4EIN

Crystal structure of mouse thymidylate synthase in binary complex with a substrate analogue and strong inhibitor, N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate

• PDB DOI: https://doi.org/10.2210/pdb4EIN/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-05 Released: 2013-04-10 
• Deposition Author(s): Dowiercial, A., Jarmula, A., Rypniewski, W.R., Wilk, P., Kierdaszuk, B., Rode, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.255 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Crystal structures of complexes of mouse thymidylate synthase crystallized with N4-OH-dCMP alone or in the presence of N5,10-methylenetetrahydrofolate

Dowiercial, A., Jarmula, A., Rypniewski, W.R., Wilk, P., Kierdaszuk, B., Rode, W.

(2013) Pteridines 

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: 70.74 kDa 
• Atom Count: 5,462 
• Modelled Residue Count: 569 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B	307	Mus musculus	Mutation(s): 0  Gene Names: Tyms EC: 2.1.1.45
UniProt
Find proteins for P07607 (Mus musculus) Explore P07607  Go to UniProtKB:  P07607

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NOH	C [auth A], D [auth B]	2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate) C9 H14 N3 O8 P YKOWBJJOJNGCAD-SHYZEUOFSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NOH	BindingDB:  4EIN	Kd: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.255 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.023	α = 90
b = 87.956	β = 96.44
c = 68.668	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): Dowiercial, A., Jarmula, A., Rypniewski, W.R., Wilk, P., Kierdaszuk, B., Rode, W.

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description