4EZ8

Crystal structure of mouse thymidylate sythase in ternary complex with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate and the cofactor product, dihydrofolate

• PDB DOI: https://doi.org/10.2210/pdb4EZ8/pdb

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


• Deposited: 2012-05-02 Released: 2013-05-08 
• Deposition Author(s): Dowiercial, A., Jarmula, A., Rypniewski, W., Wilk, P., Kierdaszuk, B., Banaszak, K., Gorecka, K., Rode, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 0.130 
• R-Value Work: 0.107 
• R-Value Observed: 0.108 

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., Wilk, P., Kierdaszuk, B., Banaszak, K., Gorecka, K., 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: 35.95 kDa 
• Atom Count: 3,141 
• Modelled Residue Count: 287 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHF	C [auth A]	DIHYDROFOLIC ACID C19 H21 N7 O6 OZRNSSUDZOLUSN-LBPRGKRZSA-N
NOH	B [auth A]	2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate) C9 H14 N3 O8 P YKOWBJJOJNGCAD-SHYZEUOFSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NOH	BindingDB:  4EZ8	Kd: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.17 Å
• R-Value Free: 0.130 
• R-Value Work: 0.107 
• R-Value Observed: 0.108 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.121	α = 90
b = 112.045	β = 90
c = 88.297	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Dowiercial, A., Jarmula, A., Rypniewski, W., Wilk, P., Kierdaszuk, B., Banaszak, K., Gorecka, K., Rode, W.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations