SMTL ID : 4r6n.1 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

hetero-2-2-mer

Ligands

1 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

10 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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.95 Hydrogen bonds: A:S.83, A:T.85 IPA.3: 2 residues within 4Å: Chain A: A.8, F.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.9 IPA.4: 3 residues within 4Å: Chain A: G.1, F.47 Ligands: MBG.1 No protein-ligand interaction detected (PLIP) IPA.5: 3 residues within 4Å: Chain A: L.34, N.35, S.37 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.34, A:L.34, A:N.35 Hydrogen bonds: A:S.37 IPA.7: 2 residues within 4Å: Chain C: G.50, F.51 No protein-ligand interaction detected (PLIP) IPA.8: 4 residues within 4Å: Chain B: Q.7 Chain C: N.110, G.111, L.133 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.133 Hydrogen bonds: C:N.110, B:Q.7, B:Q.7 Water bridges: C:G.111 IPA.9: 4 residues within 4Å: Chain C: A.8, F.9, T.10, L.34 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.10, C:L.34 Hydrogen bonds: C:A.8 IPA.10: 2 residues within 4Å: Chain C: N.74, G.77 No protein-ligand interaction detected (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 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.10, C:Y.130 Hydrogen bonds: D:T.8 Water bridges: D:S.6 IPA.13: 4 residues within 4Å: Chain C: A.8 Chain D: S.6, T.8 Ligands: IPA.12 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.8

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

EDO.6: 4 residues within 4Å: Chain A: Y.64, N.110, G.111, L.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.111, A:G.111 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

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: 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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