2XSW | pdb_00002xsw

Crystal structure of human INPP5E

• PDB DOI: https://doi.org/10.2210/pdb2XSW/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-09-30 Released: 2010-11-17 
• Deposition Author(s): Tresaugues, L., Schutz, P., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Kouznetsova, E., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., Van Der Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Inpp5E

Tresaugues, L., Schutz, P., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Kouznetsova, E., Moche, M., Nyman, T., Persson, C., Schuler, H., Siponen, M.I., Thorsell, A.G., Van Der Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 81.41 kDa 
• Atom Count: 5,785 
• Modeled Residue Count: 666 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
72 KDA INOSITOL POLYPHOSPHATE 5-PHOSPHATASE	A, B	357	Homo sapiens	Mutation(s): 0  EC: 3.1.3.36 (PDB Primary Data), 3.1.3.86 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRR6 (Homo sapiens) Explore Q9NRR6  Go to UniProtKB:  Q9NRR6
PHAROS:  Q9NRR6 GTEx:  ENSG00000148384

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], G [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.528	α = 90
b = 103.579	β = 90
c = 137.545	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Tresaugues, L., Schutz, P., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Kouznetsova, E., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., Van Der Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Nordlund, P.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description