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   PDBe-KB   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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