3KMB

COMPLEX OF 3'-SULFO-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a selectin-like mutant of mannose-binding protein complexed with sialylated and sulfated Lewis(x) oligosaccharides.

Ng, K.K.Weis, W.I.

(1997) Biochemistry 36: 979-988

  • DOI: 10.1021/bi962564e
  • Primary Citation of Related Structures:  1KMB, 2KMB, 4KMB

  • PubMed Abstract: 
  • Rat serum mannose-binding protein in which residues 211-213 have been changed to the Lys-Lys-Lys sequence found in E-selectin binds HL-60 cells and the oligosaccharide 3'-NeuAc-Le(x). To understand how this mutant, designated K3, mimics the carbohydr ...

    Rat serum mannose-binding protein in which residues 211-213 have been changed to the Lys-Lys-Lys sequence found in E-selectin binds HL-60 cells and the oligosaccharide 3'-NeuAc-Le(x). To understand how this mutant, designated K3, mimics the carbohydrate-binding properties of E-selectin, structures of K3 alone and in complexes with 3'-NeuAc-Le(x), 3'-sulfo-Le(x) and 4'-sulfo-Le(x) have been determined at 1.95-2.1 A resolution by X-ray crystallography. The region of K3 that interacts with bound oligosaccharides superimposes closely with the corresponding region of unliganded E-selectin. In each of the oligosaccharide-protein complexes, the 2- and 3-OH of Fuc coordinate Ca2+ and form a network of cooperative hydrogen bonds with amino acid side chains that also coordinate the Ca2+. Lys211 of the K3 mutant, which corresponds to Lys111 of E-selectin, interacts with each of the three bound ligands: the N zeta atom donates a hydrogen bond to the 4-OH of Gal in 3'-NeuAc-Le(x), forms a water-mediated hydrogen bond with the 4-OH of Gal in 3'-sulfo-Le(x), and forms a salt bridge with the sulfate group of 4'-sulfo-Le(x). Lys213 packs against an otherwise exposed aromatic residue and forms a water-mediated hydrogen bond with Lys211 which may help to position that residue for interactions with bound oligosaccharides. These structures are consistent with previous mutagenesis and chemical modification studies which demonstrate the importance of the Ca2+ ligands as well as Lys111 and Lys113 for carbohydrate binding in the selectins, and they provide a structural basis for understanding the selective recognition of negatively charged Le(x) derivatives by the selectins.


    Related Citations: 
    • Trimeric Structure of a C-Type Mannose-Binding Protein
      Weis, W.I.,Drickamer, K.
      (1994) Structure 2: 1227
    • Introduction of Selectin-Like Binding Specificity Into a Homologous Mannose-Binding Protein
      Blanck, O.,Iobst, S.T.,Gabel, C.,Drickamer, K.
      (1996) J.Biol.Chem. 271: 7289


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MANNOSE-BINDING PROTEIN-A
1, 2, 3
149Rattus norvegicusGene Names: Mbl1
Find proteins for P19999 (Rattus norvegicus)
Go to UniProtKB:  P19999
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SGA
Query on SGA

Download SDF File 
Download CCD File 
1, 3
O3-SULFONYLGALACTOSE
C6 H12 O9 S
HHRMGTRTCHNCRO-FDROIEKHSA-N
 Ligand Interaction
MAG
Query on MAG

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Download CCD File 
1
BETA-METHYL-N-ACETYL-D-GLUCOSAMINE
C9 H17 N O6
ZEVOCXOZYFLVKN-JGKVKWKGSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
1, 2, 3
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
1, 2, 3
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
1, 2, 3
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
3
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.100α = 90.00
b = 84.900β = 106.60
c = 97.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance