SMTL ID : 4r6p.1 (2 other biounits)

Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-4-4-mer

Ligands

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

IPA.1: 6 residues within 4Å: Chain A: Y.64, N.110, G.111, L.112, L.133 Chain F: S.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.64, A:L.112 Hydrogen bonds: A:N.110, A:G.111 Water bridges: A:Y.64 IPA.2: 7 residues within 4Å: Chain A: A.8, F.9, L.34 Chain E: A.8, F.9, T.10, L.34 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:T.10, A:L.34 Water bridges: E:F.9 IPA.3: 1 residues within 4Å: Chain C: V.40 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.40 IPA.5: 6 residues within 4Å: Chain E: Y.78, V.80, G.121, Y.122, W.123, D.125 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:Y.78, E:V.80, E:W.123 Hydrogen bonds: E:Y.122

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

EDO.4: 7 residues within 4Å: Chain C: A.8, F.9, T.10, L.34 Chain G: A.8, F.9, L.34 2 PLIP interactions: 2 interactions with chain H Water bridges: H:S.6, H:T.8

1 x ZZ1: 4-METHYL-2H-CHROMEN-2-ONE(Non-covalent)

ZZ1.6: 5 residues within 4Å: Chain G: S.76, Y.78, Y.122, W.123 Ligands: GAL.7 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:Y.78, G:Y.122, G:Y.122 Hydrogen bonds: G:S.76

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.7: 8 residues within 4Å: Chain G: G.1, Y.78, V.80, G.121, Y.122, W.123, D.125 Ligands: ZZ1.6 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:G.1, G:G.1, G:G.121, G:Y.122, G:W.123, G:W.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abhinav, K.V. et al., Jacalin-carbohydrate interactions: distortion of the ligand molecule as a determinant of affinity. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-02-18

Peptides

Agglutinin alpha chain: ACEG
Agglutinin beta-3 chain: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

Agglutinin alpha chain

Agglutinin beta-3 chain

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