6DFM

Crystal structure of human GRP78 in complex with 8-aminoadenosine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


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.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoplasmic reticulum chaperone BiP
A, B
382Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11021
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3BH
Query on 3BH
Download Ideal Coordinates CCD File 
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 
IDSourceBinding 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 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.662α = 90
b = 74.775β = 99.48
c = 89.485γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
MOLREPphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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