SMTL ID : 4r6r.1 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

hetero-4-4-mer

Ligands

3 x 147: 4-nitrophenyl beta-D-galactopyranoside(Non-covalent)

147.1: 8 residues within 4Å: Chain A: G.1, F.47, Y.78, V.80, G.121, Y.122, W.123, D.125 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.1, A:G.1, A:G.121, A:Y.122, A:W.123 147.13: 8 residues within 4Å: Chain E: G.1, S.76, Y.78, V.80, G.121, Y.122, W.123, D.125 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:Y.78, E:Y.122, E:W.123 Hydrogen bonds: E:G.1, E:G.1, E:G.121, E:Y.122, E:W.123, E:W.123 pi-Stacking: E:Y.122 147.14: 7 residues within 4Å: Chain G: G.1, Y.78, V.80, G.121, Y.122, W.123, D.125 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:Y.78, G:Y.122 Hydrogen bonds: G:G.1, G:G.1, G:G.121, G:Y.122, G:W.123, G:W.123 pi-Stacking: G:Y.122

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

EDO.2: 2 residues within 4Å: Chain A: K.55, S.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.55 Water bridges: A:S.57 EDO.3: 6 residues within 4Å: Chain A: L.34, N.35, S.37 Chain E: D.6, F.9, Y.39 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:D.6, A:S.37 EDO.4: 2 residues within 4Å: Chain A: T.23, S.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.76 EDO.5: 2 residues within 4Å: Chain A: P.38, V.40 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: F.4, D.5, Q.42, H.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.5 Water bridges: A:A.3, A:Q.42 EDO.8: 2 residues within 4Å: Chain C: T.23, W.123 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain C: Y.19, P.95, Y.96, G.97 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.19, C:G.97 EDO.10: 3 residues within 4Å: Chain C: F.51, T.52, P.53 No protein-ligand interaction detected (PLIP) EDO.11: 2 residues within 4Å: Chain C: P.53, K.55 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.16, C:K.55 EDO.12: 5 residues within 4Å: Chain D: S.3 Chain G: Y.64, N.110, G.111, L.112 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain D Hydrogen bonds: G:N.110, G:G.111, G:G.111, D:S.3, D:S.3 Water bridges: G:L.133

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

IPA.7: 5 residues within 4Å: Chain A: T.72, G.73, N.74, G.101, T.102 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.74 Hydrogen bonds: A:N.74

Links

RCSB   PDBe   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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