4E5O

Crystal structure of mouse thymidylate synthase in complex with dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate synthase
A, B, C, D, E
A, B, C, D, E, F
307Mus musculusMutation(s): 0 
Gene Names: Tyms
EC: 2.1.1.45
UniProt
Find proteins for P07607 (Mus musculus)
Explore P07607 
Go to UniProtKB:  P07607
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07607
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UMP
Query on UMP

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
I [auth C]
M [auth D]
N [auth E]
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
Query on BU1

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.35α = 90
b = 88.54β = 95.99
c = 136.76γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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