7BBP | pdb_00007bbp

Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac

• PDB DOI: https://doi.org/10.2210/pdb7BBP/pdb

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


• Deposited: 2020-12-18 Released: 2021-03-03 
• Deposition Author(s): Krojer, T., Talon, R., Fairhead, M., Szykowska, A., Burgess-Brown, N.A., Brennan, P.E., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.240 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.214 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac

Krojer, T., Talon, R., Fairhead, M., Szykowska, A., Burgess-Brown, N.A., Brennan, P.E., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.81 kDa 
• Atom Count: 4,228 
• Modeled Residue Count: 488 
• Deposited Residue Count: 532 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PH-interacting protein	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	128	Homo sapiens	Mutation(s): 0  Gene Names: PHIP, DCAF14, WDR11
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWQ0 (Homo sapiens) Explore Q8WWQ0  Go to UniProtKB:  Q8WWQ0
PHAROS:  Q8WWQ0 GTEx:  ENSG00000146247

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	E [auth FFF], F [auth GGG]	10	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q0VAS5 (Homo sapiens) Explore Q0VAS5  Go to UniProtKB:  Q0VAS5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth AAA]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	H [auth BBB], I [auth CCC]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	E [auth FFF], F [auth GGG]	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.240 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.214 (DCC) 

Diffraction Data: https://doi.org/10.5281/zenodo.4085070

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.21	α = 90
b = 58.31	β = 99.08
c = 77.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Krojer, T., Talon, R., Fairhead, M., Szykowska, A., Burgess-Brown, N.A., Brennan, P.E., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary