2BVE

Structure of the N-terminal of Sialoadhesin in complex with 2-Phenyl- Prop5Ac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic and in Silico Analysis of the Sialoside-Binding Characteristics of the Siglec Sialoadhesin.

Zaccai, N.R.May, A.P.Robinson, R.C.Burtnick, L.D.Crocker, P.Brossmer, R.Kelm, S.Jones, E.Y.

(2007) J.Mol.Biol. 365: 1469

  • DOI: 10.1016/j.jmb.2006.10.084

  • PubMed Abstract: 
  • The Siglec family of receptors mediates cell-surface interactions through recognition of sialylated glycoconjugates. Previously reported structures of the N-terminal domain of the Siglec sialoadhesin (SnD1) in complex with various sialic acid analogs ...

    The Siglec family of receptors mediates cell-surface interactions through recognition of sialylated glycoconjugates. Previously reported structures of the N-terminal domain of the Siglec sialoadhesin (SnD1) in complex with various sialic acid analogs revealed the structural template for sialic acid binding. To characterize further the carbohydrate-binding properties, we have determined the crystal structures of SnD1 in the absence of ligand, and in complex with 2-benzyl-Neu5NPro and 2-benzyl-Neu5NAc. These structures reveal that SnD1 undergoes very few structural changes on ligand binding and detail how two novel classes of sialic acid analogs bind, one of which unexpectedly can induce Siglec dimerization. In conjunction with in silico analysis, this set of structures informs us about the design of putative ligands with enhanced binding affinities and specificities to different Siglecs, and provides data with which to test the effectiveness of different computational drug design protocols.


    Organizational Affiliation

    CR-UK Receptor Structure Research Group, Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Headington, Oxford OX3 7BN, UK. nathan.zaccai@bristol.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SIALOADHESIN
A, B
119Mus musculusGene Names: Siglec1 (Sa, Sn)
Find proteins for Q62230 (Mus musculus)
Go to UniProtKB:  Q62230
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PH5
Query on PH5

Download SDF File 
Download CCD File 
A, B
2-PHENYL-PROP5AC
C19 H27 N O9
XDURJXFZCXMSHL-YZKZVDITSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PH5IC50: 215000 nM BINDINGMOAD
PH5IC50: 215000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 31.974α = 90.00
b = 70.961β = 90.00
c = 102.650γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance