SMTL ID : 4zbv.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-FUC.1: 4 residues within 4Å: Chain B: R.33, N.72, N.114 Ligands: NAG.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.72 Water bridges: B:N.114, B:N.114

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.2: 10 residues within 4Å: Chain B: L.62, A.63, T.64, L.67, L.81, D.84, G.86, W.87, N.97, S.100 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.3: 4 residues within 4Å: Chain A: Q.86, N.87, N.108, S.113 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.86 Water bridges: A:N.108 NAG.5: 3 residues within 4Å: Ligands: NAG-FUC.1, NAG-FUC.1, BMA.6 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain A: I.45, R.48, P.89, P.90, I.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.89, A:I.91, A:A.92 Salt bridges: A:R.48

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.6: 1 residues within 4Å: Ligands: NAG.5 No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Post Translational Modification)

EDO.7: 5 residues within 4Å: Chain B: N.183, N.184, N.185, R.186 Ligands: PGE.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.184, B:R.186

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

PGE.8: 5 residues within 4Å: Chain B: V.138, Y.171, N.183, R.186 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.183, B:R.186

1 x GAL: beta-D-galactopyranose(Non-functional Binders)

GAL.9: 9 residues within 4Å: Chain B: D.22, V.23, Y.24, G.25, Y.37, Q.42, N.44, R.112 Ligands: A2G.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.22, B:G.25, B:Q.42, B:N.44, B:N.44, B:R.112

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

A2G.10: 3 residues within 4Å: Chain B: G.25 Ligands: GAL.9, MBN.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.25

1 x MBN: TOLUENE(Non-covalent)

MBN.11: 1 residues within 4Å: Ligands: A2G.10 No protein-ligand interaction detected (PLIP)

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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