5ZJY: Eukaryotic translation initiation factor 4E

Stapled-peptides tailored against initiation of translation. Determined by X-ray diffraction at 1.59 Å resolution. Released 20 Mar 2019.

Method: X-ray diffraction
Resolution: 1.59 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,789
Mol. weight: 24.45 kDa
Ligands: MGP
Released: 20 Mar 2019

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

Secondary structure: helices and β-sheets

5ZJY contains 11 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
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	111-117	7	1
α-helix	119-121	3
α-helix	122-126	5
α-helix	127-138	12
α-helix	143-148	6
β-strand	149-155	7	1
β-strand	161-167	7	1
α-helix	173-187	15
β-strand	196-199	4	1
α-helix	200-204	5
β-strand	215-216	2	1

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4E	A	protein	191	Homo sapiens	P06730 (AlphaFold model)
Lys-lys-arg-tyr-ser-arg-2JN-gln-leu-leu-2JN-phe	B	protein	14	Homo sapiens

Sequence of entity 1 (A), FASTA

>5ZJY_1 Eukaryotic translation initiation factor 4E (chains A)
MVANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLM
PGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYS
DDVCGAVVNVRAKGDKIAIWTTECENREAVTHIGRVYKERLGLPPKIVIGYQSHADTATK
SGSTTKNRFVV

Sequence of entity 2 (B), FASTA

>5ZJY_2 LYS-LYS-ARG-TYR-SER-ARG-2JN-GLN-LEU-LEU-2JN-PHE (chains B)
XKKRYSRXQLLXFX

Ligands and cofactors

ID	Name	Formula	Copies
MGP	7-methyl-guanosine-5'-triphosphate	C11 H19 N5 O14 P3	1

Primary citation

Structural insights reveal a recognition feature for tailoring hydrocarbon stapled-peptides against the eukaryotic translation initiation factor 4E protein. Lama, D., Liberatore, A.M., Frosi, Y. et al. Chem Sci (2019) 10:2489-2500. DOI 10.1039/c8sc03759k · 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…
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
5EI3 1.71 Å, Co-crystal structure of eIF4E with nucleotide mimetic inhibitor.
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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