8VX7 | pdb_00008vx7

Computationally designed tunable C2 symmetric tandem repeat homodimer, bound to cyclic peptide

  • Classification: DE NOVO PROTEIN
  • Organism(s): synthetic construct
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-02-03 Released: 2025-02-05 
  • Deposition Author(s): Kennedy, M.A., Stoddard, B.L., Said, M.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.299 (Depositor), 0.297 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.258 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Computationally designed tunable C2 symmetric tandem repeat homodimer, bound to cyclic peptide

Kennedy, M.A., Stoddard, B.L., Said, M.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CID7
A, B
162synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MC18synthetic constructMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MEA
Query on MEA
C
L-PEPTIDE LINKINGC10 H13 N O2PHE
MLE
Query on MLE
C
L-PEPTIDE LINKINGC7 H15 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.299 (Depositor), 0.297 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.434α = 90
b = 79.802β = 90
c = 105.939γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesDGE-1762114
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM115545
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM139752
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01AG063845
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesU19AG065156

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release