6DWS

Crystal structure of human GRP78 in complex with (2R,3R,4S,5R)-2-(6-amino-8-((2-chlorobenzyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol

• PDB DOI: https://doi.org/10.2210/pdb6DWS/pdb

• Classification: chaperone, transferase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-27 Released: 2019-07-03 
• Deposition Author(s): Chen, Y., Antoshchenko, T., Smil, D., Zepeda, C., Huang, Y., Park, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 

Literature

Crystal structure of human GRP78 in complex with (2R,3R,4S,5R)-2-(6-amino-8-((2-chlorobenzyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol

Chen, Y., Antoshchenko, T., Smil, D., Zepeda, C., Huang, Y., Park, H.W.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 85.17 kDa 
• Atom Count: 6,291 
• Modelled Residue Count: 763 
• Deposited Residue Count: 764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum chaperone BiP	A, B	382	Homo sapiens	Mutation(s): 0  Gene Names: HSPA5, GRP78 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P11021 (Homo sapiens) Explore P11021  Go to UniProtKB:  P11021
PHAROS:  P11021 GTEx:  ENSG00000044574

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HFY	C [auth A], E [auth B]	8-{[(2-chlorophenyl)methyl]amino}adenosine C17 H19 Cl N6 O4 HXRSLQGBEUJHPP-XNIJJKJLSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.248 
• R-Value Work: 0.213 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.916	α = 90
b = 74.611	β = 98.1
c = 86.848	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Chen, Y., Antoshchenko, T., Smil, D., Zepeda, C., Huang, Y., Park, H.W.

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Derived calculations