4EZ8

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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 --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A
307Mus musculusMutation(s): 0 
Gene Names: Tyms
EC: 2.1.1.45
Find proteins for P07607 (Mus musculus)
Go to UniProtKB:  P07607
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NOH
Query on NOH

Download SDF File 
Download CCD File 
A
2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate)
C9 H14 N3 O8 P
YKOWBJJOJNGCAD-SHYZEUOFSA-N
 Ligand Interaction
DHF
Query on DHF

Download SDF File 
Download CCD File 
A
DIHYDROFOLIC ACID
C19 H21 N7 O6
OZRNSSUDZOLUSN-LBPRGKRZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NOHKd: 1000 nM (88) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.107 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 71.121α = 90.00
b = 112.045β = 90.00
c = 88.297γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-08
    Type: Initial release