1WW4

Agrocybe cylindracea galectin complexed with NeuAca2-3lactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of a Fungal Galectin from Agrocybe cylindracea for Recognizing Sialoconjugate

Ban, M.Yoon, H.J.Demirkan, E.Utsumi, S.Mikami, B.Yagi, F.

(2005) J.Mol.Biol. 351: 695-706

  • DOI: 10.1016/j.jmb.2005.06.045
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Galectin from an edible fungus Agrocybe cylindracea (ACG) has a strong preference for N-acetylneuraminyl lactose (NeuAcalpha2-3lactose). The sugar recognition mechanism of ACG was explored by the X-ray crystallographic analyses of ligand-free ACG, an ...

    Galectin from an edible fungus Agrocybe cylindracea (ACG) has a strong preference for N-acetylneuraminyl lactose (NeuAcalpha2-3lactose). The sugar recognition mechanism of ACG was explored by the X-ray crystallographic analyses of ligand-free ACG, and its complex with lactose, 3'-sulfonyl lactose and NeuAcalpha2-3lactose. The refined structure shows that ACG is a "proto"-type galectin composed of a beta-sandwich of two antiparallel sheets, each with six strands, in contrast to the five and six strands in animal galectins. ACG dimer in solution was classified as being among the "layer"-type. The carbohydrate recognition domain (CRD) of this galectin is common to those of animal galectins, except for substitution of one residue, Ala64, which corresponds to Asn46 in human galectin 1. A five-residue insertion in ACG at positions 42-46 involving Ser44 and Asn46 modified the architecture of the sugar binding site that contributes sialic acid specificity. Furthermore, it was found that the binding of a sulfate ion near the CRD in the ligand-free form led to a change in the conformation of the loop region caused by main-chain cis/trans transition between Ser44 and Pro45.


    Organizational Affiliation

    Laboratory of Food Design and Development, Graduate school of Agriculture, Kyoto University, Kyoto, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
galectin
A, B, C, D
160Agrocybe aegeritaMutation(s): 0 
EC: 3.1.21.-
Find proteins for Q6WY08 (Agrocybe aegerita)
Go to UniProtKB:  Q6WY08
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, C, D
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
A, C, D
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
B
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
SIA
Query on SIA

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Download CCD File 
A, B, C, D
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.215 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 47.264α = 89.98
b = 57.078β = 111.73
c = 64.306γ = 90.22
Software Package:
Software NamePurpose
CNSrefinement
SAINTdata scaling
CNSphasing
SAINTdata reduction
SADIEdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance