5ISO

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


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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase catalytic subunit alpha-2
A, C
552Homo sapiensMutation(s): 0 
Gene Names: PRKAA2AMPKAMPK2
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data)
Find proteins for P54646 (Homo sapiens)
Go to UniProtKB:  P54646
NIH Common Fund Data Resources
PHAROS  P54646

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit beta-1
B, D
286Homo sapiensMutation(s): 0 
Gene Names: PRKAB1AMPK
Find proteins for Q9Y478 (Homo sapiens)
Go to UniProtKB:  Q9Y478
NIH Common Fund Data Resources
PHAROS  Q9Y478

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit gamma-1
E, F
331Homo sapiensMutation(s): 0 
Gene Names: PRKAG1
Find proteins for P54619 (Homo sapiens)
Go to UniProtKB:  P54619
NIH Common Fund Data Resources
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STU
Query on STU

Download CCD File 
A, C
STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
 Ligand Interaction
992
Query on 992

Download CCD File 
A, 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
 Ligand Interaction
AMP
Query on AMP

Download CCD File 
E, F
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B,DL-PEPTIDE LINKINGC3 H8 N O6 PSER
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 = 75.42α = 90
b = 129.39β = 92.73
c = 139.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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