1JG0

Crystal structure of Escherichia coli thymidylate synthase complexed with 2'-deoxyuridine-5'-monophosphate and N,O-didansyl-L-tyrosine

• PDB DOI: https://doi.org/10.2210/pdb1JG0/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-06-22 Released: 2002-02-08 
• Deposition Author(s): Fritz, T.A., Tondi, D., Finer-Moore, J.S., Costi, M.P., Stroud, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.212 

Literature

Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase.

Fritz, T.A., Tondi, D., Finer-Moore, J.S., Costi, M.P., Stroud, R.M.

(2001) Chem Biol 8: 981-995

• PubMed: 11590022 
• DOI: https://doi.org/10.1016/s1074-5521(01)00067-9
• Primary Citation of Related Structures:  
  1JG0


• PubMed Abstract: 
  

  Protein plasticity in response to ligand binding abrogates the notion of a rigid receptor site. Thus, computational docking alone misses important prospective drug design leads. Bacterial-specific inhibitors of an essential enzyme, thymidylate synthase (TS), were developed using a combination of computer-based screening followed by in-parallel synthetic elaboration and enzyme assay [Tondi et al. (1999) Chem. Biol. 6, 319-331]. Specificity was achieved through protein plasticity and despite the very high sequence conservation of the enzyme between species.

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Organizational Affiliation: 

Macromolecular Structure Group, Department of Biochemistry, 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: 4,846 
• Modelled Residue Count: 526 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thymidylate synthase	A, B	264	Escherichia coli	Mutation(s): 1  Gene Names: Esherichia coli EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12)) Explore P0A884  Go to UniProtKB:  P0A884

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DDT	D [auth A], F [auth B]	N,O-DIDANSYL-L-TYROSINE C33 H33 N3 O7 S2 LUBOPDUYHWABFG-NDEPHWFRSA-N
UMP	C [auth A], E [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CXM	A, B	L-PEPTIDE LINKING	C6 H11 N O4 S		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
DDT	BindingDB:  1JG0	Ki: min: 1800, max: 1800 (nM) from 2 assay(s)
		IC50: 5000 (nM) from 1 assay(s)
	Binding MOAD:  1JG0	IC50: 5000 (nM) from 1 assay(s)
	PDBBind:  1JG0	IC50: 5000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.250 
• R-Value Work: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.797	α = 90
b = 87.062	β = 90
c = 127.461	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-08 
Deposition Author(s): Fritz, T.A., Tondi, D., Finer-Moore, J.S., Costi, M.P., Stroud, R.M.

Revision History  

• Version 1.0: 2002-02-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance