9UUH | pdb_00009uuh

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

PDB DOI: https://doi.org/10.2210/pdb9UUH/pdb
EM Map EMD-64511: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Citrobacter freundii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-07 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: 3.07 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9UUH

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: 322.09 kDa
Atom Count: 21,000
Modeled Residue Count: 2,528
Deposited Residue Count: 2,732
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	683	Citrobacter freundii	Mutation(s): 0 Gene Names: ppk1, ppk, AI2935V1_1415, AM363_21060, AN672_02535, HV178_06940, I9Y29_001391, KY227_003292, O4000_06400, PQQ21_001765... ppk1, ppk, AI2935V1_1415, AM363_21060, AN672_02535, HV178_06940, I9Y29_001391, KY227_003292, O4000_06400, PQQ21_001765, RYZ67_05450, SGX49_000532 EC: 2.7.4.1
UniProt
Find proteins for A0A0D7LNR8 (Citrobacter freundii) Explore A0A0D7LNR8 Go to UniProtKB: A0A0D7LNR8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0D7LNR8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-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: 3.07 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

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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.