SMTL ID : 4za3.1

Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd)-Native-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 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.32, N.71, N.113 Ligands: NAG-BMA.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.32, B:N.71 Water bridges: B:N.113

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

NAG-BMA.2: 2 residues within 4Å: Ligands: NAG-FUC.1, NAG-FUC.1 No protein-ligand interaction detected (PLIP)

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.3: 12 residues within 4Å: Chain B: L.61, A.62, T.63, A.65, L.66, Y.79, L.80, D.83, W.86, N.96, S.98, S.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.79

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: N.109, T.110, F.111, I.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.111 Water bridges: A:K.163 EDO.5: 5 residues within 4Å: Chain A: H.131, A.134, S.135, H.138, S.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.138, A:S.150 EDO.7: 4 residues within 4Å: Chain B: Q.7, R.8, T.9, T.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.7, B:R.8, B:T.9 EDO.8: 6 residues within 4Å: Chain B: R.15, D.16, A.108, S.110, C.205, D.206 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.15, B:S.110, B:S.110 Water bridges: B:A.107, B:A.108 EDO.9: 1 residues within 4Å: Chain B: K.241 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.241 EDO.10: 4 residues within 4Å: Chain B: G.142, L.143, R.144, H.145 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.144, B:H.145, B:H.145

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

NAG.6: 3 residues within 4Å: Chain A: Q.86, N.87, N.108 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.87

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 7 residues within 4Å: Chain B: D.21, V.22, Y.23, G.24, Y.36, Q.41, N.43 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.24, B:Q.41, B:N.43, B:N.43

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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