SMTL ID : 9f08.1

Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Covalent complex with 2-deoxyribose.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-hexamer

Ligands

6 x 2DR: 2-deoxy-beta-D-erythro-pentofuranose(Post Translational Modification)

2DR.1: 13 residues within 4Å: Chain A: Y.7, G.9, A.10, W.12, F.13, P.42, D.72, D.92, G.94, L.95, E.98 Chain B: N.123, M.125 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.12, A:P.42 Hydrogen bonds: A:A.10, A:D.92, A:G.94, B:N.123 2DR.2: 12 residues within 4Å: Chain A: N.123, M.125 Chain B: Y.7, G.9, A.10, W.12, F.13, D.72, D.92, G.94, L.95, E.98 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.12 Hydrogen bonds: B:A.10, B:G.94, B:L.95, A:N.123 Water bridges: B:F.8, B:A.10 2DR.3: 13 residues within 4Å: Chain C: Y.7, G.9, A.10, W.12, F.13, P.42, D.72, D.92, G.94, L.95, E.98 Chain D: N.123, M.125 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.12, C:P.42 Hydrogen bonds: C:A.10, C:D.92, C:G.94, D:N.123 2DR.4: 12 residues within 4Å: Chain C: N.123, M.125 Chain D: Y.7, G.9, A.10, W.12, F.13, D.72, D.92, G.94, L.95, E.98 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.12 Hydrogen bonds: D:A.10, D:G.94, D:L.95, C:N.123 Water bridges: D:F.8, D:A.10 2DR.5: 13 residues within 4Å: Chain E: Y.7, G.9, A.10, W.12, F.13, P.42, D.72, D.92, G.94, L.95, E.98 Chain F: N.123, M.125 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:N.123, E:A.10, E:D.92, E:G.94 Hydrophobic interactions: E:W.12, E:P.42 2DR.6: 12 residues within 4Å: Chain E: N.123, M.125 Chain F: Y.7, G.9, A.10, W.12, F.13, D.72, D.92, G.94, L.95, E.98 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:N.123, F:A.10, F:G.94, F:L.95 Hydrophobic interactions: F:W.12 Water bridges: F:F.8, F:A.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salihovic, A. et al., Gram-scale enzymatic synthesis of 2'-deoxyribonucleoside analogues using nucleoside transglycosylase-2. Chem Sci (2024)

Release Date

2024-12-04

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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