SMTL ID : 4zfu.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 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: 12 residues within 4Å: Chain B: L.62, A.63, T.64, A.66, L.67, Y.80, L.81, D.84, 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

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(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: S.42, V.43, R.48 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.42, A:R.48 Water bridges: A:V.43, A:I.45 GOL.7: 3 residues within 4Å: Chain B: Y.37, Q.42 Ligands: A2G.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.37, B:Y.37, B:Q.42

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

NAG.4: 3 residues within 4Å: Chain A: N.87, N.108, S.113 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.108

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 8 residues within 4Å: Chain A: D.70, G.72, N.109, F.111, E.160, K.163, E.191, W.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.163 Water bridges: A:E.191

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.6: 10 residues within 4Å: Chain B: D.22, V.23, Y.24, G.25, A.26, Y.37, Q.42, N.44, R.112 Ligands: GOL.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Q.42 Hydrogen bonds: B:D.22, B:G.25, B:Q.42, B:N.44, B:N.44

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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