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.

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 4F2L

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1038/nature12189
Primary Citation Related Structures:
4F2L

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54645
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-26

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.