Oxford University Press - Online Resource Centres

Taylor & Drickamer: Introduction to Glycobiology 3e

Links to proteins

A library of 3D molecular structures is provided below to help you visualize a number structures in the book. Links are provided to the 3D structures on the Research Collaboratory for Structural Bionformations (RSCB) Protein Data Bank website (www.rcsb.org/pdb/home/home.do).

Section 5.3 - Figure 5.4, GlcNAc transferase I
1FOA:  http://www.rcsb.org/pdb/explore/jmol.do?structureId=1FOA&bionumber=1
With UDP-GlcNAc donor and Mn2+ binding to DXD motif; acceptor is modeled in the figure

Section 5.3 - Figure 5.5, Blood group A transferase
1LZI: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1LZI&bionumber=1
With bound UDP and fucose acceptor; donor GalNAc is modeled in the figure

Section 5.3 - Figure 5.5, Blood group B transferase
1LZJ: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1LZJ&bionumber=1
With bound UDP and fucose acceptor; donor galactose is modeled in the figure

Section 7.5 - Figure 7.8, Langerin
3P5F: http://www.rcsb.org/pdb/explore/jmol.do?structureId=3P5F&bionumber=1
Langerin with Mana1-2Man in binding site. The sugar conformation can be viewed by selecting residues 401 and 402 in chain C and hiding residue 450, an alternative orientation of mannose in the binding site.

Section 7.5 - Figure 7.9 - Mannose-binding protein mutant with bound sialyl Lewisx
2KMB: http://www.rcsb.org/pdb/explore/jmol.do?structureId=2KMB&bionumber=1
Sialyl Lewisx conformation can be viewed by selecting chain 3 residues 222 - 225

Section 8.2 - Figure 8.2 - CD2
1GYA: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1GYA
Complete N-linked glycan seen in NMR structure

Section 8.3 - Figure 8.4 - Trypanosome variant surface glycoprotein MITat 1.2
1VSG: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1VSG&bionumber=1
Structure with N-linked glycan

Section 8.3 - Figure 8.4, Trypanosome variant surface glycoprotein ILTat 1.24
2VSG: http://www.rcsb.org/pdb/explore/jmol.do?structureId=2VSG&bionumber=1
Structure with Eo helix

Section 8.5 - Figure 8.6, IgG
1FC1: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1FC1&bionumber=1
N-linked glycans in Fc region are inside the protein

Section 9.3 - Figure 9.3/9.4, Mannose-binding protein
2MSB: http://www.rcsb.org/pdb/explore/jmol.do?structureId=2MSB&bionumber=1
Ligand binding site with mannose oligosaccharide

Section 9.3 - Figure 9.4, Mannose-binding protein
1RTM: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1RTM&bionumber=1
Trimer structure with coiled-coil neck

Section 9.6 - Figure 9.9, E-selectin
1G1T: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1G1T&bionumber=1
Shows EGF domain plus CRD with sialyl Lewisx in the binding site

Section 9.7 - Figure 9.11, DC-SIGN
1K9J: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1K9J&bionumber=1
Ligand bound is Man3GlcNAc2, used as a model for Man5

Section 9.10 - Figure 9.15, Sialoadhesin
1QFO  http://www.rcsb.org/pdb/explore/jmol.do?structureId=1QFO&bionumber=1
With bound sialyl lactose

Section 9.11 - Figure 9.18/9.19, Galectin-1
1HLC: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1HLC&bionumber=1
Lactose in binding site. Dimer organization
Section 10.6 - Figure 10.7, Cation-dependent mannose 6-phosphate receptor
1C39: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1C39&bionumber=1
Binding site has Mn2+ and Man3 with terminal residue bearing 6-PO4

Section 10.7 - Figure 10.10, Galactose-binding C-type carbohydrate-recognition domain
1AFA: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1AFA&bionumber=1
Mechanism of C-type lectin binding to b-methyl galactoside

Section 11.4 - Figure 11.5, Concanavalin A
1CVN: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1CVN&bionumber=1
Mechanism for L-type lectin binding to Man3 structure bound

Section 11.5 - Figure 11.7, Ricin toxin
2AAI: http://www.rcsb.org/pdb/explore/jmol.do?structureId=2AAI&bionumber=1
R-type lectin with lactose in the ligand-binding site (also has attached N-linked glycans)

Section 11.5 - Figure 11.7, Mannose receptor
1DQO: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1DQO&bionumber=1
R-type carbohydrate-recognition domain with SO4-4GalNAc in the binding site

Section 11.6 - Figure 11.8, Cholera toxin
2CHB: http://www.rcsb.org/pdb/explore/jmol.do?structureId=2CHB&bionumber=1
Pentamer of B subunit with each subunit bound to GM1 headgroup

Section 11.7 - Figure 11.9, PapG bacterial pilus adhesin
1J8R: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1J8R&bionumber=1
With glycolipid headgroup bound

Section 11.11 - Figure 11.10, Influenza virus haemagglutinin
1HGG: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1HGG&bionumber=1
Sialic acid in binding site

Section 11.11 - Figure 11.11, Influenza virus haemagglutinin
1RVX: http://www.rcsb.org/pdb/explore/explore.do?structureId=1RVX
Preference for a1-3 linked NeuAc

Section 11.11 - Figure 11.11, Influenza virus haemagglutinin
1RVZ: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1RVZ&bionumber=1
Preference for a1-6 linked NeuAc

Section 12.1 - Figure 12.2, Fibroblast growth factor / receptor / heparan sulphate complex
1E0O: http://www.rcsb.org/pdb/explore/jmol.do?structureId=1E0O&bionumber=1
Bridging function of heparan sulphate is illustrated