2HDN: Trypsin-modified Elongation Factor Tu

Trypsin-modified Elongation Factor Tu in complex with tetracycline at 2.8 Angstrom resolution. Determined by X-ray diffraction at 2.8 Å resolution. Released 31 Oct 2006.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Escherichia coli
Chains: 12
Atoms: 17,608
Mol. weight: 249.86 kDa
Ligands: TAC, GDP, MG
Released: 31 Oct 2006

Explore 2HDN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2HDN contains 64 α-helices and 162 β-strands across 12 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.

Chains A, C, E, G, I and K: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	1
β-strand	16-17	2	2
α-helix	24-39	16

Chains B, D, J and L: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	64-70	7	1
β-strand	75-80	6	1
α-helix	84-93	10
β-strand	101-106	6	2
α-helix	113-125	13
β-strand	130-135	6	2
α-helix	143-159	17
β-strand	169-171	3	2
α-helix	174-179	6
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	3
β-strand	216-220	5	4
β-strand	224-230	7	4
β-strand	233	1	3
β-strand	235-237	3	5
β-strand	241-245	5	3
β-strand	251-254	4	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	286-287	2
β-strand	291-293	3	3
β-strand	300-310	11	6
β-strand	322-323	2	7
β-strand	329-332	4	6
β-strand	335-342	8	6
α-helix	343-344	2
β-strand	349-350	2	7
β-strand	355-367	13	6
β-strand	373-378	6	6
β-strand	381-391	11	6

Chains F and H: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	64-70	7	14
β-strand	75-80	6	14
α-helix	84-93	10
β-strand	101-106	6	15
α-helix	113-125	13
β-strand	130-135	6	15
α-helix	143-159	17
β-strand	169-171	3	15
α-helix	174-179	6
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	16
β-strand	216-220	5	17
β-strand	224-230	7	17
β-strand	233	1	16
β-strand	235-237	3	18
β-strand	241-245	5	16
β-strand	251-254	4	16
β-strand	255-260	6	17
β-strand	263-265	3	17
β-strand	267-269	3	18
β-strand	273-278	6	17
β-strand	291-293	3	16
β-strand	300-310	11	19
β-strand	322-323	2	20
β-strand	329-332	4	19
β-strand	335-342	8	19
α-helix	343-344	2
β-strand	349-350	2	20
β-strand	355-367	13	19
β-strand	373-378	6	19
β-strand	381-391	11	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor EF-Tu	A, C, E, G, I, K	protein	37	Escherichia coli	P0CE47 (AlphaFold model)
Elongation factor EF-Tu	B, D, F, H, J, L	protein	335	Escherichia coli	P0CE47 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>2HDN_1 Elongation factor EF-Tu (chains A, C, E, G, I, K)
TKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAAR

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>2HDN_2 Elongation factor EF-Tu (chains B, D, F, H, J, L)
GITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREH
ILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKAL
EGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKV
GEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTI
KPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKM
VVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG

Ligands and cofactors

ID	Name	Formula	Copies
TAC	Tetracycline	C22 H24 N2 O8	6
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	6
MG	Magnesium ion	Mg	6

Primary citation

Molecular complementarity between tetracycline and the GTPase active site of elongation factor Tu. Heffron, S.E., Mui, S., Aorora, A. et al. Acta Crystallogr D Biol Crystallogr (2006) 62:1392-1400. DOI 10.1107/S0907444906035426 · 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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