1MPJ

X-RAY CRYSTALLOGRAPHIC STUDIES ON HEXAMERIC INSULINS IN THE PRESENCE OF HELIX-STABILIZING AGENTS, THIOCYANATE, METHYLPARABEN AND PHENOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystallographic studies on hexameric insulins in the presence of helix-stabilizing agents, thiocyanate, methylparaben, and phenol.

Whittingham, J.L.Chaudhuri, S.Dodson, E.J.Moody, P.C.Dodson, G.G.

(1995) Biochemistry 34: 15553-15563

  • Primary Citation of Related Structures:  2TCI, 3MTH

  • PubMed Abstract: 
  • Three X-ray crystallographic studies have been carried out on pig insulin in the presence of three ligands, thiocyanate, methylparaben (methyl p-hydroxybenzoate), and phenol. In each case, rhombohedral crystals were obtained, which diffracted to 1.8, ...

    Three X-ray crystallographic studies have been carried out on pig insulin in the presence of three ligands, thiocyanate, methylparaben (methyl p-hydroxybenzoate), and phenol. In each case, rhombohedral crystals were obtained, which diffracted to 1.8, 1.9, and 2.3 A, respectively. Each crystal structure was very similar to that of 4-zinc pig insulin, which was used as a starting model for PROLSQ refinement (Collaborative Computational Project, Number 4, 1994). The R factors for the refined structures of thiocyanate insulin, methylparaben insulin, and phenol insulin were 19.6, 18.4, and 19.1, respectively. Each crystal structure consists of T3R3f insulin hexamers with two zinc ions per hexamer. In the R3f trimer of the thiocyanate insulin hexamer, one thiocyanate ion is coordinated to the zinc on the hexamer 3-fold axis, but there is no evidence of zinc ion binding in the off-axis zinc ion sites seen in the 4-zinc pig insulin structure. In the methylparaben insulin and phenol insulin hexamers, the phenolic ligands are bound at the dimer-dimer interfaces in the R3f trimers in a manner similar to that of phenol in R6 phenol insulin. The binding of methylparaben appears to make the hexamer more compact by drawing the A and the B chains closer together in the binding site. In all three structures presented herein, the conformations of the first three residues of the B chain in the R3f trimer are extended rather than alpha-helical, as is seen in R6 phenol insulin. The energetics of ligand binding in the insulin hexamer are discussed.


    Related Citations: 
    • The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol
      Smith, G.D.,Dodson, G.G.
      (1992) Biopolymers 32: 441
    • Phenol Stabilizes More Helix in a New Symmetrical Zinc Insulin Hexamer
      Derewenda, U.,Derewenda, Z.,Dodson, E.J.,Dodson, G.G.,Reynolds, C.D.,Smith, G.D.,Sparks, C.,Swenson, D.
      (1989) Nature 338: 594


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHENOL INSULIN
A, C
21Sus scrofaGene Names: INS
Find proteins for P01315 (Sus scrofa)
Go to Gene View: INS
Go to UniProtKB:  P01315
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHENOL INSULIN
B, D
30Sus scrofaGene Names: INS
Find proteins for P01315 (Sus scrofa)
Go to Gene View: INS
Go to UniProtKB:  P01315
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IPH
Query on IPH

Download SDF File 
Download CCD File 
A
PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 80.700α = 90.00
b = 80.700β = 90.00
c = 37.800γ = 120.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance