5RKV | pdb_00005rkv

PanDDA analysis group deposition -- Crystal Structure of PHIP in complex with Z56877838

• PDB DOI: https://doi.org/10.2210/pdb5RKV/pdb
• Deposition Group: G_1002162 (changed state) ExploreG_1002162

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


• Deposited: 2020-06-02 Released: 2020-06-17 
• Deposition Author(s): Grosjean, H., Aimon, A., Krojer, T., Talon, R., Douangamath, A., Koekemoer, L., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Biggin, P.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

PanDDA analysis group deposition of ground-state model

Grosjean, H., Aimon, A., Krojer, T., Talon, R., Douangamath, A., Koekemoer, L., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Biggin, P.C.

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: 17.99 kDa 
• Atom Count: 1,281 
• Modeled Residue Count: 119 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PH-interacting protein	A	149	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
YI6 (Subject of Investigation/LOI)	B [auth A], C [auth A]	2-(4-ethoxyphenyl)ethanoic acid C10 H12 O3 ZVVWZNFSMIFGEP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.137	α = 90
b = 27.095	β = 100.43
c = 56.37	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Grosjean, H., Aimon, A., Krojer, T., Talon, R., Douangamath, A., Koekemoer, L., Arrowsmith, C.H., Edwards, A., Bountra, C., von Delft, F., Biggin, P.C.

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references