SMTL ID : 4o4q.1

Crystal structure of the complex formed between type 1 ribosome inactivating protein and uridine diphosphate at 1.81 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: L.6, G.8, A.9, L.129, P.130, A.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.8 Water bridges: A:A.9, A:A.9 GOL.4: 8 residues within 4Å: Chain A: N.33, I.34, V.233, T.234, S.235, N.236, I.237, Q.238 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.233, A:Q.238, A:Q.238 Water bridges: A:N.33

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

NAG.2: 3 residues within 4Å: Chain A: T.226, N.227, T.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.226, A:N.227 Water bridges: A:N.227

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.3: 13 residues within 4Å: Chain A: V.69, Y.70, I.71, M.72, F.83, E.85, G.109, N.110, Y.111, I.155, A.159, E.160, R.163 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.111 Hydrogen bonds: A:I.71, A:I.71, A:E.85, A:G.109, A:Y.111, A:E.160, A:R.163, A:R.163 Water bridges: A:Y.70, A:S.108, A:E.112 pi-Stacking: A:Y.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamini, S. et al., Crystal structure of the complex formed between type 1 ribosome inactivating protein and uridine diphosphate at 1.81 A resolution. To be Published

Release Date

2014-01-01

Peptides

rRNA N-glycosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

rRNA N-glycosidase

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