6GJ0

Human IMPase with Mn

• PDB DOI: https://doi.org/10.2210/pdb6GJ0/pdb

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


• Deposited: 2018-05-15 Released: 2018-10-17 
• Deposition Author(s): Kraft, L.V., Roe, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.210 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Literature

Co-crystallization of human inositol monophosphatase with the lithium mimetic L-690,330.

Kraft, L., Roe, S.M., Gill, R., Atack, J.R.

(2018) Acta Crystallogr D Struct Biol 74: 973-978

• PubMed: 30289407 
• DOI: https://doi.org/10.1107/S2059798318010380
• Primary Citation of Related Structures:  
  6GIU, 6GJ0


• PubMed Abstract: 
  

  Lithium, which is still the gold standard in the treatment of bipolar disorder, has been proposed to inhibit inositol monophosphatase (IMPase) and is hypothesized to exert its therapeutic effects by attenuating phosphatidylinositol (PI) cell signalling. Drug-discovery efforts have focused on small-molecule lithium mimetics that would specifically inhibit IMPase without exhibiting the undesired side effects of lithium. L-690,330 is a potent bisphosphonate substrate-based inhibitor developed by Merck Sharp & Dohme. To aid future structure-based inhibitor design, determination of the exact binding mechanism of L-690,330 to IMPase was of interest. Here, the high-resolution X-ray structure of human IMPase in complex with L690,330 and manganese ions determined at 1.39 Å resolution is reported.

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Organizational Affiliation: 

Sussex Drug Discovery Centre, University of Sussex, Chichester II, Falmer, Brighton BN1 9QJ, England.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 61.71 kDa 
• Atom Count: 4,797 
• Modelled Residue Count: 549 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol monophosphatase 1	A, B	277	Homo sapiens	Mutation(s): 0  Gene Names: IMPA1, IMPA EC: 3.1.3.25 (PDB Primary Data), 3.1.3.94 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P29218 (Homo sapiens) Explore P29218  Go to UniProtKB:  P29218
PHAROS:  P29218 GTEx:  ENSG00000133731

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	I [auth A], P [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	C [auth A], D [auth A], E [auth A], J [auth B], K [auth B], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.210 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.94	α = 90
b = 84.94	β = 90
c = 152.51	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Kraft, L.V., Roe, S.M.

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Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary