5LF8 | pdb_00005lf8

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.298 (Depositor), 0.296 (DCC)
R-Value Work:
0.227 (Depositor), 0.236 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5LF8

This is version 1.1 of the entry. See complete history.

Literature

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

Huber, K.

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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 (PDB Primary Data), 3.6.1.62 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0C025 (Homo sapiens) Explore P0C025 Go to UniProtKB: P0C025
PHAROS: P0C025 GTEx: ENSG00000186364
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C025
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EMC Query on EMC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	ETHYL MERCURY ION C₂ H₅ Hg MJOUBOKSWBMNGQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.298 (Depositor), 0.296 (DCC)
R-Value Work: 0.227 (Depositor), 0.236 (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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-08-16

Deposition Author(s):

Burgess-Brown, N.

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.