5BN9

Crystal structure of ADP bound human Hsp70 NBD mutant R272K.

• PDB DOI: https://doi.org/10.2210/pdb5BN9/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-05-25 Released: 2016-09-14 
• Deposition Author(s): Narayanan, D., Engh, R.A.
• Funding Organization(s): FRINAT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.201 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Nucleotide binding to variants of the HSP70-NBD.

Narayanan, D., Pflug, A., Christopeit, T., Kyomuhendo, P., Engh, R.A.

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)

Macromolecule Content

• Total Structure Weight: 43.55 kDa 
• Atom Count: 3,268 
• Modelled Residue Count: 379 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock 70 kDa protein 1A	A	388	Homo sapiens	Mutation(s): 1  Gene Names: HSPA1A, HSPA1, HSX70
UniProt & NIH Common Fund Data Resources
Find proteins for P0DMV8 (Homo sapiens) Explore P0DMV8  Go to UniProtKB:  P0DMV8
GTEx:  ENSG00000204389

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
EPE	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ADP	BindingDB:  5BN9	Kd: min: 320, max: 324 (nM) from 2 assay(s)
		IC50: 280 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.201 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.933	α = 90
b = 63.21	β = 90
c = 143.872	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
MOLREP	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Narayanan, D., Engh, R.A.

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Funding Organization	Location	Grant Number
FRINAT	Norway	191303

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description