2BVN: E. coli EF-Tu:GDPNP

Name: PDB 2BVN: E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa
Published: 2005-09-01
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: elongation factor

E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa. Determined by X-ray diffraction at 2.3 Å resolution. Released 1 Sept 2005.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: ESCHERICHIA COLI
Chains: 2
Atoms: 6,078
Mol. weight: 88.98 kDa
Ligands: ENX, MG, GNP
Released: 1 Sept 2005

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

Secondary structure: helices and β-sheets

2BVN contains 25 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: 13 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
α-helix	24-39	16
α-helix	60-62	3
β-strand	66-70	5	1
β-strand	75-80	6	1
α-helix	85-87	3
α-helix	88-95	8
β-strand	101-106	6	1
α-helix	113-125	13
β-strand	130-135	6	1
α-helix	137-139	3
α-helix	143-159	17
β-strand	169-171	3	1
α-helix	174-178	5
α-helix	182-198	17
α-helix	200-203	4
β-strand	205	1	2
β-strand	211-213	3	2
β-strand	217-220	4	2
β-strand	224-230	7	2
β-strand	233	1	2
β-strand	235-237	3	3
β-strand	241-246	6	2
β-strand	248-260	13	2
β-strand	263-265	3	2
β-strand	267-269	3	3
β-strand	273-279	7	2
α-helix	283-285	3
β-strand	288	1	4
β-strand	290	1	4
β-strand	291-293	3	2
β-strand	299-310	12	5
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: 12 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	7
α-helix	24-39	16
β-strand	66-70	5	7
β-strand	75-80	6	7
α-helix	85-87	3
α-helix	88-95	8
β-strand	101-106	6	7
α-helix	113-125	13
β-strand	130-135	6	7
α-helix	137-139	3
α-helix	143-159	17
β-strand	169-171	3	7
α-helix	174-178	5
α-helix	182-198	17
α-helix	200-203	4
β-strand	205	1	8
β-strand	211-213	3	8
β-strand	217-220	4	8
β-strand	224-230	7	8
β-strand	233	1	8
β-strand	235-237	3	9
β-strand	241-246	6	8
β-strand	248-260	13	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	288	1	10
β-strand	290	1	10
β-strand	291-293	3	8
β-strand	299-310	12	11
α-helix	313-315	3
β-strand	322-323	2	12
β-strand	329-332	4	11
β-strand	335-342	8	11
α-helix	343-344	2
β-strand	349-350	2	12
β-strand	355-368	14	11
β-strand	373-378	6	11
β-strand	381-391	11	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongation factor tu	A, B	protein	393	ESCHERICHIA COLI	P0CE48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2BVN_1 ELONGATION FACTOR TU (chains A, B)
SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGI
TINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHIL
LGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEG
DAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGE
EVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKP
HTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVV
TLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS

Ligands and cofactors

ID	Name	Formula	Copies
ENX	Enacyloxin iia	C33 H45 Cl2 N O11	2
MG	Magnesium ion	Mg	2
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	2

Primary citation

Enacyloxin Iia Pinpoints a Binding Pocket of Elongation Factor TU for Development of Novel Antibiotics. Parmeggiani, A., Krab, I.M., Watanabe, T. et al. J Biol Chem (2006) 281:2893. DOI 10.1074/JBC.M505951200 · PubMed

Other PDB entries of the same protein (UniProt P0CE48 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9T38 2.45 Å, Rhs2-CT endonuclease toxin in complex with cognate immunity protein RhsI2 and EF-Tu
6EZE 2.47 Å, The open conformation of E.coli Elongation Factor Tu in complex with GDPNP.
1DG1 2.5 Å, Whole, unmodified, ef-tu(elongation factor tu).
1EFU 2.5 Å, Elongation factor complex ef-tu/ef-ts from escherichia coli
3MMP 2.5 Å, Structure of the Qb replicase, an RNA-dependent RNA polymerase consisting of viral and…
1EFM 2.7 Å, Structure of the GDP domain of ef-tu and location of the amino acids homologous to ras…
8QFS 2.7 Å, Cryo-EM structure of SidH from Legionella pneumophila
5AFI 2.9 Å, 2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EM
5WDT 3.0 Å, 70S ribosome-EF-Tu H84A complex with GppNHp
5WFS 3.0 Å, 70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)
5WE4 3.1 Å, 70S ribosome-EF-Tu wt complex with GppNHp
8G7Q 3.1 Å, Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and…

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