6GRU

Crystal structure of human NUDT5

• PDB DOI:  https://doi.org/10.2210/pdb6GRU/pdb

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


• Deposited: 2018-06-12 Released: 2018-06-27 
• Deposition Author(s): Dubianok, Y., Collins, P., Krojer, T., Fairhead, M., MacLean, E., Diaz Saez, L., Strain-Damerell, C., Elkins, J., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Huber, K., von Delft, F., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.270 
• R-Value Work: 0.231 
• R-Value Observed: 0.233 

Literature

Crystal structure of human NUDT5

Dubianok, Y., Elkins, J., Bountra, C., Arrowsmith, C.H., Edwards, A., Huber, K., von Delft, F., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 92.9 kDa 
• Atom Count: 5,953 
• Modelled Residue Count: 769 
• Deposited Residue Count: 836 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-sugar pyrophosphatase	A, B, C, D	209	Homo sapiens	Mutation(s): 0  Gene Names: NUDT5, NUDIX5, HSPC115 EC: 3.6.1.13 (PDB Primary Data), 3.6.1.58 (PDB Primary Data), 2.7.7.96 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKK9 (Homo sapiens) Explore Q9UKK9  Go to UniProtKB:  Q9UKK9
PHAROS:  Q9UKK9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	H [auth B], K [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A], F [auth A], I [auth B], J [auth B], L [auth C], M [auth C], N [auth D], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.270 
• R-Value Work: 0.231 
• R-Value Observed: 0.233 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.6	α = 79.92
b = 60.14	β = 81.52
c = 80.01	γ = 75.49

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Dubianok, Y., Collins, P., Krojer, T., Fairhead, M., MacLean, E., Diaz Saez, L., Strain-Damerell, C., Elkins, J., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Huber, K., von Delft, F., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2018-06-27
  Type: Initial release