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

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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



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