7NNJ

Crystal Structure of NUDT4 (Diphosphoinositol polyphosphate phosphohydrolase 2) in complex with 4-O-Bn-1-PCP-InsP4 (AMR2105)

PDB DOI: https://doi.org/10.2210/pdb7NNJ/pdb

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

Deposited: 2021-02-24 Released: 2022-03-23
Deposition Author(s): Dubianok, Y., Arruda Bezerra, G., Raux, B., Diaz Saez, L., Riley, A.M., Potter, B.V.L., Huber, K.V.M., von Delft, F.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.245
R-Value Work: 0.195
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of NUDT4 (Diphosphoinositol polyphosphate phosphohydrolase 2) in complex with 4-O-Bn-1-PCP-InsP4 (AMR2105)

Riley, A.M., Raux, B., Diaz Saez, L., Dubianok, Y., Arruda Bezerra, G., von Delft, F., Huber, K.V.M., Potter, B.V.L.

To be published.

Macromolecule Content

Total Structure Weight: 33.54 kDa
Atom Count: 2,257
Modelled Residue Count: 264
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diphosphoinositol polyphosphate phosphohydrolase 2	A, B	140	Homo sapiens	Mutation(s): 0 Gene Names: NUDT4, DIPP2, KIAA0487, HDCMB47P EC: 3.6.1.52
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZJ9 (Homo sapiens) Explore Q9NZJ9 Go to UniProtKB: Q9NZJ9
PHAROS: Q9NZJ9 GTEx: ENSG00000173598
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NZJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UJN (Subject of Investigation/LOI) Query on UJN Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B]	K [auth B]	[oxidanyl-[(2S,3R,5S,6S)-4-phenylmethoxy-2,3,5,6-tetraphosphonooxy-cyclohexyl]oxy-phosphoryl]methylphosphonic acid C₁₄ H₂₆ O₂₃ P₆ WTIJGFYHWWTXHU-BUCHIQEDSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B]	C [auth A], D [auth A], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B]	E [auth A], F [auth A], G [auth A], I [auth B], J [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]