3IRK

Solution Structure of Heparin dp30


Experimental Data Snapshot

ERROR: Experimental Data Snapshots data not found.

wwPDB Validation

Currently 3irk does not have a wwPDB validation report.


This is version 1.1 of the entry. See complete history

Literature

Semi-rigid solution structures of heparin by constrained X-ray scattering modelling: new insight into heparin-protein complexes.

Khan, S.Gor, J.Mulloy, B.Perkins, S.J.

(2010) J.Mol.Biol. 395: 504-521

  • DOI: 10.1016/j.jmb.2009.10.064
  • Primary Citation of Related Structures:  3IRI, 3IRJ, 3IRL

  • PubMed Abstract: 
  • The anionic polysaccharides heparin and heparan sulphate play essential roles in the regulation of many physiological processes. Heparin is often used as an analogue for heparan sulphate. Despite knowledge of an NMR solution structure and 19 crystal ...

    The anionic polysaccharides heparin and heparan sulphate play essential roles in the regulation of many physiological processes. Heparin is often used as an analogue for heparan sulphate. Despite knowledge of an NMR solution structure and 19 crystal structures of heparin-protein complexes for short heparin fragments, no structures for larger heparin fragments have been reported up to now. Here, we show that solution structures for six purified heparin fragments dp6-dp36 (where dp stands for degree of polymerisation) can be determined by a combination of analytical ultracentrifugation, synchrotron X-ray scattering, and constrained modelling. Analytical ultracentrifugation velocity data for dp6-dp36 showed sedimentation coefficients that increased linearly from 1.09 S to 1.84 S with size. X-ray scattering of dp6-dp36 gave radii of gyration R(G) that ranged from 1.33 nm to 3.12 nm and maximum lengths that ranged from 3.0 nm to 12.3 nm. The higher resolution of X-ray scattering revealed an increased bending of heparin with increased size. Constrained molecular modelling of 5000 randomised heparin conformers resulted in 9-15 best-fit structures for each of dp18, dp24, dp30, and dp36 that indicated flexibility and the presence of short linear segments in mildly bent structures. Comparisons of these solution structures with crystal structures of heparin-protein complexes revealed similar ranges of phi (phi) and psi (psi) angles between iduronate and glucosamine rings. We conclude that heparin in solution has a semi-rigid and extended conformation that is preformed for its optimal binding to protein targets without major conformational changes.


    Organizational Affiliation

    Department of Structural and Molecular Biology, Division of Biosciences, Darwin Building, University College London, Gower Street, London WC1E 6BT, UK.




Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SGN
Query on SGN

Download SDF File 
Download CCD File 
A
N,O6-DISULFO-GLUCOSAMINE
C6 H13 N O11 S2
DQTRACMFIGDHSN-UKFBFLRUSA-N
 Ligand Interaction
IDS
Query on IDS

Download SDF File 
Download CCD File 
A
2-O-sulfo-alpha-L-idopyranuronic acid
O2-SULFO-GLUCURONIC ACID
C6 H10 O10 S
COJBCAMFZDFGFK-VCSGLWQLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

ERROR: Experimental Data Snapshots data not found.
Software Package:
Software NamePurpose
GNOMmodel building
SCTPL7phasing
DISCOVERYrefinement
Localdata reduction
IDO2data scaling
INSIGHTrefinement
GNOMphasing
SCTPL7model building
Localdata collection

Structure Validation

Currently 3IRK does not have a wwPDB validation report.



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance