5S8F

XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N00572d (space group C2)

• PDB DOI: https://doi.org/10.2210/pdb5S8F/pdb
• Deposition Group: G_1002187 (changed state) ExploreG_1002187

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


• Deposited: 2020-12-17 Released: 2021-01-13 
• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 0.187 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

XChem group deposition

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: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 15.36 kDa 
• Atom Count: 1,163 
• Modelled Residue Count: 119 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PH-interacting protein	A	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZHA (Subject of Investigation/LOI)	B [auth A]	~{N}-(5-oxidanylidene-7,8-dihydro-6~{H}-naphthalen-2-yl)ethanamide C12 H13 N O2 WEBCZGJWXXPNHB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 0.187 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.94	α = 90
b = 27.52	β = 100.19
c = 56.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
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.

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references