6IN1 | pdb_00006in1

Crystal structure of the first bromodomain of BRD4 in complex with 18-Crown-6

• PDB DOI: https://doi.org/10.2210/pdb6IN1/pdb

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


• Deposited: 2018-10-24 Released: 2019-10-30 
• Deposition Author(s): Yokoyama, T., Kosaka, Y., Matsumoto, K., Kitakami, R., Nabeshima, Y., Mizuguchi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Crown Ethers as Transthyretin Amyloidogenesis Inhibitor

Yokoyama, T., Kosaka, Y., Matsumoto, K., Kitakami, R., Nabeshima, Y., Mizuguchi, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.85 kDa 
• Atom Count: 1,273 
• Modeled Residue Count: 128 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	135	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LOC	B [auth A]	N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide C22 H25 N O6 IAKHMKGGTNLKSZ-INIZCTEOSA-N
O4B	C [auth A]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C12 H24 O6 XEZNGIUYQVAUSS-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.633	α = 90
b = 44.896	β = 90
c = 78.251	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Yokoyama, T., Kosaka, Y., Matsumoto, K., Kitakami, R., Nabeshima, Y., Mizuguchi, M.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations