8PSR

ERK2 covalently bound to SynthRevD-12-opt artificial peptide

• PDB DOI: https://doi.org/10.2210/pdb8PSR/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-07-13 Released: 2024-07-24 
• Deposition Author(s): Sok, P., Poti, A., Gogl, G., Remenyi, A.
• Funding Organization(s): National Research Development and Innovation Office (NKFIH)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.209 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Targeting a key protein-protein interaction surface on mitogen-activated protein kinases by a Michael acceptor-based cyclic warhead scaffold

Sok, P., Poti, A., Balint, D., Soos, T., Remenyi, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 44.87 kDa 
• Atom Count: 3,351 
• Modelled Residue Count: 372 
• Deposited Residue Count: 383 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	364	Homo sapiens	Mutation(s): 0  Gene Names: MAPK1, ERK2, PRKM1, PRKM2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482  Go to UniProtKB:  P28482
GTEx:  ENSG00000100030

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SynthRevD-12-opt	B	19	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.209 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.13	α = 90
b = 62.13	β = 90
c = 214.98	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Sok, P., Poti, A., Gogl, G., Remenyi, A.

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Funding Organization	Location	Grant Number
National Research Development and Innovation Office (NKFIH)	Hungary	KKP 126963

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release