8V9O

Imaging scaffold engineered to bind the therapeutic protein target BARD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.81 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

X-ray structure of a designed rigidified imaging scaffold engineered to bind the therapeutic protein target BARD1

Agdanowski, M.P.Castells-Graells, R.Sawaya, M.R.Yeates, T.O.Arbing, M.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tetrahedral Nanocage Cage, Non-Fusion Component
A, B, C
178synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tetrahedral Nanocage Cage Component Fused to Anti-BARD1 Darpin
D, E, F
322synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.81 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.01α = 90
b = 195.57β = 90
c = 228.37γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM129854
Department of Energy (DOE, United States)United StatesDE-FC02-02ER63421

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release