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


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 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endoplasmic reticulum chaperone BiPA, B382Homo sapiensMutation(s): 0 
Gene Names: HSPA5GRP78
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11021
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HFY
Query on HFY

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
8-{[(2-chlorophenyl)methyl]amino}adenosine
C17 H19 Cl N6 O4
HXRSLQGBEUJHPP-XNIJJKJLSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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 = 54.916α = 90
b = 74.611β = 98.1
c = 86.848γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release