7D6Y | pdb_00007d6y

eIF4E in Complex with a Disulphide-Free Autonomous VH Domain

PDB DOI: https://doi.org/10.2210/pdb7D6Y/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-10-02 Released: 2021-10-06
Deposition Author(s): Brown, C.J., Frosi, Y., Jiang, S., Lin, Y.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.206 (Depositor), 0.215 (DCC)
R-Value Work:
0.181 (Depositor), 0.192 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Engineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways

Frosi, Y., Lin, Y.C., Jiang, S., Ramlan, S.R., Hew, K., Asial, I., Engman, A.H., Goh, M., Thean, D., Nordlund, P., Lane, D.P., Brown, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 43.02 kDa
Atom Count: 2,977
Modeled Residue Count: 314
Deposited Residue Count: 378
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 4E	A	217	Homo sapiens	Mutation(s): 0 Gene Names: EIF4E, EIF4EL1, EIF4F
UniProt & NIH Common Fund Data Resources
Find proteins for P06730 (Homo sapiens) Explore P06730 Go to UniProtKB: P06730
PHAROS: P06730 GTEx: ENSG00000151247
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06730
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VH Domain (1C5)	B	161	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGO Query on MGO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	[[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE C₁₂ H₂₀ N₄ O₁₄ P₃ LPHBJZOLBGBNJF-XYHAGOFUSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.206 (Depositor), 0.215 (DCC)
R-Value Work: 0.181 (Depositor), 0.192 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.848	α = 90
b = 45.324	β = 93.192
c = 39.763	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-10-06
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.