PDBsum entry 8ybe

Sugar binding protein

PDB id: 8ybe

Contents

Protein chain

370 a.a.

Ligands

GLC-GLC

Waters ×197

References listed in PDB file

Key reference

Title

Atomic resolution structure of mbp using cryo-Em

Authors

Y.Yoo, K.Park, H.Kim.

Ref.

TO BE PUBLISHED ...

Secondary reference #1

Title

Crystal structures of the maltodextrin/maltose-Binding protein complexed with reduced oligosaccharides: flexibility of tertiary structure and ligand binding.

Authors

X.Duan, J.A.Hall, H.Nikaido, F.A.Quiocho.

Ref.

J Mol Biol, 2001, 306, 1115-1126. [DOI no: 10.1006/jmbi.2001.4456]

PubMed id

11237621

Figure 2.
Figure 2. Binding of maltotriitol to the MBP closed form in the C2 space group crystal. The sugar residues are labeled -G1 for the glucitol, followed by G1, G2, and G3 for the glucose residues. (a) Difference (F[o] -F[c]) omit electron density map (blue) at 2.3 Å resolution of the maltotriitol contoured at 2s level. (b) Stereo view of the hydrogen bonds ( slant 3.4 Å) (broken lines) and stacking interactions between the maltotriitol and MBP. With the exception of E111 and E153, all the polar residues (blue color) that are involved in hydrogen-bonding interactions originate from domain I. E111 and E153 (red color) are located in domain II and the hinge connecting the two domains, respectively. The aromatic residues (colored green) originate from domain I (W62) and domain II (W230, Y155, W340).

Figure 3.
Figure 3. The binding site of MBP with bound maltotetraitol in the C2 or closed structure. The identifications of the amino acid residues and the sugar residues are identical with those shown in Figure 2. The additional Tyr341 residue originates from domain II. (a) The 2.3 Å difference electron density map of maltotetraitol patterned after Figure 2(a). (b) Stereo view of the hydrogen bonds ( slant 3.4 Å) (broken lines) and stacking interactions.

The above figures are reproduced from the cited reference with permission from Elsevier