4F2L | pdb_00004f2l

Structure of a regulatory domain of AMPK

• PDB DOI: https://doi.org/10.2210/pdb4F2L/pdb

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


• Deposited: 2012-05-08 Released: 2013-06-26 
• Deposition Author(s): Xin, F.J., Zhang, Y.Y., Wang, J., Wang, Z.X., Wu, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.212 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Conserved regulatory elements in AMPK

Chen, L., Xin, F.J., Wang, J., Hu, J., Zhang, Y.Y., Wan, S., Cao, L.S., Lu, C., Li, P., Yan, S.F., Neumann, D., Schlattner, U., Xia, B., Wang, Z.X., Wu, J.W.

(2013) Nature 498: E8-E10

• PubMed: 23765502 
• DOI: https://doi.org/10.1038/nature12189
• Primary Citation of Related Structures:  
  4F2L

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Organizational Affiliation: 
• MOE Key Laboratory of Protein Sciences and Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.41 kDa 
• Atom Count: 604 
• Modeled Residue Count: 61 
• Deposited Residue Count: 61 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase catalytic subunit alpha-1	A	61	Rattus norvegicus	Mutation(s): 0  Gene Names: Prkaa1, Ampk1 EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (PDB Primary Data), 2.7.11.31 (UniProt)
UniProt
Find proteins for P54645 (Rattus norvegicus) Explore P54645  Go to UniProtKB:  P54645

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.212 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.117	α = 90
b = 36.258	β = 90
c = 98.755	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AutoSol	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-26 
Deposition Author(s): Xin, F.J., Zhang, Y.Y., Wang, J., Wang, Z.X., Wu, J.W.

Revision History  

• Version 1.0: 2013-06-26
  Type: Initial release
  
• Version 1.1: 2014-09-03
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary