5LOR | pdb_00005lor

human NUDT22

PDB DOI: https://doi.org/10.2210/pdb5LOR/pdb

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

Deposited: 2016-08-09 Released: 2017-08-16
Deposition Author(s): Carter, M., Stenmark, P.
Funding Organization(s): Swedish Research Council, Wenner-Gren Foundation, Swedish Cancer Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.244 (Depositor), 0.250 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and functional studies of human NUDT22

Carter, M., Ann-Sofie, J., Patrick, H., Puigvert, J.C., Carranza, M.M., Vallin, K.S.A., Helleday, T., Stenmark, P.

To be published.

Macromolecule Content

Total Structure Weight: 71.62 kDa
Atom Count: 4,571
Modelled Residue Count: 581
Deposited Residue Count: 660
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate-linked moiety X motif 22	A, B	330	Homo sapiens	Mutation(s): 0 Gene Names: NUDT22, PP11246 EC: 3.6.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRQ3 (Homo sapiens) Explore Q9BRQ3 Go to UniProtKB: Q9BRQ3
PHAROS: Q9BRQ3 GTEx: ENSG00000149761
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BRQ3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG Query on UPG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.244 (Depositor), 0.250 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.332	α = 90
b = 46.565	β = 94.27
c = 120.678	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--
Wenner-Gren Foundation	Sweden	--
Swedish Cancer Society	Sweden	--

Revision History (Full details and data files)

Version 1.0: 2017-08-16
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Refinement description

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.