1TRG

E. COLI THYMIDYLATE SYNTHASE IN SYMMETRIC COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The additivity of substrate fragments in enzyme-ligand binding.

Stout, T.J.Sage, C.R.Stroud, R.M.

(1998) Structure 6: 839-848

  • DOI: 10.1016/S0969-2126(98)00086-0
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Enzymes have evolved to recognise their target substrates with exquisite selectivity and specificity. Whether fragments of the substrate--perhaps never available to the evolving enzyme--are bound in the same manner as the parent substrate addresses t ...

    Enzymes have evolved to recognise their target substrates with exquisite selectivity and specificity. Whether fragments of the substrate--perhaps never available to the evolving enzyme--are bound in the same manner as the parent substrate addresses the fundamental basis of specificity. An understanding of the relative contributions of individual portions of ligand molecules to the enzyme-binding interaction may offer considerable insight into the principles of substrate recognition.


    Related Citations: 
    • Water-Mediated Substrate/Product Discrimination: The Product Complex of Thymidylate Synthase at 1.83 A
      Fauman, E.B., Rutenber, E.E., Maley, G.F., Maley, F., Stroud, R.M.
      (1994) Biochemistry 33: 1502
    • Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding Dump and an Anti-Folate
      Montfort, W.R., Perry, K.M., Fauman, E.B., Finer-Moore, J.S., Maley, G.F., Hardy, L., Maley, F., Stroud, R.M.
      (1990) Biochemistry 29: 6964
    • Erratum. Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding Dump and an Anti-Folate
      Montfort, W.R., Perry, K.M., Fauman, E.B., Finer-Moore, J.S., Maley, G.F., Hardy, L., Maley, F., Stroud, R.M.
      (1990) Biochemistry 29: 10864

    Organizational Affiliation

    Department of Biochemistry, School of Medicine, University of California, San Francisco 94143-0448, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A
265Escherichia coliMutation(s): 0 
Gene Names: thyA
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A884
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CB3
Query on CB3

Download CCD File 
A
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID
C24 H23 N5 O6
LTKHPMDRMUCUEB-IBGZPJMESA-N
 Ligand Interaction
UMP
Query on UMP

Download CCD File 
A
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CB3IC50:  60   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.96α = 90
b = 71.96β = 90
c = 115.1γ = 120
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance