5ISO

STRUCTURE OF FULL LENGTH HUMAN AMPK (NON-PHOSPHORYLATED AT T-LOOP) IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR, A BENZIMIDAZOLE DERIVATIVE (991)

• PDB DOI: https://doi.org/10.2210/pdb5ISO/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-15 Released: 2017-03-29 
• Deposition Author(s): Xiao, B., Hubbard, J.A., Gamblin, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.230 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

STRUCTURE OF FULL LENGTH HUMAN AMPK (NON-PHOSPHORYLATED AT T-LOOP) IN COMPLEX WITH A SMALL MOLECULE ACTIVATOR, A BENZIMIDAZOLE DERIVATIVE (991)

Xiao, B., Hubbard, J.A., Gamblin, S.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 268.85 kDa 
• Atom Count: 14,898 
• Modelled Residue Count: 1,835 
• Deposited Residue Count: 2,338 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase catalytic subunit alpha-2	A, D [auth C]	552	Homo sapiens	Mutation(s): 0  Gene Names: PRKAA2, AMPK, AMPK2 EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P54646 (Homo sapiens) Explore P54646  Go to UniProtKB:  P54646
PHAROS:  P54646 GTEx:  ENSG00000162409

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit beta-1	B, E [auth D]	286	Homo sapiens	Mutation(s): 0  Gene Names: PRKAB1, AMPK
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y478 (Homo sapiens) Explore Q9Y478  Go to UniProtKB:  Q9Y478
PHAROS:  Q9Y478 GTEx:  ENSG00000111725

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit gamma-1	C [auth E], F	331	Homo sapiens	Mutation(s): 0  Gene Names: PRKAG1
UniProt & NIH Common Fund Data Resources
Find proteins for P54619 (Homo sapiens) Explore P54619  Go to UniProtKB:  P54619
PHAROS:  P54619 GTEx:  ENSG00000181929

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STU	G [auth A], L [auth C]	STAUROSPORINE C28 H26 N4 O3 HKSZLNNOFSGOKW-FYTWVXJKSA-N
992	H [auth A], M [auth C]	5-[[6-chloranyl-5-(1-methylindol-5-yl)-1H-benzimidazol-2-yl]oxy]-2-methyl-benzoic acid C24 H18 Cl N3 O3 FHWSAZXFPUMKFL-UHFFFAOYSA-N
AMP	I [auth E], J [auth E], K [auth E], N [auth F], O [auth F], P [auth F]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B, E [auth D]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.230 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.42	α = 90
b = 129.39	β = 92.73
c = 139.28	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Xiao, B., Hubbard, J.A., Gamblin, S.J.

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2019-06-12
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description