6P39 | pdb_00006p39

Crystal Structure Analysis of TAF1 Bromodomain

• PDB DOI: https://doi.org/10.2210/pdb6P39/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-23 Released: 2020-05-27 
• Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.212 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of TAF1 Bromodomain

Seo, H.-S., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.48 kDa 
• Atom Count: 1,080 
• Modeled Residue Count: 128 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 1	A	138	Homo sapiens	Mutation(s): 0  Gene Names: TAF1, BA2R, CCG1, CCGS, TAF2A EC: 2.3.1.48 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P21675 (Homo sapiens) Explore P21675  Go to UniProtKB:  P21675
PHAROS:  P21675 GTEx:  ENSG00000147133

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NQY (Subject of Investigation/LOI)	B [auth A]	3-methoxy-4-{[(6aR)-5-methyl-6-oxo-6,6a,7,8,9,10-hexahydro-5H-dipyrido[1,2-a:3',2'-e]pyrazin-2-yl]amino}-N-(1-methylpiperidin-4-yl)benzamide C26 H34 N6 O3 AVGGLPRMVXANOV-OAQYLSRUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NQY	BindingDB:  6P39	IC50: 63 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.212 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.6	α = 90
b = 96.6	β = 90
c = 91.13	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary