6PMT

Structure of Mortalin-NBD with adenosine-5'-monophosphate and thiodiphosphate

• PDB DOI: https://doi.org/10.2210/pdb6PMT/pdb

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


• Deposited: 2019-07-02 Released: 2020-07-08 
• Deposition Author(s): Moseng, M.A., Nix, J.C., 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: 2.30 Å
• R-Value Free: 0.205 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Structure of the mortalin nucleotide binding domain in complex with adenosine monophosphate

Moseng, M.A., Nix, J.C., Page, R.C.

To be published.

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: 42.05 kDa 
• Atom Count: 2,967 
• Modelled Residue Count: 376 
• 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
AMP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
PIS (Subject of Investigation/LOI)	C [auth A]	TRIHYDROGEN THIODIPHOSPHATE H3 O6 P2 S HWTUHTNZLQJJEV-UHFFFAOYSA-M
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.205 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.829	α = 90
b = 56.548	β = 90
c = 141.363	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Moseng, M.A., Nix, J.C., 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: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description