1EV3 | pdb_00001ev3

Structure of the rhombohedral form of the M-cresol/insulin R6 hexamer


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.78 Å
  • R-Value Free:&nbsp
    0.266 (Depositor)&nbsp
  • R-Value Work:&nbsp
    0.200 (Depositor), 0.200 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.200&nbsp(Depositor)&nbsp

wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


This is version 1.3 of the entry. See complete&nbsphistory.&nbsp


Literature

R6 hexameric insulin complexed with m-cresol or resorcinol.

Smith, G.D.,&nbspCiszak, E.,&nbspMagrum, L.A.,&nbspPangborn, W.A.,&nbspBlessing, R.H.

(2000) Acta Crystallogr D Biol Crystallogr&nbsp56: 1541-1548

  • DOI:&nbsphttps://doi.org/10.1107/s0907444900012749
  • Primary Citation of Related Structures: &nbsp
    1EV3, 1EV6, 1EVR

  • PubMed Abstract:&nbsp

    The structures of three R(6) human insulin hexamers have been determined. Crystals of monoclinic m-cresol-insulin, monoclinic resorcinol-insulin and rhombohedral m-cresol-insulin diffracted to 1. 9, 1.9 and 1.78 A, respectively, and have been refined to residuals of 0.195, 0.179 and 0.200, respectively. In all three structures, a phenolic derivative is found to occupy the phenolic binding site, where it forms hydrogen bonds to the carbonyl O atom of CysA6 and the N atom of CysA11. Two additional phenolic derivative binding sites were identified within or between hexamers. The structures of all three hexamers are nearly identical, although a large displacement of the N-terminus of one B chain in both monoclinic structures results from coordination to a sodium ion which is located between symmetry-related hexamers. Other minor differences in structure arise from differences in packing in the monoclinic cell compared with the rhombohedral cell. Based upon the differences in conformation of the GluB13 side chains in T(6), T(3)R(f)(3) and R(6) hexamers, the deprotonation of these side chains appears to be associated with the T-->R conformational transition.


  • Organizational Affiliation:&nbsp

    Hauptman-Woodward Medical Research Institute, 73 High Street, Buffalo, NY 14203, USA. [email protected]


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INSULIN
A, C
21N/AMutation(s): 0&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP01308&nbsp(Homo sapiens)
Explore&nbspP01308&nbsp
Go to UniProtKB: &nbspP01308
PHAROS: &nbspP01308
GTEx: &nbspENSG00000254647&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
INSULIN
B, D
30N/AMutation(s): 0&nbsp
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP01308&nbsp(Homo sapiens)
Explore&nbspP01308&nbsp
Go to UniProtKB: &nbspP01308
PHAROS: &nbspP01308
GTEx: &nbspENSG00000254647&nbsp
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands&nbsp3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CRS
Query on CRS

Download Ideal Coordinates CCD File&nbsp
E [auth A],
H [auth C],
I [auth C]
M-CRESOL
C7 H8 O
RLSSMJSEOOYNOY-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File&nbsp
F [auth B],
J [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File&nbsp
G [auth B],
K [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.78 Å
  • R-Value Free:&nbsp 0.266 (Depositor)&nbsp
  • R-Value Work:&nbsp 0.200 (Depositor), 0.200 (DCC)&nbsp
  • R-Value Observed:&nbsp0.200&nbsp(Depositor)&nbsp
Space Group:&nbspH 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.866α = 90
b = 78.866β = 90
c = 39.465γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View&nbspFull Validation Report



Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary