SMTL ID : 4mej.1

Crystal structure of Lactobacillus helveticus purine deoxyribosyl transferase (PDT) with the tricyclic purine 8,9-dihydro-9-oxoimidazo[2,1-b]purine (N2,3-ethenoguanine)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 9 residues within 4Å: Chain A: V.5, P.6 Chain B: P.6, T.7, A.39 Chain C: V.5, P.6, T.7 Ligands: SO4.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.6 SO4.5: 9 residues within 4Å: Chain A: K.9, N.81, T.83 Chain B: K.9, N.81 Chain C: K.9, N.81, T.83 Ligands: SO4.1 7 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 3 interactions with chain B Water bridges: A:K.9, C:K.9, B:K.9 Salt bridges: A:K.9, C:K.9, B:K.9 Hydrogen bonds: B:N.81

3 x 28Y: 3H-imidazo[2,1-b]purin-4(5H)-one(Non-covalent)

28Y.2: 5 residues within 4Å: Chain A: P.44, F.45, W.67, T.71, D.75 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.75 pi-Stacking: A:F.45, A:F.45, A:F.45 28Y.3: 5 residues within 4Å: Chain C: P.44, F.45, W.67, T.71, D.75 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.75 pi-Stacking: C:F.45, C:F.45 28Y.4: 5 residues within 4Å: Chain B: P.44, F.45, W.67, T.71, D.75 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.75 pi-Stacking: B:F.45, B:F.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, W. et al., Glycosylation of a tricyclic purine analog at alternative sites by nucleoside 2 -deoxyribosyltransferases. Plos One (2014)

Release Date

2014-10-15

Peptides

Nucleoside deoxyribosyltransferase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Nucleoside deoxyribosyltransferase

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