8QR9 | pdb_00008qr9

Crystal structure of ERK2 in complex with a covalently bound macrocyclic ligand

PDB DOI: https://doi.org/10.2210/pdb8QR9/pdb

Classification: SIGNALING PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-06 Released: 2025-04-16
Deposition Author(s): Gelin, M., Labesse, G.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.222 (Depositor), 0.223 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of ERK2 in complex with a covalently bound macrocyclic ligand

Gelin, M., Labesse, G., Guichou, J.-F., Pons, J.-L., Barluenga, S., Katickeyan, G., Winssinger, N.

To be published.

Macromolecule Content

Total Structure Weight: 43.24 kDa
Atom Count: 3,243
Modelled Residue Count: 346
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	364	Rattus norvegicus	Mutation(s): 0 Gene Names: Mapk1 EC: 2.7.11.24
UniProt
Find proteins for P63086 (Rattus norvegicus) Explore P63086 Go to UniProtKB: P63086
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63086
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WMX (Subject of Investigation/LOI) Query on WMX Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	(4~{S},9~{S},10~{S})-17-(ethoxymethoxy)-4-methyl-9,10,19-tris(oxidanyl)-3-oxabicyclo[13.4.0]nonadeca-1(19),15,17-triene-2,8-dione C₂₂ H₃₂ O₈ KDOYDBOXSWPABK-UAXOWTEWSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]