SMTL ID : 4zlb.1

Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd) in complex with lactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 11 residues within 4Å: Chain B: L.62, A.63, T.64, A.66, L.67, L.81, D.84, G.86, W.87, N.97, S.100 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.2: 4 residues within 4Å: Chain B: R.33, N.72, N.114 Ligands: NAG-BMA.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.72, B:N.114 Water bridges: B:N.114, B:N.114

1 x NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-BMA.3: 3 residues within 4Å: Ligands: NAG-FUC.2, NAG-FUC.2, XYP.6 No protein-ligand interaction detected (PLIP)

1 x BGC- GAL: beta-D-galactopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-GAL.4: 8 residues within 4Å: Chain B: D.22, V.23, Y.24, G.25, Y.37, Q.42, N.44, R.112 6 PLIP interactions: 6 interactions with chain B Water bridges: B:Y.24 Hydrogen bonds: B:D.22, B:G.25, B:Q.42, B:N.44, B:N.44, B:R.112

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.5: 4 residues within 4Å: Chain A: Q.86, N.87, N.108, S.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.86

1 x XYP: beta-D-xylopyranose(Non-functional Binders)

XYP.6: 2 residues within 4Å: Ligands: NAG-BMA.3, NAG-BMA.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandran, T. et al., Structural studies on a non-toxic homologue of type II RIPs from bitter gourd: Molecular basis of non-toxicity, conformational selection and glycan structure. J.Biosci. (2015)

Release Date

2016-03-23

Peptides

rRNA N-glycosidase: A
rRNA N-glycosidase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

rRNA N-glycosidase

rRNA N-glycosidase

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