SMTL ID : 6ifb.1

Structure of rhamnose bound beta-trefoil lectin from Entamoeba histolytica

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-dimer

Ligands

2 x RM4: beta-L-rhamnopyranose(Non-covalent)

RM4.1: 8 residues within 4Å: Chain A: D.23, I.24, Q.25, G.26, A.27, Y.38, H.41, N.45 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.23, A:G.26, A:A.27, A:H.41, A:N.45 RM4.4: 8 residues within 4Å: Chain B: D.23, I.24, Q.25, G.26, A.27, Y.38, H.41, N.45 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.23, B:G.26, B:A.27, B:H.41, B:N.45

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: A.27, G.43, E.44, F.61 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.44 Water bridges: A:N.45 GOL.5: 5 residues within 4Å: Chain B: Q.29, E.30, N.31, K.64, D.79 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.30, B:K.64 Water bridges: B:N.31, B:D.79, B:D.79

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

IPA.3: 5 residues within 4Å: Chain A: K.52, F.90, D.92, T.98, I.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.52 IPA.6: 3 residues within 4Å: Chain B: R.101, E.107, F.124 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.124, B:F.124 Hydrogen bonds: B:R.101, B:R.101 IPA.7: 3 residues within 4Å: Chain B: T.67, L.83, R.85 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.67 Hydrogen bonds: B:R.85, B:R.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khan, F. et al., Crystal structures of a beta-trefoil lectin from Entamoeba histolytica in monomeric and a novel disulfide bond-mediated dimeric forms. Glycobiology (2020)

Release Date

2019-09-25

Peptides

lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

lectin