1AXW | pdb_00001axw

E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH METHOTREXATE (MTX) AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)

• PDB DOI: https://doi.org/10.2210/pdb1AXW/pdb

• Classification: METHYLTRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-10-23 Released: 1998-10-28 
• Deposition Author(s): Stout, T.J., Sage, C.R., Stroud, R.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.265 (Depositor) 
• R-Value Work: 
  0.217 (Depositor) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Discovery of Thymidylate Synthase Inhibitors Using Flexible Docking and an Empirically Tuned Scoring Function

Welch, W., Sage, C.R., Stout, T.J., Klein, T., Ruppert, J., Stroud, R.M., Jain, A.

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: 62.61 kDa 
• Atom Count: 4,600 
• Modelled Residue Count: 530 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE SYNTHASE	A, B	265	Escherichia coli	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTX	D [auth A], F [auth B]	METHOTREXATE C20 H22 N8 O5 FBOZXECLQNJBKD-ZDUSSCGKSA-N
UMP	C [auth A], E [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MTX	BindingDB:  1AXW	IC50: min: 1800, max: 9.00e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.265 (Depositor) 
• R-Value Work:  0.217 (Depositor) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.34	α = 90
b = 127.34	β = 90
c = 68.06	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-28 
Deposition Author(s): Stout, T.J., Sage, C.R., Stroud, R.M.

Revision History  

• Version 1.0: 1998-10-28
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Derived calculations, Other, Refinement description