5M7Z | pdb_00005m7z

Translation initiation factor 4E in complex with (SP)-m2(7,2'O)GppSepG mRNA 5' cap analog (beta-Se-ARCA D2)

PDB DOI: https://doi.org/10.2210/pdb5M7Z/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-10-28 Released: 2017-12-20
Deposition Author(s): Warminski, M., Nowak, E., Kowalska, J., Jemielity, J., Nowotny, M.
Funding Organization(s): Ministry of Science and Higher Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.219 (Depositor), 0.223 (DCC)
R-Value Observed:
0.220 (Depositor)

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 (SP)-m2(7,2'O)GppSepG mRNA 5' cap analog (beta-Se-ARCA D2)

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

To be published.

Macromolecule Content

Total Structure Weight: 91.44 kDa
Atom Count: 5,730
Modeled Residue Count: 658
Deposited Residue Count: 760
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63073
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7LO Query on 7LO Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], J [auth C]	[[[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-selanyl-phosphoryl] [(2~{R},3~{S},4~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C₂₂ H₃₂ N₁₀ O₁₇ P₃ Se LVNVABJMRYMPGM-DCILJVRDSA-O		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]