2HYV

Human Annexin A2 with heparin hexasaccharide bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Crystallographic analysis of calcium-dependent heparin binding to annexin A2.

Shao, C., Zhang, F., Kemp, M.M., Linhardt, R.J., Waisman, D.M., Head, J.F., Seaton, B.A.

(2006) J.Biol.Chem. 281: 31689-31695

  • DOI: 10.1074/jbc.M604502200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Annexin A2 and heparin bind to one another with high affinity and in a calcium-dependent manner, an interaction that may play a role in mediating fibrinolysis. In this study, three heparin-derived oligosaccharides of different lengths were co-crystal ...

    Annexin A2 and heparin bind to one another with high affinity and in a calcium-dependent manner, an interaction that may play a role in mediating fibrinolysis. In this study, three heparin-derived oligosaccharides of different lengths were co-crystallized with annexin A2 to elucidate the structural basis of the interaction. Crystal structures were obtained at high resolution for uncomplexed annexin A2 and three complexes of heparin oligosaccharides bound to annexin A2. The common heparin-binding site is situated at the convex face of domain IV of annexin A2. At this site, annexin A2 binds up to five sugar residues from the nonreducing end of the oligosaccharide. Unlike most heparin-binding consensus patterns, heparin binding at this site does not rely on arrays of basic residues; instead, main-chain and side-chain nitrogen atoms and two calcium ions play important roles in the binding. Especially significant is a novel calcium-binding site that forms upon heparin binding. Two sugar residues of the heparin derivatives provide oxygen ligands for this calcium ion. Comparison of all four structures shows that heparin binding does not elicit a significant conformational change in annexin A2. Finally, surface plasmon resonance measurements were made for binding interactions between annexin A2 and heparin polysaccharide in solution at pH 7.4 or 5.0. The combined data provide a clear basis for the calcium dependence of heparin binding to annexin A2.

    Organizational Affiliation: 

    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Annexin A2
A
308Homo sapiensMutation(s): 0 
Gene Names: ANXA2 (ANX2, ANX2L4, CAL1H, LPC2D)
Find proteins for P07355 (Homo sapiens)
Go to Gene View: ANXA2
Go to UniProtKB:  P07355
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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
UAP
Query on UAP
Download SDF File 
Download CCD File 
A
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid
C6 H8 O9 S
VJIMUKBSNUBECH-YKKSOZKNSA-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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.709α = 90.00
b = 54.292β = 90.00
c = 68.571γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Advisory, Refinement description