5EI3: Eukaryotic translation initiation factor 4E

Name: PDB 5EI3: Co-crystal structure of eIF4E with nucleotide mimetic inhibitor.
Published: 2016-09-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Determined by X-ray diffraction at 1.71 Å resolution. Released 7 Sept 2016.

Method: X-ray diffraction
Resolution: 1.71 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 2,103
Mol. weight: 27.58 kDa
Ligands: 5O8
Released: 7 Sept 2016

Explore 5EI3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EI3 contains 12 α-helices and 8 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: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
β-strand	38-48	11	1
α-helix	57-59	3
β-strand	60-68	9	1
α-helix	69-76	8
α-helix	82-84	3
α-helix	86	1
β-strand	90-95	6	1
β-strand	111-116	6	1
α-helix	121-124	4
α-helix	126-138	13
α-helix	143-148	6
β-strand	149-155	7	1
β-strand	162-167	6	1
α-helix	173-187	15
β-strand	196-199	4	1
α-helix	200-205	6
α-helix	210-213	4
β-strand	215-216	2	1

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	626-630	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4E	A	protein	217	Homo sapiens	P06730 (AlphaFold model)
Eukaryotic translation initiation factor 4 gamma	B	protein	14	synthetic construct	Q04637 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5EI3_1 Eukaryotic translation initiation factor 4E (chains A)
MATVEPETTPTPNPPTTEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKSKTWQANL
RLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQ
QRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIG
RVYKERLGLPPKIVIGYQSHADTATKSGSTTKNRFVV

Sequence of entity 2 (B), FASTA

>5EI3_2 Eukaryotic translation initiation factor 4 gamma (chains B)
KKRYDREFLLGFQF

Ligands and cofactors

ID	Name	Formula	Copies
5O8	~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-1…	C18 H20 F3 N6 O6 S	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Design of nucleotide-mimetic and non-nucleotide inhibitors of the translation initiation factor eIF4E: Synthesis, structural and functional characterisation. Soukarieh, F., Nowicki, M.W., Bastide, A. et al. Eur J Med Chem (2016) 124:200-217. DOI 10.1016/j.ejmech.2016.08.047 · PubMed

Other PDB entries of the same protein (UniProt P06730 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4TPW 1.5 Å, The co-complex structure of the translation initiation factor eIF4E with the inhibitor…
5T46 1.53 Å, Crystal structure of the human eIF4E-eIF4G complex
8QM8 1.58 Å, Potential drug binding sites for translation initiation factor eIF4E
4TQB 1.59 Å, The co-complex structure of the translation initiation factor eIF4E with the inhibitor…
5ZJY 1.59 Å, Stapled-peptides tailored against initiation of translation
7D6Y 1.67 Å, eIF4E in Complex with a Disulphide-Free Autonomous VH Domain
5ZJZ 1.67 Å, Stapled-peptides tailored against initiation of translation
4UED 1.75 Å, Complex of human eIF4E with the 4E binding protein 4E-BP1
5ZK9 1.76 Å, Stapled-peptides tailored against initiation of translation
4TQC 1.8 Å, The co-complex structure of the translation initiation factor eIF4E with the inhibitor…
5ZML 1.8 Å, Stapled-peptides tailored against initiation of translation
7XTP 1.83 Å, eIF4E in Complex with a Disulphide-Free Autonomous VH Domain

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