8QRA | pdb_00008qra

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

PDB DOI: https://doi.org/10.2210/pdb8QRA/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: 1.55 Å
R-Value Free:
0.182 (Depositor), 0.182 (DCC)
R-Value Work:
0.142 (Depositor), 0.142 (DCC)
R-Value Observed:
0.144 (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: 42.86 kDa
Atom Count: 3,235
Modeled Residue Count: 341
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WM6 (Subject of Investigation/LOI) Query on WM6 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]	(4~{R},5~{S},6~{S})-4,5,6,15,17-pentakis(oxidanyl)-2,12-dioxabicyclo[12.4.0]octadeca-1(14),15,17-triene-7,13-dione C₁₆ H₂₀ O₉ JTDNYLVWHABXBF-UGFHNGPFSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.182 (Depositor), 0.182 (DCC)
R-Value Work: 0.142 (Depositor), 0.142 (DCC)
R-Value Observed: 0.144 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.65	α = 90
b = 69.84	β = 109.38
c = 59.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
MOSFLM	data reduction
PHENIX	phasing
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE18-0025

Revision History (Full details and data files)

Version 1.0: 2025-04-16
Type: Initial release

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.