5AME | pdb_00005ame

Crystal structure of the bromodomain of human surface epitope engineered BRD1A in complex with 3D Consortium fragment 4-acetyl- piperazin-2-one (SGC - Diamond I04-1 fragment screening)

• PDB DOI: https://doi.org/10.2210/pdb5AME/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-03-10 Released: 2015-03-18 
• Deposition Author(s): Pearce, N.M., Fairhead, M., Strain-Damerell, C., Talon, R., Wright, N., Ng, J.T., Bradley, A., Cox, O., Bowkett, D., Collins, P., Brandao-Neto, J., Douangamath, A., Krojer, T., Burgess-Brown, N., Brennan, P., Arrowsmith, C.H., Edwards, E., Bountra, C., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: other

Literature

Crystal Structure of the Bromodomain of Human Surface Epitope Engineered Brd1A in Complex with 3D Consortium Fragment 4-Acetyl-Piperazin-2-One

Pearce, N.M., Fairhead, M., Strain-Damerell, C., Talon, R., Wright, N., Ng, J.T., Bradley, A., Cox, O., Bowkett, D., Collins, P., Brandao-Neto, J., Douangamath, A., Krojer, T., Burgess-Brown, N., Brennan, P., Arrowsmith, C.H., Edwards, E., Bountra, C., von Delft, F.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.67 kDa 
• Atom Count: 2,361 
• Modeled Residue Count: 246 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROMODOMAIN-CONTAINING PROTEIN 1	A, B	135	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens) Explore O95696  Go to UniProtKB:  O95696
PHAROS:  O95696 GTEx:  ENSG00000100425

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PW3	C [auth B]	4-acetyl-piperazin-2-one C6 H10 N2 O2 ISNPMTVERREURB-UHFFFAOYSA-N
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.554	α = 90
b = 56.537	β = 90
c = 101.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-18 
Deposition Author(s): Pearce, N.M., Fairhead, M., Strain-Damerell, C., Talon, R., Wright, N., Ng, J.T., Bradley, A., Cox, O., Bowkett, D., Collins, P., Brandao-Neto, J., Douangamath, A., Krojer, T., Burgess-Brown, N., Brennan, P., Arrowsmith, C.H., Edwards, E., Bountra, C., von Delft, F.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2019-03-06
  Changes: Data collection, Experimental preparation
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description