6P2U | pdb_00006p2u

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

• PDB DOI: https://doi.org/10.2210/pdb6P2U/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

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

• PubMed: 31177526 
• DOI: https://doi.org/10.1002/1873-3468.13475
• Primary Citation of Related Structures:  
  6P2U


• 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. 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.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 42 kDa 
• Atom Count: 3,113 
• Modelled Residue Count: 379 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stress-70 protein, mitochondrial	A	385	Homo sapiens	Mutation(s): 0  Gene Names: HSPA9, GRP75, HSPA9B, mt-HSP70
UniProt & NIH Common Fund Data Resources
Find proteins for P38646 (Homo sapiens) Explore P38646  Go to UniProtKB:  P38646
PHAROS:  P38646 GTEx:  ENSG00000113013

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO7 (Subject of Investigation/LOI)	B [auth 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
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.04	α = 90
b = 68.25	β = 90
c = 121.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-19 
Deposition Author(s): Moseng, M.A., Page, R.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM128595
National Science Foundation (NSF, United States)	United States	MCB 15-52113

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2019-07-03
  Changes: Data collection, Database references
• Version 1.2: 2019-08-28
  Changes: Data collection, Database references
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description