6FXV

Crystal structure of ERK2 in complex with an adenosine derivative

• PDB DOI: https://doi.org/10.2210/pdb6FXV/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-09 Released: 2019-03-20 
• Deposition Author(s): Gelin, M., Labesse, G.
• Funding Organization(s): FRISBI

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.193 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Starting Model: experimental

Literature

None

Gelin, M., Pochet, S., Labesse, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43.06 kDa 
• Atom Count: 3,166 
• Modelled Residue Count: 337 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

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, Erk2, Mapk, Prkm1 EC: 2.7.11.24
UniProt
Find proteins for P63086 (Rattus norvegicus) Explore P63086  Go to UniProtKB:  P63086

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E9W	F [auth A]	azanylidene-[[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[2-oxidanylidene-2-(prop-2-ynylamino)ethyl]sulfanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylimino]azanium C15 H18 N9 O4 S JLTMRFGYLXJIRU-FRJWGUMJSA-O
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	B [auth A], C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.193 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.788	α = 90
b = 70.583	β = 109.02
c = 59.85	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Gelin, M., Labesse, G.

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Funding Organization	Location	Grant Number
FRISBI	France	ANR-10-INSB-05

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary