3U6K: Ef-tu

Ef-tu (escherichia coli) in complex with nvp-ldk733. Determined by X-ray diffraction at 2.45 Å resolution. Released 8 Feb 2012.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Escherichia coli
Chains: 4
Atoms: 6,311
Mol. weight: 90.47 kDa
Ligands: MG, GDP
Released: 8 Feb 2012

Explore 3U6K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3U6K contains 31 α-helices and 60 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: 18 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
α-helix	24-38	15
α-helix	46-50	5
α-helix	52-53	2
β-strand	54-57	4	2
β-strand	60-63	4	2
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	113-124	12
β-strand	130-135	6	1
α-helix	137-139	3
α-helix	145-159	15
α-helix	164-166	3
β-strand	169-171	3	1
α-helix	174-179	6
α-helix	184-198	15
α-helix	200-204	5
α-helix	205-207	3
α-helix	209-210	2
β-strand	211-213	3	3
β-strand	217-220	4	4
β-strand	224-230	7	4
β-strand	233	1	3
β-strand	235-237	3	5
β-strand	241-246	6	3
β-strand	248-254	7	3
β-strand	255-260	6	4
β-strand	263-265	3	4
β-strand	267-269	3	5
β-strand	273-278	6	4
α-helix	283-285	3
β-strand	288	1	6
β-strand	290	1	6
β-strand	291-293	3	3
β-strand	300-310	11	7
α-helix	311-312	2
α-helix	313-315	3
α-helix	321	1
β-strand	322-323	2	8
β-strand	329-332	4	7
β-strand	335-342	8	7
α-helix	343	1
β-strand	349-350	2	8
β-strand	355-367	13	7
β-strand	373-377	5	7
β-strand	382-391	10	7

Chain B: 13 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	9
β-strand	16-17	2	10
α-helix	24-38	15
α-helix	52-53	2
β-strand	54-56	3	11
β-strand	61-63	3	11
β-strand	65-71	7	9
β-strand	74-80	7	9
α-helix	84-93	10
β-strand	101-106	6	10
α-helix	113-125	13
β-strand	130-135	6	10
α-helix	143-158	16
β-strand	169-171	3	10
α-helix	174-179	6
α-helix	185-198	14
α-helix	200-204	5
α-helix	209-210	2
β-strand	211-213	3	12
β-strand	217-220	4	12
β-strand	224-230	7	12
β-strand	233	1	12
β-strand	235-237	3	13
β-strand	241-245	5	12
β-strand	251-260	10	12
β-strand	263-265	3	12
β-strand	267-269	3	13
β-strand	273-279	7	12
α-helix	283-285	3
β-strand	288	1	14
β-strand	290	1	14
β-strand	291-293	3	12
β-strand	300-310	11	15
α-helix	311-312	2
α-helix	313-315	3
β-strand	322	1	16
β-strand	329-332	4	15
β-strand	335-342	8	15
α-helix	343-344	2
β-strand	350	1	16
β-strand	355-367	13	15
β-strand	373-378	6	15
β-strand	381-391	11	15

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-LDK733	C, D	protein	12		Q7M0J8

Sequence of entity 1 (A, B), FASTA

>3U6K_1 Elongation factor Tu 1 (chains A, B)
MAKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG
ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE
GDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG
EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK
PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV
VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG

Sequence of entity 2 (C, D), FASTA

>3U6K_2 Thiocillin GE2270 analogue NVP-LDK733 (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
3U6B 2.12 Å, Ef-tu (escherichia coli) in complex with nvp-ldi028
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…

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