SMTL ID : 4lwx.1

Crystal structure of the complex of Ribosome inactivating protein from Momordica Balsamina with peptidoglycan fragment at 1.78 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: T.226, N.227, T.229 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.226, A:N.227 Water bridges: A:N.227, A:S.230

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: L.6, G.8, A.9, L.129, P.130, A.175, Y.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.8 Water bridges: A:A.9 GOL.3: 8 residues within 4Å: Chain A: N.33, I.34, V.233, T.234, S.235, N.236, I.237, Q.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.235, A:Q.238

1 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.4: 11 residues within 4Å: Chain A: V.69, Y.70, I.71, G.109, N.110, Y.111, I.155, A.159, R.163 Ligands: LAC.5, ALA.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:N.110 Hydrogen bonds: A:V.69, A:I.71, A:I.71, A:G.109, A:Y.111, A:R.163, A:R.163 Salt bridges: A:R.163

1 x LAC: LACTIC ACID(Non-covalent)

LAC.5: 9 residues within 4Å: Chain A: Y.70, I.71, M.72, E.85, G.109, N.110 Ligands: NDG.4, ALA.6, GLN.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.70 Hydrogen bonds: Q.7

1 x ALA: ALANINE(Non-covalent)

ALA.6: 7 residues within 4Å: Chain A: E.85, S.108, G.109, N.110 Ligands: NDG.4, LAC.5, GLN.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:N.110, Q.7 Hydrogen bonds: A:G.109

1 x GLN: GLUTAMINE(Non-covalent)

GLN.7: 3 residues within 4Å: Chain A: Y.70 Ligands: LAC.5, ALA.6 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrophobic interactions: A.6 Water bridges: A:N.68, A:N.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamini, S. et al., Crystal structure of the complex of Ribosome inactivating protein from Momordica Balsamina with peptidoglycan fragment at 1.78 A resolution. To be Published

Release Date

2013-08-28

Peptides

rRNA N-glycosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

rRNA N-glycosidase

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