5BN8 | pdb_00005bn8

Crystal structure of nucleotide-free human Hsp70 NBD.

• PDB DOI: https://doi.org/10.2210/pdb5BN8/pdb

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


• 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: 1.34 Å
• R-Value Free: 
  0.154 (Depositor), 0.155 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.132 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

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: 43.48 kDa 
• Atom Count: 3,708 
• Modeled 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): 0  Gene Names: HSPA1A, HSPA1, HSX70
UniProt & NIH Common Fund Data Resources
Find proteins for P0DMV8 (Homo sapiens) Explore P0DMV8  Go to UniProtKB:  P0DMV8
PHAROS:  P0DMV8 GTEx:  ENSG00000204389

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PO4	E [auth A], F [auth A], G [auth A], H [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.154 (Depositor), 0.155 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.132 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.129	α = 90
b = 63.7	β = 90
c = 144.118	γ = 90

Software Package:

Software Name	Purpose
REFMAC	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, Derived calculations, Refinement description