SMTL ID : 9gn2.1

Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Complex with ribose and cytosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-hexamer

Ligands

3 x CYT: 6-AMINOPYRIMIDIN-2(1H)-ONE(Non-covalent)

CYT.1: 10 residues within 4Å: Chain A: W.12, P.42, Q.46, V.52, W.64, D.72 Chain B: L.124, M.125, Y.157 Ligands: RIB.2 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.124 Hydrogen bonds: B:Y.157, A:Q.46, A:Q.46 pi-Stacking: A:W.12 CYT.3: 10 residues within 4Å: Chain C: W.12, P.42, Q.46, V.52, W.64, D.72 Chain D: L.124, M.125, Y.157 Ligands: RIB.4 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.124 Hydrogen bonds: D:Y.157, C:Q.46, C:Q.46 pi-Stacking: C:W.12 CYT.5: 10 residues within 4Å: Chain E: W.12, P.42, Q.46, V.52, W.64, D.72 Chain F: L.124, M.125, Y.157 Ligands: RIB.6 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:L.124 Hydrogen bonds: F:Y.157, E:Q.46, E:Q.46 pi-Stacking: E:W.12

3 x RIB: alpha-D-ribofuranose(Post Translational Modification)

RIB.2: 14 residues within 4Å: Chain A: Y.7, F.8, G.9, A.10, F.13, P.42, D.72, D.92, G.94, L.95, E.98 Chain B: N.123, M.125 Ligands: CYT.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.10, A:A.10, A:G.94, B:N.123 RIB.4: 14 residues within 4Å: Chain C: Y.7, F.8, G.9, A.10, F.13, P.42, D.72, D.92, G.94, L.95, E.98 Chain D: N.123, M.125 Ligands: CYT.3 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.10, C:A.10, C:G.94, D:N.123 RIB.6: 14 residues within 4Å: Chain E: Y.7, F.8, G.9, A.10, F.13, P.42, D.72, D.92, G.94, L.95, E.98 Chain F: N.123, M.125 Ligands: CYT.5 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:N.123, E:Y.7, E:A.10, E:A.10, E:G.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salihovic, A. et al., Biocatalytic synthesis of ribonucleoside analogues using nucleoside transglycosylase-2. Chem Sci (2025)

Release Date

2024-12-25

Peptides

Nucleoside deoxyribosyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Nucleoside deoxyribosyltransferase

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