SMTL ID : 4r6q.1 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-4-4-mer

Ligands

4 x NBZ: NITROBENZENE(Non-covalent)

NBZ.1: 5 residues within 4Å: Chain A: S.76, Y.78, Y.122, W.123 Ligands: GLA.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.78, A:W.123 pi-Stacking: A:Y.122 NBZ.4: 5 residues within 4Å: Chain C: S.76, Y.78, Y.122, W.123 Ligands: GLA.5 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.78, C:Y.122, C:W.123 pi-Stacking: C:Y.122 NBZ.8: 5 residues within 4Å: Chain E: S.76, Y.78, Y.122, W.123 Ligands: GLA.9 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:Y.78, E:W.123 pi-Stacking: E:Y.122 NBZ.12: 4 residues within 4Å: Chain G: Y.78, Y.122, W.123 Ligands: GLA.13 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:Y.78, G:W.123 pi-Stacking: G:Y.122

4 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.2: 8 residues within 4Å: Chain A: G.1, Y.78, V.80, G.121, Y.122, W.123, D.125 Ligands: NBZ.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.1, A:G.1, A:G.121, A:Y.122, A:W.123, A:W.123 Water bridges: A:G.1, A:G.1, A:Y.78, A:Y.78 GLA.5: 9 residues within 4Å: Chain C: G.1, F.47, Y.78, V.80, G.121, Y.122, W.123, D.125 Ligands: NBZ.4 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.1, C:G.1, C:G.121, C:Y.122, C:W.123, C:W.123 Water bridges: C:Y.78 GLA.9: 9 residues within 4Å: Chain E: G.1, F.47, Y.78, V.80, G.121, Y.122, W.123, D.125 Ligands: NBZ.8 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:G.1, E:G.1, E:G.121, E:Y.122, E:W.123, E:W.123 Water bridges: E:G.1, E:Y.78 GLA.13: 9 residues within 4Å: Chain G: G.1, Y.78, V.80, G.121, Y.122, W.123, D.125 Ligands: NBZ.12, EDO.15 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

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

EDO.3: 5 residues within 4Å: Chain B: Q.2, S.3 Chain E: Y.64, N.110, G.111 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:G.111, E:G.111, B:S.3, B:S.3 Water bridges: E:N.110 EDO.6: 7 residues within 4Å: Chain C: N.16, L.17, D.27, F.28, Q.29, N.43, K.45 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.16, C:N.43, C:K.45 EDO.11: 4 residues within 4Å: Chain F: P.13, G.15, A.16, K.17 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.17, F:K.17 EDO.14: 5 residues within 4Å: Chain D: Q.2, S.3 Chain G: Y.64, N.110, G.111 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain G Water bridges: D:Q.7 Hydrogen bonds: G:G.111, G:G.111 EDO.15: 5 residues within 4Å: Chain G: G.1, S.119, D.125, Y.126 Ligands: GLA.13 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.1, G:S.119

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

IPA.7: 7 residues within 4Å: Chain C: A.8, F.9, T.10, L.34 Chain G: A.8, F.9, L.34 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.34 IPA.10: 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:A.8, E:T.10 Hydrogen bonds: A:A.8 IPA.16: 5 residues within 4Å: Chain E: N.110 Chain G: Y.130 Chain H: Q.7, T.8, I.10 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:Y.130, H:I.10 Hydrogen bonds: H:T.8

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

Related Entries With Identical Sequence