5LTU | pdb_00005ltu

Crystal Structure of NUDT4A- Diphosphoinositol polyphosphate phosphohydrolase 2

• PDB DOI: https://doi.org/10.2210/pdb5LTU/pdb

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


• Deposited: 2016-09-07 Released: 2017-09-20 
• Deposition Author(s): Srikannathasan, V., Nunez, C.A., Tallant, C., Siejka, P., Mathea, S., Newman, J., Strain-Damerell, C., Elkins, J.M., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 
  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human NUDT4A- Diphosphoinositol polyphosphate phosphohydrolase 2

Srikannathasan, V., Huber, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.16 kDa 
• Atom Count: 2,078 
• Modeled Residue Count: 257 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diphosphoinositol polyphosphate phosphohydrolase 2	A, B	180	Homo sapiens	Mutation(s): 0  Gene Names: NUDT4, DIPP2, KIAA0487, HDCMB47P EC: 3.6.1.52 (PDB Primary Data), 3.6.1 (PDB Primary Data), 3.6.1.61 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZJ9 (Homo sapiens) Explore Q9NZJ9  Go to UniProtKB:  Q9NZJ9
PHAROS:  Q9NZJ9 GTEx:  ENSG00000173598

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free:  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.71	α = 90
b = 41.03	β = 122.55
c = 74.32	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Aimless	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Srikannathasan, V., Nunez, C.A., Tallant, C., Siejka, P., Mathea, S., Newman, J., Strain-Damerell, C., Elkins, J.M., Burgess-Brown, N., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2018-02-07
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description