SMTL ID : 5j50.2 (1 other biounit)

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

Coordinates

PDB Format

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: 11 residues within 4Å: Chain A: G.1, F.47, Y.78, V.80, G.121, Y.122, W.123, D.125 Chain B: A.16 Ligands: PEG.3, NPO.6 2 PLIP interactions: 2 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: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.9 2 PLIP interactions: 2 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, C:G.1 Water bridges: C:Y.78, C:V.79

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: G.1 Ligands: A2G-GAL.1, A2G-GAL.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.1

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

EDO.4: 5 residues within 4Å: Chain A: N.16, L.17, D.27, P.53, V.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.27, A:D.27, A:V.54, A:V.54 EDO.5: 4 residues within 4Å: Chain A: R.13, G.36, F.60, P.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.13, A:G.36 EDO.7: 4 residues within 4Å: Chain A: T.72 Chain B: W.14, G.15 Chain C: N.105 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:G.15, B:G.15, C:N.105 Water bridges: C:N.105, A:P.103 EDO.8: 4 residues within 4Å: Chain C: Y.64, N.110, G.111, L.112 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.110, C:G.111 EDO.10: 4 residues within 4Å: Chain A: N.105 Chain C: F.104 Chain D: W.14, G.15 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: A:N.105, D:P.13, D:G.15 Water bridges: A:N.105, C:P.103

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:W.123 Hydrogen bonds: A:Y.122 Water bridges: A:Y.78 pi-Stacking: A:Y.122 NPO.9: 5 residues within 4Å: Chain C: S.76, Y.78, Y.122, W.123 Ligands: A2G-GAL.2 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.78, C:W.123 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
E

C
G

B
F

D
H

Agglutinin alpha chain

Agglutinin beta-3 chain

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