9URJ | pdb_00009urj

binary complex of polyP-bound polyphosphate kinase 1 (PPK1)

PDB DOI: https://doi.org/10.2210/pdb9URJ/pdb
EM Map EMD-64459: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-30 Released: 2026-03-04
Deposition Author(s): Jiang, W.J., Zhao, J., Wei, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.11 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9URJ

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

Literature

Structural Insights into PPK1 Catalyzed Triple Phosphoryl Transfer Underlying Polyphosphate Biosynthesis

Jiang, W.J., Zhao, J., Wei, W.

To be published.

Macromolecule Content

Total Structure Weight: 321.41 kDa
Atom Count: 20,676
Modeled Residue Count: 2,496
Deposited Residue Count: 2,736
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyphosphate kinase	A, B, C, D	684	Escherichia coli K-12	Mutation(s): 0 Gene Names: ppk, b2501, JW2486 EC: 2.7.4.1
UniProt
Find proteins for P0A7B1 (Escherichia coli (strain K12)) Explore P0A7B1 Go to UniProtKB: P0A7B1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7B1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7TT (Subject of Investigation/LOI) Query on 7TT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	Tetraphosphate H₆ O₁₃ P₄ YDHWWBZFRZWVHO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.11 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-03-04
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.