6C9H

non-phosphorylated AMP-activated protein kinase bound to pharmacological activator R734


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of AMP-activated protein kinase bound to novel pharmacological activators in phosphorylated, non-phosphorylated, and nucleotide-free states.

Yan, Y.Zhou, X.E.Novick, S.J.Shaw, S.J.Li, Y.Brunzelle, J.S.Hitoshi, Y.Griffin, P.R.Xu, H.E.Melcher, K.

(2019) J. Biol. Chem. 294: 953-967


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase catalytic subunit alpha-1
A
494Homo sapiensMutation(s): 0 
Gene Names: PRKAA1 (AMPK1)
EC: 2.7.11.1
Find proteins for Q13131 (Homo sapiens)
Go to Gene View: PRKAA1
Go to UniProtKB:  Q13131
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit beta-1
B
204Homo sapiensMutation(s): 1 
Gene Names: PRKAB1 (AMPK)
Find proteins for Q9Y478 (Homo sapiens)
Go to Gene View: PRKAB1
Go to UniProtKB:  Q9Y478
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit gamma-1
C
331Homo sapiensMutation(s): 0 
Gene Names: PRKAG1
Find proteins for P54619 (Homo sapiens)
Go to Gene View: PRKAG1
Go to UniProtKB:  P54619
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STU
Query on STU

Download SDF File 
Download CCD File 
A
STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
C
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
R34
Query on R34

Download SDF File 
Download CCD File 
A
5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide
C24 H19 Cl N4 O3
SCEVBRBKKQZTKM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.213 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 124.016α = 90.00
b = 124.016β = 90.00
c = 404.180γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesGM102545
National Institutes of Health/National Human Genome Research InstituteUnited StatesDK071662
National Natural Science Foundation of ChinaChina31300245
Ministry of Science and Technology (China)China2012ZX09301001
Ministry of Science and Technology (China)China2012CB910403
Ministry of Science and Technology (China)China2013CB910600
Ministry of Science and Technology (China)ChinaXDB08020303
Ministry of Science and Technology (China)China2013ZX09507001

Revision History 

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Database references
  • Version 1.2: 2019-01-30
    Type: Data collection, Database references