6DO2

Crystal structure of human GRP78 in complex with 7-deaza-2'-C-methyladenosine

• PDB DOI: https://doi.org/10.2210/pdb6DO2/pdb

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


• Deposited: 2018-06-08 Released: 2019-06-12 
• Deposition Author(s): Ferrie, R.P., Chen, Y., Antoshchenko, T., Cooney, O.M., Huang, Y., Park, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal structure of human GRP78 in complex with 7-deaza-2'-C-methyladenosine

Ferrie, R.P., Chen, Y., Antoshchenko, T., Cooney, O.M., Huang, Y., Park, H.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 84.87 kDa 
• Atom Count: 6,322 
• Modelled Residue Count: 764 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H5V (Subject of Investigation/LOI)	C [auth A], D [auth B]	7-(2-C-methyl-beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine C12 H16 N4 O4 IRZRJANZDIOOIF-GAJNKVMBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.41	α = 90
b = 75.02	β = 99.11
c = 89.48	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Ferrie, R.P., Chen, Y., Antoshchenko, T., Cooney, O.M., Huang, Y., Park, H.W.

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references