9WRZ | pdb_00009wrz

Crystal structure of NUDIX hydrolase E83A mutant from Limisphaera ngatamarikiensis in complex with ITP

PDB DOI: https://doi.org/10.2210/pdb9WRZ/pdb

Classification: HYDROLASE
Organism(s): Limisphaera ngatamarikiensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-09-12 Released: 2026-09-16
Deposition Author(s): Wu, W.Q., Li, Z.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.291 (Depositor), 0.296 (DCC)
R-Value Work:
0.247 (Depositor), 0.256 (DCC)
R-Value Observed:
0.251 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of NUDIX hydrolase E83A mutant from Limisphaera ngatamarikiensis in complex with ITP

Wu, W.Q., Li, Z.X.

To be published.

Macromolecule Content

Total Structure Weight: 96 kDa
Atom Count: 6,288
Modeled Residue Count: 779
Deposited Residue Count: 844
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUDIX domain-containing protein	A, B, C, D	211	Limisphaera ngatamarikiensis	Mutation(s): 1 Gene Names: G4L39_03320
UniProt
Find proteins for A0A6M1RLF6 (Limisphaera ngatamarikiensis) Explore A0A6M1RLF6 Go to UniProtKB: A0A6M1RLF6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6M1RLF6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CZU (Subject of Investigation/LOI) Query on CZU Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate C₁₀ H₁₅ N₄ O₁₄ P₃ HAEJPQIATWHALX-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]