SMTL ID : 2x3t.2 (1 other biounit)

Glutaraldehyde-crosslinked wheat germ agglutinin isolectin 1 crystal soaked with a synthetic glycopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-dimer

Ligands

1 x DBB- DBB: GLYCOPEPTIDE(Non-functional Binders)

DBB-DBB.1: 2 residues within 4Å: Ligands: GYV.12, GYV.13 No protein-ligand interaction detected (PLIP)

6 x GYV: 2-acetamido-1-O-carbamoyl-2-deoxy-alpha-D-glucopyranose(Non-covalent)

GYV.2: 9 residues within 4Å: Chain A: D.86, S.105, W.107, F.109, E.115, F.116 Chain B: A.71, E.72 Ligands: DBB.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.107, A:E.115, A:F.116 Hydrogen bonds: A:D.86, A:S.105, A:W.107, B:E.72 GYV.4: 9 residues within 4Å: Chain A: D.129, S.148, W.150, S.152, G.158, Y.159 Chain B: G.28, D.29 Ligands: DBB.5 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.159 Hydrogen bonds: A:D.129, A:S.148, A:S.152, A:Y.159, B:D.29, B:D.29 GYV.7: 7 residues within 4Å: Chain A: P.157 Chain B: S.19, Y.21, Y.23, D.29, Y.30 Ligands: DBB.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.29 Hydrogen bonds: B:S.19 GYV.9: 7 residues within 4Å: Chain A: S.114, E.115 Chain B: S.62, Y.66, E.72, Y.73 Ligands: DBB.10 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.72, B:Y.73 Hydrogen bonds: B:S.62, A:S.114, A:E.115, A:E.115, A:E.115 GYV.12: 9 residues within 4Å: Chain A: A.71, E.72 Chain B: D.86, S.105, W.107, F.109, E.115, F.116 Ligands: DBB-DBB.1 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.115, B:F.116 Hydrogen bonds: B:D.86, B:D.86, B:S.105, A:E.72 Water bridges: A:A.71 GYV.13: 8 residues within 4Å: Chain A: S.62, Y.64, Y.66, E.72, Y.73 Chain B: S.114, E.115 Ligands: DBB-DBB.1 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.114, B:E.115, A:S.62, A:Y.73 Hydrophobic interactions: A:Y.73

4 x DBB: D-ALPHA-AMINOBUTYRIC ACID(Non-covalent)(Non-functional Binders)

DBB.3: 2 residues within 4Å: Chain A: W.107 Ligands: GYV.2 No protein-ligand interaction detected (PLIP) DBB.5: 2 residues within 4Å: Chain B: D.29 Ligands: GYV.4 No protein-ligand interaction detected (PLIP) DBB.8: 1 residues within 4Å: Ligands: GYV.7 No protein-ligand interaction detected (PLIP) DBB.10: 1 residues within 4Å: Ligands: GYV.9 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: G.124, A.125, C.126, D.129, C.153 Chain B: M.26 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.124, A:C.126, A:D.129, A:C.153 GOL.11: 10 residues within 4Å: Chain A: M.26, G.27, W.41 Chain B: G.124, A.125, C.126, T.128, D.129, Y.145, C.153 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.128, B:C.153, A:G.27, A:W.41

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

2010-06-30

Peptides

AGGLUTININ ISOLECTIN 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AGGLUTININ ISOLECTIN 1

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