7D6Y: EIF4E

eIF4E in Complex with a Disulphide-Free Autonomous VH Domain. Determined by X-ray diffraction at 1.67 Å resolution. Released 6 Oct 2021.

Method: X-ray diffraction
Resolution: 1.67 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,977
Mol. weight: 43.02 kDa
Ligands: MGO
Released: 6 Oct 2021

Explore 7D6Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7D6Y contains 16 α-helices and 21 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	111-116	6	1
α-helix	121	1
α-helix	122-126	5
α-helix	127-138	12
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	200-203	4
β-strand	215-216	2	1

Chain B: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	2
β-strand	12-13	2	3
β-strand	19-26	8	2
α-helix	30-32	3
β-strand	35-40	6	4
β-strand	47-53	7	4
β-strand	58-61	4	4
β-strand	66	1	2
β-strand	69-74	6	2
β-strand	79-84	6	2
α-helix	89-91	3
β-strand	93-100	8	4
α-helix	101	1
α-helix	102-104	3
α-helix	109-116	8
α-helix	117-120	4
β-strand	121-124	4	4
β-strand	128-130	3	4
β-strand	131-132	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic translation initiation factor 4E	A	protein	217	Homo sapiens	P06730 (AlphaFold model)
VH Domain (1C5)	B	protein	161	Homo sapiens

Sequence of entity 1 (A), FASTA

>7D6Y_1 Eukaryotic translation initiation factor 4E (chains A)
MATVEPETTPTPNPPTTEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKSKTWQANL
RLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQ
QRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIG
RVYKERLGLPPKIVIGYQSHADTATKSGSTTKNRFVV

Sequence of entity 2 (B), FASTA

>7D6Y_2 VH Domain (1C5) (chains B)
MSEVQLVESGGGLVQPGGSLRLSSAISGFSISSTSIDWVRQAPGKGLEWVARISPSSGST
SYADSVKGRFTISADTSKNTVYLQMNSLRAEDTAVYYTGRVAKDLNSSSPSFVVNTYSSF
GFDYRGQGTLVTVSSGAAEQKLISEEDLNGAAAFEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MGO	[[(2R,3S,4R,5R)-5-(6-amino-3-methyl-4-oxo-5H-IMIDAZO[4,5-c]pyridin-1-yl)-3,4-di…	C12 H20 N4 O14 P3	1

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

Primary citation

Engineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways. Frosi, Y., Lin, Y.C., Jiang, S. et al. To be published.

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
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

Browse structure collections

About this viewer

MolViewer shows 7D6Y directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.