7JIJ

ATP-bound AMP-activated protein kinase

• PDB DOI: https://doi.org/10.2210/pdb7JIJ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-07-23 Released: 2021-07-28 
• Deposition Author(s): Yan, Y., Zhou, X.E., Powell, K., Xu, T., Brunzelle, J.S., Xu, H.X., Melcher, K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.50 Å
• R-Value Free: 0.323 
• R-Value Work: 0.249 
• R-Value Observed: 0.253 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 155.81 kDa 
• Atom Count: 9,372 
• Modelled Residue Count: 1,161 
• Deposited Residue Count: 1,361 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin ABC transporter substrate-binding protein MalE	A [auth M]	373	Escherichia coli	Mutation(s): 0  Gene Names: malE, GRW33_05015
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase catalytic subunit alpha-1	B [auth A]	484	Homo sapiens	Mutation(s): 0  Gene Names: PRKAA1, AMPK1 EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13131 (Homo sapiens) Explore Q13131  Go to UniProtKB:  Q13131
PHAROS:  Q13131 GTEx:  ENSG00000132356

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit beta-2	C [auth B]	198	Homo sapiens	Mutation(s): 0  Gene Names: PRKAB2
UniProt & NIH Common Fund Data Resources
Find proteins for O43741 (Homo sapiens) Explore O43741  Go to UniProtKB:  O43741
PHAROS:  O43741 GTEx:  ENSG00000131791

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase subunit gamma-1	D [auth G]	306	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

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	E [auth C]	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	F [auth G]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP	H [auth G]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP	G	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B [auth A]	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	E [auth C]	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.50 Å
• R-Value Free: 0.323 
• R-Value Work: 0.249 
• R-Value Observed: 0.253 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.688	α = 90
b = 126.688	β = 90
c = 332.384	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Yan, Y., Zhou, X.E., Powell, K., Xu, T., Brunzelle, J.S., Xu, H.X., Melcher, K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM129436

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 1.1: 2021-09-08
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description