3U6B: Ef-tu

Ef-tu (escherichia coli) in complex with nvp-ldi028. Determined by X-ray diffraction at 2.12 Å resolution. Released 8 Feb 2012.

Method: X-ray diffraction
Resolution: 2.12 Å
Organism: Escherichia coli
Chains: 4
Atoms: 6,044
Mol. weight: 90.44 kDa
Ligands: MG, GDP
Released: 8 Feb 2012

Explore 3U6B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3U6B contains 31 α-helices and 51 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	10	1
β-strand	11-17	7	1
α-helix	24-38	15
β-strand	65-70	6	1
β-strand	75-80	6	1
α-helix	84-93	10
β-strand	100-106	7	1
α-helix	113-125	13
β-strand	130-135	6	1
α-helix	143-159	17
α-helix	164-166	3
β-strand	169-171	3	1
α-helix	174-178	5
α-helix	182-198	17
α-helix	200-204	5
α-helix	205-207	3
α-helix	209-210	2
β-strand	211-213	3	2
β-strand	217-218	2	3
β-strand	226-230	5	3
β-strand	233	1	2
β-strand	235-237	3	4
β-strand	241-245	5	2
β-strand	251-254	4	2
β-strand	255-260	6	3
β-strand	263-265	3	3
β-strand	267-269	3	4
β-strand	273-278	6	3
α-helix	283-285	3
β-strand	291-293	3	2
β-strand	299-310	12	5
α-helix	311-312	2
α-helix	313-315	3
β-strand	322-323	2	6
β-strand	329-332	4	5
β-strand	335-342	8	5
α-helix	343-344	2
β-strand	349-350	2	6
β-strand	355-368	14	5
β-strand	373-378	6	5
β-strand	381-391	11	5

Chain B: 16 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
α-helix	9-10	2
β-strand	11-17	7	7
α-helix	24-39	16
β-strand	65-70	6	7
β-strand	75-80	6	7
α-helix	84-93	10
β-strand	100-106	7	7
α-helix	113-124	12
β-strand	130-135	6	7
α-helix	143-159	17
α-helix	164-166	3
β-strand	169-171	3	7
α-helix	174-178	5
α-helix	182-198	17
α-helix	200-204	5
α-helix	205-207	3
α-helix	209-210	2
β-strand	211-213	3	8
β-strand	217-218	2	8
β-strand	226-230	5	8
β-strand	233	1	8
β-strand	235-237	3	9
β-strand	241-245	5	8
β-strand	251-260	10	8
β-strand	263-265	3	8
β-strand	267-269	3	9
β-strand	273-279	7	8
α-helix	283-285	3
β-strand	291-293	3	8
β-strand	299-310	12	10
α-helix	311-312	2
α-helix	313-315	3
β-strand	322	1	11
β-strand	329-332	4	10
β-strand	335-342	8	10
α-helix	343-344	2
β-strand	350	1	11
β-strand	355-368	14	10
β-strand	373-378	6	10
β-strand	381-391	11	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Tu 1	A, B	protein	394	Escherichia coli	P0CE47 (AlphaFold model)
Thiocillin GE2270 analogue NVP-LDI028	C, D	protein	12		Q7M0J8

Sequence of entity 1 (A, B), FASTA

>3U6B_1 Elongation factor Tu 1 (chains A, B)
MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG
ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE
GDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG
EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK
PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV
VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG

Sequence of entity 2 (C, D), FASTA

>3U6B_2 Thiocillin GE2270 analogue NVP-LDI028 (chains C, D)
SCNCVCGFCCSX

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Primary citation

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. et al. J Med Chem (2011) 54:8099-8109. DOI 10.1021/jm200938f · PubMed

Other PDB entries of the same protein (UniProt P0CE47 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9TBU 1.23 Å, E. coli EF-Tu-T62A:GDP AMPylated at T65
4PC3 1.83 Å, Elongation factor Tu:Ts complex with partially bound GDP
5JBQ 2.01 Å, Ef-tu (escherichia coli) in complex with thiomuracin analog
1EFC 2.05 Å, Intact elongation factor from e.coli
2HCJ 2.12 Å, Trypsin-modified Elongation Factor Tu in complex with tetracycline
4P3Y 2.15 Å, Crystal structure of Acinetobacter baumannii DsbA in complex with EF-Tu
5MI8 2.18 Å, Structure of the phosphomimetic mutant of EF-Tu T383E
8FR3 2.23 Å, E. coli EF-Tu in complex with KKL-55
4G5G 2.3 Å, ef-tu (Escherichia coli) complexed with nvp-ldu796
1D8T 2.35 Å, Crystal structure of elongation factor, tu (ef-tu-mggdp) complexed with GE2270A, a…
5I4Q 2.35 Å, Contact-dependent inhibition system from Escherichia coli NC101 - ternary…
3U6K 2.45 Å, Ef-tu (escherichia coli) in complex with nvp-ldk733

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