5FBQ

PI4KB in complex with Rab11 and the MI358 Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5FBQ/pdb

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


• 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: 3.79 Å
• R-Value Free: 0.302 
• R-Value Work: 0.248 
• R-Value Observed: 0.251 

Starting Model: experimental

Literature

PI4KB in complex with Rab11 and the MI358 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: 91.09 kDa 
• Atom Count: 5,027 
• Modelled Residue Count: 629 
• 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): 0  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
5W6	C [auth A]	~{N}-[2-[[6-chloranyl-3-[3-[4-(hydroxymethyl)piperidin-1-yl]sulfonyl-4-methoxy-phenyl]-2-methyl-imidazo[1,2-b]pyridazin-8-yl]amino]ethyl]ethanamide C24 H31 Cl N6 O5 S IEPPNMCWFCTFFK-UHFFFAOYSA-N
GDP	D [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5W6	BindingDB:  5FBQ	IC50: 15 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.79 Å
• R-Value Free: 0.302 
• R-Value Work: 0.248 
• R-Value Observed: 0.251 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.759	α = 90
b = 101.155	β = 90
c = 188.486	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASES	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