SMTL ID : 9f09.1

Nucleoside-2'-deoxyribosyltransferase from Lactobacillus leichmannii. Complex with 2-deoxyribose, 7-Bromo-1H-imidazo[4,5-b]pyridine and 2'-deoxycytidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-hexamer

Ligands

3 x DCZ: 2'-DEOXYCYTIDINE(Non-covalent)

DCZ.1: 17 residues within 4Å: Chain A: Y.7, G.9, A.10, W.12, F.13, P.42, Q.46, W.64, D.72, D.92, G.94, L.95, E.98 Chain B: N.123, L.124, M.125, Y.157 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.12, A:P.42, B:L.124 Hydrogen bonds: A:A.10, A:Q.46, A:D.92, A:G.94, A:L.95, B:N.123, B:Y.157 Water bridges: A:F.8, A:A.10 pi-Stacking: A:W.12 DCZ.5: 17 residues within 4Å: Chain C: Y.7, G.9, A.10, W.12, F.13, P.42, Q.46, W.64, D.72, D.92, G.94, L.95, E.98 Chain D: N.123, L.124, M.125, Y.157 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:W.12, C:P.42, D:L.124 Hydrogen bonds: C:A.10, C:Q.46, C:D.92, C:G.94, C:L.95, D:N.123, D:Y.157 Water bridges: C:F.8, C:A.10 pi-Stacking: C:W.12 DCZ.9: 17 residues within 4Å: Chain E: Y.7, G.9, A.10, W.12, F.13, P.42, Q.46, W.64, D.72, D.92, G.94, L.95, E.98 Chain F: N.123, L.124, M.125, Y.157 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:W.12, E:P.42, F:L.124 Hydrogen bonds: E:A.10, E:Q.46, E:D.92, E:G.94, E:L.95, F:N.123, F:Y.157 Water bridges: E:F.8, E:A.10 pi-Stacking: E:W.12

6 x 01: 7-bromanyl-3~{H}-imidazo[4,5-b]pyridine

01.2: 10 residues within 4Å: Chain A: N.123, L.124, M.125, Y.157 Chain B: W.12, W.64, T.68, D.72 Ligands: 2DR.3, 01.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.123 Hydrophobic interactions: B:T.68 pi-Stacking: B:W.12 01.4: 10 residues within 4Å: Chain A: L.124, Y.157 Chain B: W.12, P.42, Q.46, V.52, W.64, T.68, D.72 Ligands: 01.2 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.68 pi-Stacking: B:W.12 Halogen bonds: B:Q.46 01.6: 10 residues within 4Å: Chain C: N.123, L.124, M.125, Y.157 Chain D: W.12, W.64, T.68, D.72 Ligands: 2DR.7, 01.8 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:N.123 Hydrophobic interactions: D:T.68 pi-Stacking: D:W.12 01.8: 10 residues within 4Å: Chain C: L.124, Y.157 Chain D: W.12, P.42, Q.46, V.52, W.64, T.68, D.72 Ligands: 01.6 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.68 pi-Stacking: D:W.12 Halogen bonds: D:Q.46 01.10: 10 residues within 4Å: Chain E: N.123, L.124, M.125, Y.157 Chain F: W.12, W.64, T.68, D.72 Ligands: 2DR.11, 01.12 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:T.68 pi-Stacking: F:W.12 Hydrogen bonds: E:N.123 01.12: 10 residues within 4Å: Chain E: L.124, Y.157 Chain F: W.12, P.42, Q.46, V.52, W.64, T.68, D.72 Ligands: 01.10 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:T.68 pi-Stacking: F:W.12 Halogen bonds: F:Q.46

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

2DR.3: 12 residues within 4Å: Chain A: N.123, M.125 Chain B: Y.7, G.9, A.10, F.13, D.72, D.92, G.94, L.95, E.98 Ligands: 01.2 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.123, B:A.10, B:D.92, B:G.94, B:L.95 2DR.7: 12 residues within 4Å: Chain C: N.123, M.125 Chain D: Y.7, G.9, A.10, F.13, D.72, D.92, G.94, L.95, E.98 Ligands: 01.6 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:A.10, D:D.92, D:G.94, D:L.95, C:N.123 2DR.11: 12 residues within 4Å: Chain E: N.123, M.125 Chain F: Y.7, G.9, A.10, F.13, D.72, D.92, G.94, L.95, E.98 Ligands: 01.10 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:A.10, F:D.92, F:G.94, F:L.95, E:N.123

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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