SMTL ID : 5j51.1 (1 other biounit)

Structure of tetrameric jacalin complexed with Gal alpha-(1,4) Gal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

hetero-2-2-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: A.3, F.4, K.117, G.118, Y.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.117, A:K.117, A:Y.126, A:Y.126 EDO.2: 2 residues within 4Å: Chain A: N.16, N.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.16, A:N.43 EDO.3: 3 residues within 4Å: Chain A: S.46, F.47, T.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.46 EDO.9: 6 residues within 4Å: Chain B: Q.7 Chain C: N.110, G.111, L.112, L.133 Ligands: EDO.10 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.110, C:N.110, B:Q.7 EDO.10: 6 residues within 4Å: Chain C: Y.64, N.110, G.111, L.112 Ligands: EDO.9, EDO.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.111, C:G.111 EDO.11: 2 residues within 4Å: Chain C: Y.64 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.64, C:Y.64 EDO.12: 5 residues within 4Å: Chain C: F.4, D.5, D.6, Q.42, H.44 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.5, C:D.6 Water bridges: C:Q.42, C:Q.42 EDO.13: 6 residues within 4Å: Chain C: N.16, L.17, D.27, N.43, K.45, P.53 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.43, C:N.43 Water bridges: C:V.54 EDO.14: 4 residues within 4Å: Chain C: Y.19, N.20, K.21, T.52 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.21, C:T.52 Water bridges: C:E.22 EDO.15: 1 residues within 4Å: Chain C: V.40 No protein-ligand interaction detected (PLIP) EDO.16: 2 residues within 4Å: Chain C: Q.42, N.43 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.42, C:N.43 EDO.17: 2 residues within 4Å: Chain C: K.55, Y.96 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.55 EDO.18: 1 residues within 4Å: Chain C: P.53 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.55 Water bridges: C:V.54

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

IPA.4: 2 residues within 4Å: Chain A: V.40 Ligands: IPA.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.40 IPA.5: 1 residues within 4Å: Ligands: IPA.4 No protein-ligand interaction detected (PLIP) IPA.6: 3 residues within 4Å: Chain A: R.13, F.60, P.61 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.60 Hydrogen bonds: A:R.13, A:F.60 IPA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) IPA.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 6 residues within 4Å: Chain A: Y.78, V.80, G.121, Y.122, W.123, D.125 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.121, A:Y.122, A:W.123, A:W.123 Water bridges: A:G.1, A:G.1, A:G.1

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Abhinav, K.V. et al., Effect of linkage on the location of reducing and nonreducing sugars bound to jacalin. IUBMB Life (2016)

Release Date

2016-12-14

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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