5FBR | pdb_00005fbr

PI4KB in complex with Rab11 and the MI359 Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5FBR/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-12-14 Released: 2016-12-28 
• Deposition Author(s): Chalupska, D., Mejdrova, I., Nencka, R., Boura, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.28 Å
• R-Value Free: 
  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

PI4KB in complex with Rab11 and the MI359 Inhibitor

Chalupska, D., Mejdrova, I., Nencka, R., Boura, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 91.17 kDa 
• Atom Count: 5,081 
• Modeled Residue Count: 632 
• Deposited Residue Count: 793 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4-kinase beta,Phosphatidylinositol 4-kinase beta	A	572	Homo sapiens	Mutation(s): 0  Gene Names: PI4KB, PIK4CB EC: 2.7.1.67
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBF8 (Homo sapiens) Explore Q9UBF8  Go to UniProtKB:  Q9UBF8
PHAROS:  Q9UBF8 GTEx:  ENSG00000143393

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-11A	B	221	Homo sapiens	Mutation(s): 1  Gene Names: RAB11A, RAB11 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62491 (Homo sapiens) Explore P62491  Go to UniProtKB:  P62491
PHAROS:  P62491 GTEx:  ENSG00000103769

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5W7	C [auth A]	~{N}-[2-[[3-[3-[(4-azanylcyclohexyl)sulfamoyl]-4-methoxy-phenyl]-6-chloranyl-2-methyl-imidazo[1,2-b]pyridazin-8-yl]amino]ethyl]ethanamide C24 H32 Cl N7 O4 S HORACVGDHNAIMC-IYARVYRRSA-N
GSP	D [auth B]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C10 H16 N5 O13 P3 S XOFLBQFBSOEHOG-UUOKFMHZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5W7	BindingDB:  5FBR	IC50: 27 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.28 Å
• R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.266	α = 90
b = 103.937	β = 90
c = 187.646	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Chalupska, D., Mejdrova, I., Nencka, R., Boura, E.

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description