFRACTION100
1.8497-1.88990.22331550.15811435X-RAY DIFFRACTION100
1.8899-1.93380.23661710.15611464X-RAY DIFFRACTION100
1.9338-1.98220.20371600.1541456X-RAY DIFFRACTION100
1.9822-2.03580.18221650.14911436X-RAY DIFFRACTION100
2.0358-2.09570.18511720.14041444X-RAY DIFFRACTION100
2.0957-2.16330.19081590.14551452X-RAY DIFFRACTION100
2.1633-2.24060.18531620.1411459X-RAY DIFFRACTION100
2.2406-2.33040.19691540.14341456X-RAY DIFFRACTION100
2.3304-2.43640.19791580.15131481X-RAY DIFFRACTION100
2.4364-2.56480.18171840.13941434X-RAY DIFFRACTION100
2.5648-2.72550.20341340.15281490X-RAY DIFFRACTION100
2.7255-2.93590.19631480.15951466X-RAY DIFFRACTION100
2.9359-3.23130.19671690.16041449X-RAY DIFFRACTION100
3.2313-3.69860.17941580.15091480X-RAY DIFFRACTION99
3.6986-4.65890.1861510.14171439X-RAY DIFFRACTION97
4.6589-42.31630.21241450.17421276X-RAY DIFFRACTION85

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