5LF8

Human Nucleoside diphosphate-linked moiety X motif 17 (NUDT17)

• PDB DOI: https://doi.org/10.2210/pdb5LF8/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-06-30 Released: 2017-08-16 
• Deposition Author(s): Mathea, S., Tallant, C., Salah, E., Wang, D., Velupillai, S., Nowak, R., Oerum, S., Krojer, T., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Huber, K., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.298 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Human Nucleoside diphosphate-linked moiety X motif 17 (NUDT17)

Huber, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.52 kDa 
• Atom Count: 1,784 
• Modelled Residue Count: 253 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate-linked moiety X motif 17	A	328	Homo sapiens	Mutation(s): 0  Gene Names: NUDT17 EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for P0C025 (Homo sapiens) Explore P0C025  Go to UniProtKB:  P0C025
PHAROS:  P0C025 GTEx:  ENSG00000186364

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EMC	C [auth A], D [auth A]	ETHYL MERCURY ION C2 H5 Hg MJOUBOKSWBMNGQ-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.298 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.913	α = 90
b = 151.913	β = 90
c = 81.495	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Mathea, S., Tallant, C., Salah, E., Wang, D., Velupillai, S., Nowak, R., Oerum, S., Krojer, T., Burgess-Brown, N., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Huber, K., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references