SMTL ID : 4zfw.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.54 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(Non-functional Binders)

NAG-NAG.1: 13 residues within 4Å: Chain B: L.62, A.63, T.64, A.66, L.67, Y.80, L.81, D.84, G.86, W.87, N.97, S.99, S.100 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.80

1 x NAG- NAG- BMA- XYP- FUC: beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG-NAG-BMA-XYP-FUC.2: 3 residues within 4Å: Chain B: R.33, N.72, N.114 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Post Translational Modification)(Non-covalent)

GOL.3: 8 residues within 4Å: Chain A: G.128, I.129, M.130, S.174, M.178, E.179, D.180 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.129, A:M.130, A:S.174, A:D.180 GOL.4: 3 residues within 4Å: Chain A: M.130, D.180 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.180

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

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:N.87

1 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.6: 9 residues within 4Å: Chain B: D.22, V.23, Y.24, G.25, Y.37, Q.42, N.44, R.112 Ligands: GAL.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.22, B:G.25, B:Q.42, B:N.44, B:N.44, B:R.112 Water bridges: B:R.112

1 x GAL: beta-D-galactopyranose(Post Translational Modification)

GAL.7: 9 residues within 4Å: Chain B: D.22, V.23, Y.24, G.25, Y.37, Q.42, N.44, R.112 Ligands: GLA.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.22, B:G.25, B:Q.42, B:N.44, B:N.44, B:R.112 Water bridges: B:R.112

Links

RCSB   PDBe   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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