5QK3 | pdb_00005qk3

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z239136710

PDB DOI: https://doi.org/10.2210/pdb5QK3/pdb
Deposition Group: G_1002057 (changed state) | Explore G_1002057

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

Deposited: 2018-10-31 Released: 2018-12-19
Deposition Author(s): Dubianok, Y., Collins, P., Krojer, T., Wright, N., Strain-Damerell, C., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Huber, K., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.266 (Depositor), 0.276 (DCC)
R-Value Work:
0.228 (Depositor), 0.242 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)

Dubianok, Y., Collins, P., Krojer, T., Wright, N., Strain-Damerell, C., Burgess-Brown, N., Bountra, C., Arrowsmith, C.H., Edwards, A., Huber, K., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 93.1 kDa
Atom Count: 5,999
Modeled Residue Count: 770
Deposited Residue Count: 836
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 GTEx: ENSG00000165609
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UKK9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K3A Query on K3A Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	N-(5-methyl-1H-pyrazol-3-yl)acetamide C₆ H₉ N₃ O LUFRABHJXNJTNZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C]	H [auth A], J [auth B], M [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	E [auth A] F [auth A] K [auth B] L [auth B] N [auth C] E [auth A], F [auth A], K [auth B], L [auth B], N [auth C], O [auth C], P [auth D], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.266 (Depositor), 0.276 (DCC)
R-Value Work: 0.228 (Depositor), 0.242 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.49	α = 79.15
b = 60.02	β = 81.35
c = 80.13	γ = 75.43

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-12-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-12-19
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-10-30
Changes: Structure summary
Version 1.3: 2026-02-18
Changes: Refinement description