1TDU

E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE (DURD)

• PDB DOI:  https://doi.org/10.2210/pdb1TDU/pdb

• Classification: METHYLTRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-06-25 Released: 1998-07-01 
• Deposition Author(s): Stout, T.J., Sage, C.R., Stroud, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Literature

The additivity of substrate fragments in enzyme-ligand binding.

Stout, T.J., Sage, C.R., Stroud, R.M.

(1998) Structure 6: 839-848

• PubMed: 9687366 
• DOI: https://doi.org/10.1016/S0969-2126(98)00086-0
• Primary Citation of Related Structures:  
  1AN5, 1AOB, 1BDU, 1BID, 1DDU, 1TDU, 1TJS, 1TRG


• 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 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.

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Organizational Affiliation: 

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

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: 62.69 kDa 
• Atom Count: 4,570 
• Modelled Residue Count: 530 
• Deposited Residue Count: 530 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE SYNTHASE	A, B	265	Escherichia coli	Mutation(s): 0  Gene Names: thyA EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12)) Explore P0A884  Go to UniProtKB:  P0A884

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CB3	E [auth A], H [auth B]	10-PROPARGYL-5,8-DIDEAZAFOLIC ACID C24 H23 N5 O6 LTKHPMDRMUCUEB-IBGZPJMESA-N
DUR	D [auth A], G [auth B]	2'-DEOXYURIDINE C9 H12 N2 O5 MXHRCPNRJAMMIM-SHYZEUOFSA-N
PO4	C [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
CB3	BindingDB:  1TDU	IC50: 60 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.246 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.299	α = 90
b = 127.299	β = 90
c = 67.983	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-07-01 
Deposition Author(s): Stout, T.J., Sage, C.R., Stroud, R.M.

Revision History  

• Version 1.0: 1998-07-01
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Other, Refinement description