9GN2

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

• PDB DOI: https://doi.org/10.2210/pdb9GN2/pdb

• Classification: TRANSFERASE
• Organism(s): Lactobacillus leichmannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-30 Released: 2024-12-25 
• Deposition Author(s): Ascham, A., Salihovic, A., Burley, G., Grogan, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Work: 0.190 

Starting Model: experimental

Literature

Biocatalytic synthesis of ribonucleoside analogues using nucleoside transglycosylase-2

Salihovic, A., Ascham, A., Rosenqvist, P.S., Taladriz-Sender, A., Hoskisson, P.A., Hodgson, D.R.W., Grogan, G., Burley, G.A.

(2024) Chem Sci 

• DOI: https://doi.org/10.1039/d4sc07521h

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 36.46 kDa 
• Atom Count: 2,613 
• Modelled Residue Count: 314 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside deoxyribosyltransferase	A, B	157	Lactobacillus leichmannii	Mutation(s): 0  Gene Names: ntd EC: 2.4.2.6
UniProt
Find proteins for Q9R5V5 (Lactobacillus leichmannii) Explore Q9R5V5  Go to UniProtKB:  Q9R5V5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIB (Subject of Investigation/LOI)	D [auth A]	alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N
CYT (Subject of Investigation/LOI)	C [auth A]	6-AMINOPYRIMIDIN-2(1H)-ONE C4 H5 N3 O OPTASPLRGRRNAP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Work: 0.190 
• Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.981	α = 90
b = 148.981	β = 90
c = 148.981	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-25 
Deposition Author(s): Ascham, A., Salihovic, A., Burley, G., Grogan, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-12-25
  Type: Initial release