Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.47 kDa 
• Atom Count: 6,311 
• Modelled Residue Count: 796 
• Deposited Residue Count: 812 
• Unique protein chains: 2

 3U6K

Ef-tu (escherichia coli) in complex with nvp-ldk733

• PDB DOI: 10.2210/pdb3U6K/pdb

• Classification: translation factor/antibiotic
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-10-12 Released: 2012-02-08 
• Deposition Author(s): Palestrant, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.298 
• R-Value Work: 0.224 
• R-Value Observed: 0.228 

Literature

Antibacterial optimization of 4-aminothiazolyl analogues of the natural product GE2270 A: identification of the cycloalkylcarboxylic acids.

LaMarche, M.J., Leeds, J.A., Amaral, K., Brewer, J.T., Bushell, S.M., Dewhurst, J.M., Dzink-Fox, J., Gangl, E., Goldovitz, J., Jain, A., Mullin, S., Neckermann, G., Osborne, C., Palestrant, D., Patane, M.A., Rann, E.M., Sachdeva, M., Shao, J., Tiamfook, S., Whitehead, L., Yu, D.

(2011) J Med Chem 54: 8099-8109

• PubMed: 21999529 
• DOI: 10.1021/jm200938f
• Primary Citation of Related Structures:  
  3U6B, 3U6K


• PubMed Abstract: 
  

4-Aminothiazolyl analogues of the antibiotic natural product GE2270 A (1) were designed, synthesized, and optimized for their activity against Gram positive bacterial infections. Optimization efforts focused on improving the physicochemical properties (e.g., aqueous solubility and chemical stability) of the 4-aminothiazolyl natural product template while improving the in vitro and in vivo antibacterial activity. Structure-activity relationships were defined, and the solubility and efficacy profiles were improved over those of previous analogues and 1. These studies identified novel, potent, soluble, and efficacious elongation factor-Tu inhibitors, which bear cycloalkylcarboxylic acid side chains, and culminated in the selection of development candidates amide 48 and urethane 58.

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Organizational Affiliation: 

Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor Tu 1	A, B	394	Escherichia coli K-12	Mutation(s): 0  Gene Names: tufA, b3339, JW3301
UniProt
Find proteins for P0CE47 (Escherichia coli (strain K12)) Explore P0CE47  Go to UniProtKB:  P0CE47

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiocillin GE2270 analogue NVP-LDK733	C, D	12	N/A	Mutation(s): 0
UniProt
Find proteins for Q7M0J8 (Planobispora rosea) Explore Q7M0J8  Go to UniProtKB:  Q7M0J8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	E [auth A], G [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  6 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BB6	C, D	PEPTIDE LINKING	C4 H7 N O2 S		CYS
BB7	C, D	PEPTIDE LINKING	C5 H9 N O3 S		CYS
BB8	C, D	L-PEPTIDE LINKING	C9 H11 N O3		PHE
BB9	C, D	PEPTIDE LINKING	C3 H5 N O2 S		CYS
MEN	C, D	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN
MH6	C, D	PEPTIDE LINKING	C3 H5 N O3		SER

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001073	C, D	Thiocillin GE2270 analogue NVP-LDK733	Thiopeptide / Antibiotic		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.298 
• R-Value Work: 0.224 
• R-Value Observed: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.372	α = 90
b = 82.216	β = 90
c = 129.9	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Palestrant, D.J.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Structure summary
• Version 1.2: 2012-12-12
  Changes: Other