6GKK

Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 1 (m7GppSpApG D1)

PDB DOI: https://doi.org/10.2210/pdb6GKK/pdb

Classification: TRANSLATION
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-05-21 Released: 2019-06-19
Deposition Author(s): Warminski, M., Nowak, E., Kowalska, J., Jemielity, J., Nowotny, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.234
R-Value Work: 0.195
R-Value Observed: 0.196

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 1 (m7GppSpApG D1)

Warminski, M., Nowak, E., Kubacka, D., Kowalska, J., Nowotny, M., Jemielity, J.

To be published.

Macromolecule Content

Total Structure Weight: 91.13 kDa
Atom Count: 6,191
Modelled Residue Count: 723
Deposited Residue Count: 760
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 4E	A, B, C, D	190	Mus musculus	Mutation(s): 0 Gene Names: Eif4e
UniProt & NIH Common Fund Data Resources
Find proteins for P63073 (Mus musculus) Explore P63073 Go to UniProtKB: P63073
IMPC: MGI:95305
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63073
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WZO Query on WZO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D]	E [auth A], H [auth B], J [auth C], K [auth D]	[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl [phosphonooxy(sulfanyl)phosphoryl] hydrogen phosphate C₁₂ H₂₁ N₅ O₁₃ P₃ S NSORGZXNYGWJBQ-ZRDSBRMSSA-O		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	F [auth A], G [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B]