6FI3 | pdb_00006fi3

Crystal structure of ERK2 in complex with an adenosine derivative

• PDB DOI: https://doi.org/10.2210/pdb6FI3/pdb

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


• Deposited: 2018-01-16 Released: 2019-01-30 
• Deposition Author(s): Gelin, M., Labesse, G.
• Funding Organization(s): FRISBI

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ERK2 in complex with an adenosine derivative

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: 42.85 kDa 
• Atom Count: 3,188 
• Modeled Residue Count: 339 
• 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
DJ2	F [auth A]	(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-(azanyloxymethyl)oxolane-3,4-diol C10 H14 N6 O4 NHSVFFNZROZDBB-KQYNXXCUSA-N
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: 1.52 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.564	α = 90
b = 69.957	β = 108.56
c = 59.529	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-30 
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: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary