1AFB

STRUCTURAL BASIS OF GALACTOSE RECOGNITION IN C-TYPE ANIMAL LECTINS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis of galactose recognition by C-type animal lectins.

Kolatkar, A.R.Weis, W.I.

(1996) J Biol Chem 271: 6679-6685

  • Primary Citation of Related Structures:  
    1AFD, 1AFB, 1AFA

  • PubMed Abstract: 
  • The asialoglycoprotein receptors and many other C-type (Ca2+-dependent) animal lectins specifically recognize galactose- or N-acetylgalactosamine-terminated oligosaccharides. Analogous binding specificity can be engineered into the homologous rat mannose-binding protein A by changing three amino acids and inserting a glycine-rich loop (Iobst, S ...

    The asialoglycoprotein receptors and many other C-type (Ca2+-dependent) animal lectins specifically recognize galactose- or N-acetylgalactosamine-terminated oligosaccharides. Analogous binding specificity can be engineered into the homologous rat mannose-binding protein A by changing three amino acids and inserting a glycine-rich loop (Iobst, S. T., and Drickamer, K. (1994) J. Biol. Chem. 269, 15512-15519). Crystal structures of this mutant complexed with beta-methyl galactoside and N-acetylgalactosamine (GalNAc) reveal that as with wild-type mannose-binding proteins, the 3- and 4-OH groups of the sugar directly coordinate Ca2+ and form hydrogen bonds with amino acids that also serve as Ca2+ ligands. The different stereochemistry of the 3- and 4-OH groups in mannose and galactose, combined with a fixed Ca2+ coordination geometry, leads to different pyranose ring locations in the two cases. The glycine-rich loop provides selectivity against mannose by holding a critical tryptophan in a position optimal for packing with the apolar face of galactose but incompatible with mannose binding. The 2-acetamido substituent of GalNAc is in the vicinity of amino acid positions identified by site-directed mutagenesis (Iobst, S. T., and Drickamer, K. (1996) J. Biol. Chem. 271, 6686-6693) as being important for the formation of a GalNAc-selective binding site.


    Related Citations: 
    • Trimeric Structure of a C-Type Mannose-Binding Protein
      Weis, W.I., Drickamer, K.
      (1994) Structure 2: 1227
    • Binding of Sugar Ligands to Ca+2-Dependent Animal Lectins II. Generation of High-Affinity Galactose Binding by Site-Directed Mutagenesis
      Iobst, S.T., Drickamer, K.
      (1994) J Biol Chem 269: 15512

    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MANNOSE-BINDING PROTEIN-AA [auth 1], B [auth 2], C [auth 3]154Rattus norvegicusMutation(s): 5 
Gene Names: Mbl1
UniProt
Find proteins for P19999 (Rattus norvegicus)
Explore P19999 
Go to UniProtKB:  P19999
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGA (Subject of Investigation/LOI)
Query on NGA

Download Ideal Coordinates CCD File 
D [auth 1], I [auth 2], M [auth 3]2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth 1] , F [auth 1] , G [auth 1] , J [auth 2] , K [auth 2] , L [auth 2] , N [auth 3] , O [auth 3] , 
E [auth 1],  F [auth 1],  G [auth 1],  J [auth 2],  K [auth 2],  L [auth 2],  N [auth 3],  O [auth 3],  P [auth 3]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth 1], Q [auth 3]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.8α = 90
b = 84.5β = 104.3
c = 97.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary