SMTL ID : 2x52.1

CRYSTAL STRUCTURE OF WHEAT GERM AGGLUTININ ISOLECTIN 3 IN COMPLEX WITH A SYNTHETIC DIVALENT CARBOHYDRATE LIGAND

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x GYT: BIS-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSYLOXYCARBONYL)-4,7,10-TRIOXA-1,13-TRIDECANEDIAMINE(Non-covalent)

GYT.1: 14 residues within 4Å: Chain A: S.62, Y.64, H.66, A.71, E.72, Y.73 Chain B: D.86, S.105, Q.106, W.107, Y.109, S.114, E.115, F.116 19 PLIP interactions: 11 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:Y.73, B:E.115, B:F.116 Hydrogen bonds: A:S.62, A:A.71, A:E.72, A:Y.73, A:Y.73, B:D.86, B:S.105, B:S.114, B:E.115, B:E.115 Water bridges: A:S.43, A:S.43, A:R.84, A:R.84, B:S.114 Salt bridges: A:H.66 GYT.2: 13 residues within 4Å: Chain A: S.19, Y.21, Y.23, G.28, D.29, Y.30 Chain B: D.129, S.148, W.150, S.152, P.157, G.158, Y.159 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Y.159, A:D.29, A:Y.30 Hydrogen bonds: B:D.129, B:S.148, B:S.152, B:Y.159, A:S.19, A:G.28, A:D.29, A:D.29, A:Y.30 Water bridges: B:C.153, B:G.158 GYT.3: 13 residues within 4Å: Chain A: D.86, S.105, W.107, Y.109, S.114, E.115, F.116 Chain B: S.62, Y.64, H.66, A.71, E.72, Y.73 18 PLIP interactions: 9 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:E.72, B:Y.73, A:E.115, A:F.116 Hydrogen bonds: B:S.62, B:A.71, B:E.72, B:Y.73, A:D.86, A:S.105, A:S.114, A:E.115, A:E.115, A:E.115 Water bridges: B:S.43, B:R.84, A:S.114 Salt bridges: B:H.66 GYT.4: 14 residues within 4Å: Chain A: D.129, S.148, W.150, S.152, P.157, G.158, Y.159 Chain B: S.19, Y.21, Y.23, G.28, D.29, Y.30, W.41 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:Y.159, B:Y.30 Hydrogen bonds: A:D.129, A:S.148, A:S.152, A:Y.159, B:S.19, B:G.28, B:D.29, B:D.29, B:Y.30 Water bridges: A:D.129, A:C.153, B:Y.23, B:Y.23

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: M.26, G.27, W.41 Chain B: G.124, A.125, C.126, D.129, Y.145, C.153, G.154 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.126, B:D.129 Water bridges: B:D.129, B:K.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schwefel, D. et al., Structural Basis of Multivalent Binding to Wheat Germ Agglutinin. J.Am.Chem.Soc. (2010)

Release Date

2010-02-23

Peptides

AGGLUTININ ISOLECTIN 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AGGLUTININ ISOLECTIN 3