5OPD: Phosphorylated EF-Tu

Structure of phosphorylated EF-Tu in complex with GTP. Determined by X-ray diffraction at 2.75 Å resolution. Released 29 Aug 2018.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Escherichia coli O9:H4 (strain HS)
Chains: 2
Atoms: 6,070
Mol. weight: 93.35 kDa
Ligands: GTP, MG
Released: 29 Aug 2018

Explore 5OPD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OPD contains 29 α-helices and 56 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: 14 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	1
β-strand	17-19	3	2
α-helix	25-39	15
α-helix	47-51	5
β-strand	66-71	6	1
β-strand	76-81	6	1
α-helix	85-93	9
β-strand	102-107	6	2
α-helix	114-126	13
β-strand	131-136	6	2
α-helix	144-160	17
β-strand	170-172	3	2
α-helix	175-180	6
α-helix	183-198	16
α-helix	201-205	5
α-helix	206-208	3
β-strand	212-214	3	3
β-strand	217-220	4	4
β-strand	221	1	5
β-strand	226-231	6	4
β-strand	234	1	3
β-strand	236-238	3	6
β-strand	242-246	5	3
α-helix	251	1
β-strand	252-255	4	3
β-strand	256-261	6	4
β-strand	264-266	3	4
β-strand	268-270	3	6
β-strand	274-279	6	4
α-helix	284-286	3
β-strand	292-294	3	3
β-strand	300-311	12	7
α-helix	312-313	2
α-helix	314-316	3
β-strand	323	1	8
β-strand	330-332	3	7
β-strand	339-343	5	7
α-helix	344-345	2
β-strand	351	1	8
β-strand	356-369	14	7
β-strand	374-379	6	7
β-strand	382-392	11	7

Chain B: 15 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	9
β-strand	17-18	2	10
α-helix	25-39	15
α-helix	48-51	4
β-strand	66-71	6	9
β-strand	76-81	6	9
α-helix	85-93	9
α-helix	95-97	3
β-strand	102-107	6	10
α-helix	114-126	13
β-strand	131-136	6	10
α-helix	138-140	3
α-helix	144-160	17
α-helix	165-167	3
β-strand	170-172	3	10
α-helix	175-180	6
α-helix	183-198	16
α-helix	201-202	2
α-helix	206-208	3
α-helix	210-211	2
β-strand	212-214	3	11
β-strand	217-220	4	12
β-strand	221	1	5
β-strand	226-231	6	12
β-strand	234	1	11
β-strand	236-238	3	13
β-strand	242-246	5	11
β-strand	252-255	4	11
β-strand	256-261	6	12
β-strand	264-266	3	12
β-strand	268-270	3	13
β-strand	274-279	6	12
α-helix	284-286	3
β-strand	292-294	3	11
β-strand	301-311	11	14
α-helix	314-316	3
β-strand	323	1	15
β-strand	330-332	3	14
β-strand	337-343	7	14
β-strand	351	1	15
β-strand	356-368	13	14
β-strand	374-378	5	14
β-strand	383-392	10	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor Tu 1	A, B	protein	400	Escherichia coli O9:H4 (strain HS)	P0CE47 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5OPD_1 Elongation factor Tu 1 (chains A, B)
MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARG
ITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHI
LLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALE
GDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVG
EEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIK
PHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMV
VTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2

Water and common crystallization additives (GOL, NA, IOD) are not listed.

Primary citation

Structure of phosphorylated EF-Tu in complex with GTP. Garcia-Pino, A. To be published.

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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