5BYB

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PA)2-IP4

• PDB DOI: https://doi.org/10.2210/pdb5BYB/pdb

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


• Deposited: 2015-06-10 Released: 2015-07-22 
• Deposition Author(s): Wang, H., Shears, S.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.189 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Synthetic tools for studying the chemical biology of InsP8.

Riley, A.M., Wang, H., Shears, S.B., L Potter, B.V.

(2015) Chem Commun (Camb) 51: 12605-12608

• PubMed: 26153667 
• DOI: https://doi.org/10.1039/c5cc05017k
• Primary Citation of Related Structures:  
  5BYA, 5BYB


• PubMed Abstract: 
  

  To synthesise stabilised mimics of InsP8, the most phosphorylated inositol phosphate signalling molecule in Nature, we replaced its two diphosphate (PP) groups with either phosphonoacetate (PA) or methylenebisphosphonate (PCP) groups. Utility of the PA and PCP analogues was verified by structural and biochemical analyses of their interactions with enzymes of InsP8 metabolism.

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Organizational Affiliation: 

Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK.

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: 39.24 kDa 
• Atom Count: 2,893 
• Modelled Residue Count: 317 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2	A	330	Homo sapiens	Mutation(s): 0  Gene Names: PPIP5K2, HISPPD1, KIAA0433, VIP2 EC: 2.7.4.21 (PDB Primary Data), 2.7.4.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O43314 (Homo sapiens) Explore O43314  Go to UniProtKB:  O43314
PHAROS:  O43314 GTEx:  ENSG00000145725

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4WY	C [auth A]	{[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(2-oxoethane-2,1-diyl)]}bis(phosphonic acid) C10 H22 O26 P6 KMLKNZLYFKMCMH-COQVWMOOSA-N
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
EDO	J [auth A], K [auth A], L [auth A], M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	G [auth A], H [auth A], I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	D [auth A], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.246 
• R-Value Work: 0.189 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.807	α = 90
b = 110.411	β = 90
c = 41.423	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Wang, H., Shears, S.B.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2015-08-05
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description