8UFF

Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAAGTGGG) in Ternary Complex with DB1976

  • Classification: TRANSCRIPTION
  • Organism(s): synthetic construct, Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-10-04 Released: 2024-10-09 
  • Deposition Author(s): Terrell, J.R., Poon, G.M.K., Wilson, W.D.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.166 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Literature

Structural studies on the PU.1 inhibitory mechanism by diamidine minor groove binders

Terrell, J.R., Paul, A., Ogbonna, E.N., Farahat, A.A., Poon, G.M.K., Wilson, W.D.

To be published.

Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor PU.1C [auth F]106Homo sapiensMutation(s): 0 
Gene Names: SPI1
UniProt & NIH Common Fund Data Resources
Find proteins for P17947 (Homo sapiens)
Explore P17947 
Go to UniProtKB:  P17947
PHAROS:  P17947
GTEx:  ENSG00000066336 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17947
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')A [auth C]16synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')B [auth D]16synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y5U (Subject of Investigation/LOI)
Query on Y5U
Download Ideal Coordinates CCD File 
D
(2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide)
C20 H16 N8 Se
NXECULIQZLOKFU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.913α = 90
b = 60.292β = 116.358
c = 44.393γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL155178
National Science Foundation (NSF, United States)United StatesMCB2028902
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM137160
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM111749

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release