6DFM | pdb_00006dfm

Crystal structure of human GRP78 in complex with 8-aminoadenosine

• PDB DOI: https://doi.org/10.2210/pdb6DFM/pdb

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


• Deposited: 2018-05-15 Released: 2019-05-15 
• 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: 2.14 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal structure of human GRP78 in complex with 8-aminoadenosine

Ferrie, R.P., Chen, Y., Antoshchenko, T., Cooney, O.M., 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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 84.88 kDa 
• Atom Count: 6,410 
• Modeled 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
3BH	C [auth A], D [auth B]	(2R,3R,4S,5R)-2-(6,8-diaminopurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol C10 H14 N6 O4 DVGWFQILDUEEGX-UUOKFMHZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3BH	BindingDB:  6DFM	Kd: 6800 (nM) from 1 assay(s)
		-TΔS: -6.56e+0 (kJ/mol) from 1 assay(s)
		ΔH: -5.53e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.662	α = 90
b = 74.775	β = 99.48
c = 89.485	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Ferrie, R.P., Chen, Y., Antoshchenko, T., Cooney, O.M., Huang, Y., Park, H.W.

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references