3K2J

Crystal Structure of the 3rd Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)

• PDB DOI: https://doi.org/10.2210/pdb3K2J/pdb

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


• Deposited: 2009-09-30 Released: 2009-10-13 
• Deposition Author(s): Filippakopoulos, P., Picaud, S., Keates, T., Chaikuad, A., Pike, A.C.W., Krojer, T., Sethi, R., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 

Starting Models: experimental

Literature

Crystal Structure of the 3rd Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)

Filippakopoulos, P., Picaud, S., Keates, T., Chaikuad, A., Pike, A.C.W., Krojer, T., Sethi, R., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Bountra, C., Knapp, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.5 kDa 
• Atom Count: 2,013 
• Modelled Residue Count: 242 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein polybromo-1	A, B	130	Homo sapiens	Mutation(s): 0  Gene Names: PB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86U86 (Homo sapiens) Explore Q86U86  Go to UniProtKB:  Q86U86
PHAROS:  Q86U86 GTEx:  ENSG00000163939

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.270 
• R-Value Work: 0.224 
• R-Value Observed: 0.227 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.39	α = 90
b = 81.39	β = 90
c = 79.475	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Filippakopoulos, P., Picaud, S., Keates, T., Chaikuad, A., Pike, A.C.W., Krojer, T., Sethi, R., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary