SMTL ID : 5j4x.1 (1 other biounit)

Structure of tetrameric jacalin complexed with Gal beta-(1,3) Gal-beta-OMe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-2-2-mer

Ligands

1 x MBG- GAL: beta-D-galactopyranose-(1-3)-methyl beta-D-galactopyranoside(Non-covalent)

MBG-GAL.1: 8 residues within 4Å: Chain A: G.1, Y.78, V.80, G.121, Y.122, W.123, D.125 Chain B: A.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.1, A:G.1, A:G.1, A:G.121, A:Y.122, A:W.123, A:W.123 Water bridges: A:D.125

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

EDO.2: 1 residues within 4Å: Chain A: N.35 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.35 EDO.3: 2 residues within 4Å: Chain A: Y.19, K.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.19 EDO.4: 4 residues within 4Å: Chain A: Y.64, N.110, G.111, L.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.64, A:E.109, A:N.110, A:G.111 EDO.6: 3 residues within 4Å: Chain C: D.5, G.7, Y.130 No protein-ligand interaction detected (PLIP) EDO.7: 7 residues within 4Å: Chain C: N.16, L.17, S.18, D.27, Q.29, N.43, K.45 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.17, C:N.43, C:N.43 Water bridges: C:K.45, C:V.54 EDO.8: 1 residues within 4Å: Chain C: D.59 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.59, C:F.60 EDO.9: 2 residues within 4Å: Chain C: Y.122, W.123 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain A: N.110 Chain D: Q.7, T.8, I.10 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain D Water bridges: A:N.110, D:S.6, D:T.8 Hydrogen bonds: D:T.8

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.5: 5 residues within 4Å: Chain A: A.8, F.9, T.10, L.34, N.35 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abhinav, K.V. et al., Distortion of the ligand molecule as a strategy for modulating binding affinity: Further studies involving complexes of jacalin with beta-substituted disaccharides. IUBMB Life (2017)

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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