4HN2 | pdb_00004hn2

Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with AMPPNP and a substrate analog 5PA-IP5

• PDB DOI: https://doi.org/10.2210/pdb4HN2/pdb
• Entry: 4HN2 supersedes: 4GB4

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


• Deposited: 2012-10-18 Released: 2012-10-31 
• Deposition Author(s): Wang, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.222 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

First synthetic analogues of diphosphoinositol polyphosphates: interaction with PP-InsP(5) kinase.

Riley, A.M., Wang, H., Weaver, J.D., Shears, S.B., Potter, B.V.

(2012) Chem Commun (Camb) 48: 11292-11294

• PubMed: 23032903 
• DOI: https://doi.org/10.1039/c2cc36044f
• Primary Citation Related Structures: 
  4HN2


• PubMed Abstract: 
  

  We synthesised analogues of diphosphoinositol polyphosphates (PP-InsPs) in which the diphosphate is replaced by an α-phosphonoacetic acid (PA) ester. Structural analysis revealed that 5-PA-InsP(5) mimics 5-PP-InsP(5) binding to the kinase domain of PPIP5K2; both molecules were phosphorylated by the enzyme. PA-InsPs are promising candidates for further studies into the biology of PP-InsPs.

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Organizational Affiliation: 
• Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of 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: 38.87 kDa 
• Atom Count: 3,096 
• Modeled Residue Count: 325 
• 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: HISPPD1, KIAA0433, PPIP5K2, 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0EJ	C [auth A]	(2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]oxy}ethyl)phosphonic acid C8 H20 O25 P6 JGWVNODNEALCIO-QEEWUKHFSA-N
ANP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	D [auth A], E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.222 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.666	α = 90
b = 110.768	β = 90
c = 41.536	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Wang, H.
• This entry supersedes: 4GB4

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2012-11-07
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description