SMTL ID : 2uvo.1 (1 other biounit)

High Resolution Crystal Structure of Wheat Germ Agglutinin in Complex with N-Acetyl-D-Glucosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

5 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.1: 8 residues within 4Å: Chain A: S.62, Y.64, Y.66, E.72, Y.73 Chain B: S.114, E.115 Ligands: NAG.2 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.72, A:Y.73 Hydrogen bonds: A:S.62, A:Y.73, A:Y.73, B:S.114, B:E.115, B:E.115 Water bridges: A:S.43, B:S.114 NDG.3: 8 residues within 4Å: Chain A: D.86, S.105, W.107, F.109, E.115, F.116 Chain B: A.71, E.72 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:W.107, A:E.115, A:F.116 Hydrogen bonds: A:D.86, A:S.105, B:A.71, B:E.72, B:E.72, B:E.72 Water bridges: B:R.84, B:R.84 NDG.7: 8 residues within 4Å: Chain A: S.114, E.115 Chain B: S.62, Y.64, Y.66, E.72, Y.73 Ligands: NAG.8 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:S.114, A:E.115, A:E.115, B:S.62, B:Y.73 Water bridges: A:E.115, B:S.43, B:S.43, B:Y.73 Hydrophobic interactions: B:E.72, B:Y.73 NDG.9: 8 residues within 4Å: Chain A: A.71, E.72 Chain B: D.86, S.105, W.107, F.109, E.115, F.116 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:E.115, B:F.116 Hydrogen bonds: B:D.86, B:S.105, A:A.71, A:E.72, A:E.72, A:E.72 Water bridges: A:R.84, A:R.84 NDG.10: 9 residues within 4Å: Chain A: G.28, D.29 Chain B: D.129, S.148, W.150, S.152, G.158, Y.159 Ligands: NAG.11 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.159 Hydrogen bonds: B:D.129, B:S.148, B:S.152, B:S.152, B:Y.159, A:G.28, A:D.29, A:D.29 Water bridges: B:C.153

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 8 residues within 4Å: Chain A: S.62, Y.64, Y.66, E.72, Y.73 Chain B: S.114, E.115 Ligands: NDG.1 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.72, A:Y.73 Hydrogen bonds: A:S.62, A:Y.73, A:Y.73, B:S.114, B:E.115 Water bridges: A:S.43, B:S.114 NAG.4: 8 residues within 4Å: Chain A: D.129, S.148, W.150, S.152, G.158, Y.159 Chain B: G.28, D.29 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:G.28, B:D.29, B:D.29, B:D.29, A:D.129, A:S.148, A:S.152, A:Y.159, A:Y.159 Hydrophobic interactions: A:Y.159 Water bridges: A:D.129 NAG.6: 6 residues within 4Å: Chain A: P.157 Chain B: S.19, Y.21, Y.23, D.29, Y.30 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.29, B:Y.30 Hydrogen bonds: B:S.19, B:Y.30, B:Y.30 NAG.8: 8 residues within 4Å: Chain A: S.114, E.115 Chain B: S.62, Y.64, Y.66, E.72, Y.73 Ligands: NDG.7 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:S.114, A:E.115, B:S.62, B:Y.73 Hydrophobic interactions: B:E.72, B:Y.73 Water bridges: B:S.43, B:S.43, B:Y.73 NAG.11: 9 residues within 4Å: Chain A: G.28, D.29 Chain B: D.129, S.148, W.150, S.152, G.158, Y.159 Ligands: NDG.10 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.159 Hydrogen bonds: B:D.129, B:S.148, B:S.152, B:S.152, B:Y.159, A:G.28, A:D.29, A:D.29 Water bridges: B:C.153

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: G.124, A.125, C.126, D.129, Y.145, C.153 Chain B: M.26, G.27, W.41 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.125, A:D.129 Water bridges: A:K.130, A:C.153, A:C.153, B:G.27 GOL.12: 9 residues within 4Å: Chain A: M.26, G.27, W.41 Chain B: G.124, A.125, C.126, Y.145, C.153, G.154 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:C.126, B:T.128 Water bridges: B:R.139, B:C.153, A:G.27

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

2008-05-27

Peptides

AGGLUTININ ISOLECTIN 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AGGLUTININ ISOLECTIN 1

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