6P2U

Structure of Mortalin-NBD with N6-propargyladenosine-5'-diphosphate

  • Classification: CHAPERONE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)

  • Deposited: 2019-05-22 Released: 2019-06-19 
  • Deposition Author(s): Moseng, M.A., Page, R.C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); National Science Foundation (NSF, United States) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


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

Literature

2- and N6-functionalized adenosine-5'-diphosphate analogs for the inhibition of mortalin.

Moseng, M.A., Nix, J.C., Page, R.C.

(2019) Febs Lett. 593: 2030-2039

  • DOI: 10.1002/1873-3468.13475

  • PubMed Abstract: 

    • Our early efforts to find a covalent inhibitor of mortalin, a member of the 70 kD heat shock protein (Hsp70) family, led us to solve the structure of the mortalin nucleotide-binding domain (NBD) in complex with N6-propargyladenosine-5'-diphosphate. T ...

    Our early efforts to find a covalent inhibitor of mortalin, a member of the 70 kD heat shock protein (Hsp70) family, led us to solve the structure of the mortalin nucleotide-binding domain (NBD) in complex with N6-propargyladenosine-5'-diphosphate. The acquired structure emphasizes the ability of the nucleotide-binding pocket to accommodate modified ADP compounds. A library of ADP analogs modified at either the 2- or N6-positions of adenosine was screened against the mortalin-NBD. Competitive inhibition and binding assays of the analogs demonstrate that modifications at the 2- or N6-positions have potential to bind and inhibit mortalin uniquely compared to other Hsp70 homologs, and that modifications at the 2-position confer the greatest selectivity in binding and inhibition of the mortalin-NBD.

    Organizational Affiliation: 

    Molecular Biology Consortium, Beamline 4.2.2, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Stress-70 protein, mitochondrial
A
385Homo sapiensMutation(s): 0 
Gene Names: HSPA9 (GRP75, HSPA9B, mt-HSP70)
Find proteins for P38646 (Homo sapiens)
Go to Gene View: HSPA9
Go to UniProtKB:  P38646
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NO7
Query on NO7
Download SDF File 
Download CCD File 
A
9-{5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-alpha-D-ribofuranosyl}-N-(prop-2-yn-1-yl)-9H-purin-6-amine
C13 H17 N5 O10 P2
DYWGWOPDXRINLT-HMMKDHSLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.040α = 90.00
b = 68.250β = 90.00
c = 121.220γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM128595
National Science Foundation (NSF, United States)United StatesMCB 15-52113

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-03
    Type: Data collection, Database references
  • Version 1.2: 2019-08-28
    Type: Data collection, Database references
  • Version 1.3: 2019-11-27
    Type: Author supporting evidence