SMTL ID : 5j50.1 (1 other biounit)

Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-mer

Ligands

2 x A2G- GAL: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G-GAL.1: 9 residues within 4Å: Chain A: G.1, F.47, Y.78, V.80, G.121, Y.122, W.123, D.125 Ligands: NPO.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.47 Hydrogen bonds: A:G.1, A:G.1, A:G.121, A:Y.122, A:W.123, A:W.123, A:G.1 Water bridges: A:Y.78, A:S.119, A:D.125, A:G.1, A:V.79 A2G-GAL.2: 10 residues within 4Å: Chain C: G.1, F.47, Y.78, V.80, G.121, Y.122, W.123, D.125 Chain D: A.16 Ligands: NPO.7 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.47 Hydrogen bonds: C:G.1, C:G.1, C:G.121, C:Y.122, C:W.123, C:W.123 Water bridges: C:G.1, C:V.79, C:D.125

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: K.2, K.45, S.46, F.47 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.2, A:K.45, A:S.46, A:F.47 EDO.4: 4 residues within 4Å: Chain A: Y.19, P.95, Y.96, G.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.97, A:G.97 EDO.5: 3 residues within 4Å: Chain A: S.57, E.63, Y.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.63, A:Y.93 EDO.8: 5 residues within 4Å: Chain C: G.73, N.74, R.82, S.100, G.101 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.74, C:R.82 EDO.9: 2 residues within 4Å: Chain C: K.55, S.57 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.57 Water bridges: C:K.55, C:K.55 EDO.10: 3 residues within 4Å: Chain C: R.13, V.31, P.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.13 EDO.11: 2 residues within 4Å: Chain C: R.13, F.60 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.13, C:R.13, C:F.60

2 x NPO: P-NITROPHENOL(Non-covalent)

NPO.6: 5 residues within 4Å: Chain A: S.76, Y.78, Y.122, W.123 Ligands: A2G-GAL.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.78, A:Y.122, A:W.123 Water bridges: A:Y.78 pi-Stacking: A:Y.122 NPO.7: 3 residues within 4Å: Chain C: Y.78, Y.122 Ligands: A2G-GAL.2 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.78 Water bridges: C:Y.78, C:Y.78 pi-Stacking: C:Y.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abhinav, K.V. et al., Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP. To Be Published

Release Date

2017-02-08

Peptides

Agglutinin alpha chain: AC
Agglutinin beta-3 chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Agglutinin alpha chain

Agglutinin beta-3 chain

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