4E5O | pdb_00004e5o

Crystal structure of mouse thymidylate synthase in complex with dUMP

• PDB DOI: https://doi.org/10.2210/pdb4E5O/pdb
• Entry: 4E5O supersedes: 3IHH

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-14 Released: 2012-04-18 
• Deposition Author(s): Dowiercial, A., Jarmula, A., Rypniewski, W., Sokolowska, M., Fraczyk, T., Ciesla, J., Rode, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.292 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Mouse thymidylate synthase does not show the inactive conformation, observed for the human enzyme

Dowiercial, A., Jarmula, A., Wilk, P., Rypniewski, W., Kowalska, M., Fraczyk, T., Ciesla, J., Rode, W.

(2016) Struct Chem 

• DOI: https://doi.org/10.1007/s11224-016-0840-8

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 212.43 kDa 
• Atom Count: 15,512 
• Modeled Residue Count: 1,698 
• Deposited Residue Count: 1,842 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B, C, D, E, F	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
UMP	G [auth A], H [auth B], I [auth C], M [auth D], N [auth E], O [auth F], P [auth F]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
BU1	J [auth C], K [auth C], L [auth C]	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.292 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.35	α = 90
b = 88.54	β = 95.99
c = 136.76	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: 2012-04-18 
Deposition Author(s): Dowiercial, A., Jarmula, A., Rypniewski, W., Sokolowska, M., Fraczyk, T., Ciesla, J., Rode, W.
• This entry supersedes: 3IHH

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2016-11-02
  Changes: Database references
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description