SMTL ID : 4z9w.1

Structural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd)-Native-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.1: 4 residues within 4Å: Chain B: R.33, N.72, N.114 Ligands: BMA.7 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: N.87, N.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.108 Water bridges: A:N.87 NAG.5: 11 residues within 4Å: Chain B: L.62, A.63, T.64, A.66, L.67, L.81, D.84, W.87, N.97, S.100 Ligands: NAG.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.63 Hydrogen bonds: B:T.64, B:D.84, B:N.97 Water bridges: B:K.98, B:S.100 NAG.6: 2 residues within 4Å: Chain B: Y.80 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.80

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

EDO.3: 8 residues within 4Å: Chain A: K.15, Q.169 Chain B: I.142, G.143, Q.256, W.257, T.258 Ligands: EDO.16 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.15 Water bridges: A:K.15, A:Q.169, A:Q.169, B:Q.256, B:W.257 EDO.4: 4 residues within 4Å: Chain A: N.109, T.110, F.111, I.155 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.111 EDO.8: 2 residues within 4Å: Chain B: K.199, L.245 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain B: A.234, Q.235, V.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.235 Water bridges: B:Q.235 EDO.10: 7 residues within 4Å: Chain B: M.147, W.159, L.160, E.161, V.238, Y.239, K.241 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.159 Water bridges: B:S.162 EDO.11: 5 residues within 4Å: Chain B: R.16, D.17, C.206, D.207, G.208 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.16 Water bridges: B:D.17, B:S.111, B:S.111, B:D.177, B:D.207 EDO.12: 2 residues within 4Å: Chain B: D.237, Y.239 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain B: Q.8, R.9, T.10, T.48 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.8, B:R.9, B:T.10 Water bridges: B:T.10, B:T.10 EDO.14: 6 residues within 4Å: Chain B: D.22, V.23, Y.24, G.25, Y.37, N.44 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.22, B:G.25, B:N.44 EDO.15: 3 residues within 4Å: Chain B: D.195, S.196, S.197 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.197, B:S.197 Water bridges: B:D.195, B:S.197 EDO.16: 6 residues within 4Å: Chain A: K.15 Chain B: G.143, L.144, R.145, H.146 Ligands: EDO.3 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.145, B:R.145, B:H.146, B:H.146 Water bridges: A:K.15

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

BMA.7: 1 residues within 4Å: Ligands: NAG-FUC-NAG.1 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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