3BGX

E. coli Thymidylate Synthase C146S mutant complexed with dTMP and MTF

• PDB DOI: https://doi.org/10.2210/pdb3BGX/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-11-27 Released: 2008-12-09 
• Deposition Author(s): Roberts, S.A., Montfort, W.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Literature

Structural Studies of Early Events in Catalysis by Thymidylate Synthase

Arendall III, W.B., Roberts, S.A., Hyatt, D.C., Weichsel, A., Dahlgren, A.L., Montfort, W.R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.52 kDa 
• Atom Count: 2,336 
• Modelled Residue Count: 264 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	264	Escherichia coli	Mutation(s): 1  Gene Names: thyA EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12)) Explore P0A884  Go to UniProtKB:  P0A884

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MEF	E [auth A]	N-({4-[(6aR)-3-amino-1-oxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-L-glutamic acid C20 H23 N7 O6 QYNUQALWYRSVHF-OLZOCXBDSA-N
TMP	D [auth A]	THYMIDINE-5'-PHOSPHATE C10 H15 N2 O8 P GYOZYWVXFNDGLU-XLPZGREQSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CXM	A	L-PEPTIDE LINKING	C6 H11 N O4 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.230 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.03	α = 90
b = 72.03	β = 90
c = 115.46	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MADNESS	data collection
PROCOR	data reduction
corect	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Roberts, S.A., Montfort, W.R.

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-04-18
  Changes: Data collection
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Data collection, Structure summary