SMTL ID : 4r6n.3 (2 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

hetero-4-4-mer

Ligands

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

MBG.1: 8 residues within 4Å: Chain A: G.1, Y.78, V.80, G.121, Y.122, W.123, D.125 Ligands: IPA.4 7 PLIP interactions: 7 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:Y.78 MBG.15: 7 residues within 4Å: Chain E: G.1, Y.78, V.80, G.121, Y.122, W.123, D.125 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.1, E:G.1, E:G.121, E:Y.122, E:W.123, E:W.123 MBG.22: 8 residues within 4Å: Chain G: G.1, Y.78, V.80, G.121, Y.122, W.123, D.125 Ligands: IPA.23 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

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

IPA.2: 6 residues within 4Å: Chain A: S.69, G.70, S.83, L.84, T.85, P.95 Ligand excluded by PLIP IPA.3: 6 residues within 4Å: Chain A: A.8, F.9 Chain E: A.8, F.9, T.10, L.34 Ligand excluded by PLIP IPA.4: 3 residues within 4Å: Chain A: G.1, F.47 Ligands: MBG.1 Ligand excluded by PLIP IPA.5: 6 residues within 4Å: Chain A: L.34, N.35, S.37 Chain E: D.6, F.9, Y.39 Ligand excluded by PLIP IPA.7: 2 residues within 4Å: Chain C: G.50, F.51 Ligand excluded by PLIP IPA.8: 4 residues within 4Å: Chain B: Q.7 Chain C: N.110, G.111, L.133 Ligand excluded by PLIP IPA.9: 7 residues within 4Å: Chain C: A.8, F.9, T.10, L.34 Chain G: A.8, F.9, L.34 Ligand excluded by PLIP IPA.10: 2 residues within 4Å: Chain C: N.74, G.77 Ligand excluded by PLIP IPA.12: 6 residues within 4Å: Chain A: N.110 Chain C: Y.130 Chain D: Q.7, T.8, I.10 Ligands: IPA.13 Ligand excluded by PLIP IPA.13: 6 residues within 4Å: Chain C: A.8 Chain D: S.6, T.8 Chain G: T.10, N.35 Ligands: IPA.12 Ligand excluded by PLIP IPA.16: 2 residues within 4Å: Chain E: Y.39, V.40 Ligand excluded by PLIP IPA.17: 4 residues within 4Å: Chain E: T.92, Y.93, G.94, Y.96 Ligand excluded by PLIP IPA.18: 3 residues within 4Å: Chain E: G.50, F.51, T.52 Ligand excluded by PLIP IPA.19: 7 residues within 4Å: Chain E: N.16, D.27, Q.29, N.43, K.45, P.53 Ligands: EDO.21 Ligand excluded by PLIP IPA.23: 2 residues within 4Å: Chain G: Y.122 Ligands: MBG.22 Ligand excluded by PLIP IPA.24: 5 residues within 4Å: Chain G: G.73, N.74, R.82, S.100, G.101 Ligand excluded by PLIP IPA.25: 4 residues within 4Å: Chain E: N.110 Chain H: Q.7, T.8, I.10 Ligand excluded by PLIP IPA.26: 3 residues within 4Å: Chain G: V.79 Chain H: A.16, K.17 Ligand excluded by PLIP

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

EDO.6: 5 residues within 4Å: Chain A: Y.64, N.110, G.111, L.112 Chain F: S.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:G.111, A:G.111, F:S.3, F:S.3 Water bridges: A:Y.64 EDO.11: 6 residues within 4Å: Chain C: N.16, L.17, D.27, N.43, K.45, P.53 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.17, C:N.43, C:N.43 Water bridges: C:V.54 EDO.14: 5 residues within 4Å: Chain C: T.72, F.104 Chain D: W.14, G.15, A.16 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.15, D:A.16 Water bridges: A:N.105, A:N.105 EDO.20: 4 residues within 4Å: Chain E: E.109 Chain G: K.117, Y.126, S.128 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:K.117, G:S.128, G:S.128 EDO.21: 3 residues within 4Å: Chain E: D.27, P.53 Ligands: IPA.19 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.27, E:K.45 Water bridges: E:G.50

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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