9HS3 | pdb_00009hs3

Crystal structure of the Escherichia coli nucleosidase PpnN (E264A, pppGpp form)

PDB DOI: https://doi.org/10.2210/pdb9HS3/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-12-18 Released: 2025-11-12
Deposition Author(s): Baerentsen, R.L., Brodersen, D.E.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.278 (Depositor), 0.278 (DCC)
R-Value Work:
0.221 (Depositor), 0.215 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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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

Catalytic mechanism and differential alarmone regulation of a conserved stringent nucleosidase

Baerentsen, R.L., Kronborg, K., Brodersen, D.E., Zhang, Y.E.

(2025) Structure

DOI: https://doi.org/10.1016/j.str.2025.10.012

Macromolecule Content

Total Structure Weight: 209.3 kDa
Atom Count: 14,254
Modeled Residue Count: 1,783
Deposited Residue Count: 1,832
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase	A, B, C, D	458	Escherichia coli K-12	Mutation(s): 1 Gene Names: ppnN, ygdH, b2795, JW2766 EC: 3.2.2 (PDB Primary Data), 3.2.2.10 (PDB Primary Data), 3.2.2.4 (PDB Primary Data)
UniProt
Find proteins for P0ADR8 (Escherichia coli (strain K12)) Explore P0ADR8 Go to UniProtKB: P0ADR8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ADR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0O2 (Subject of Investigation/LOI) Query on 0O2 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	F [auth A], H [auth B], K [auth D], L [auth D]	guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate) C₁₀ H₁₈ N₅ O₂₀ P₅ KCPMACXZAITQAX-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth D] Focus chain L [auth D]
HSX (Subject of Investigation/LOI) Query on HSX Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D]	E [auth A], G [auth B], I [auth C], J [auth D]	5-O-phosphono-alpha-D-ribofuranose C₅ H₁₁ O₈ P KTVPXOYAKDPRHY-AIHAYLRMSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain J [auth D]