9CIT | pdb_00009cit

Crystal structure of pyrophosphate-dependent phosphofructokinase from Candidatus Prometheoarchaeum syntrophicum with phosphoenolpyruvate, phosphate and Mg2+

PDB DOI: https://doi.org/10.2210/pdb9CIT/pdb

Classification: TRANSFERASE
Organism(s): Promethearchaeum syntrophicum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-04 Released: 2025-07-09
Deposition Author(s): Compton, J.A., Yosaatmadja, Y., Bashiri, G., Vickers, C.J., Patrick, W.M.
Funding Organization(s): Marsden Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.275 (Depositor), 0.280 (DCC)
R-Value Work:
0.216 (Depositor)
R-Value Observed:
0.219 (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

Structure and function of an unusual, multi-tasking phosphofructokinase from an Asgard archaeon

Compton, J.A., Yosaatmadja, Y., Bashiri, G., Vickers, C.J., Patrick, W.M.

To be published.

Macromolecule Content

Total Structure Weight: 187.91 kDa
Atom Count: 11,029
Modeled Residue Count: 1,532
Deposited Residue Count: 1,696
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphofructokinase	A [auth B], B [auth A], C, D	424	Promethearchaeum syntrophicum	Mutation(s): 0 Gene Names: DSAG12_00460 EC: 2.7.1
UniProt
Find proteins for A0A5B9D762 (Promethearchaeum syntrophicum) Explore A0A5B9D762 Go to UniProtKB: A0A5B9D762
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5B9D762
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEP (Subject of Investigation/LOI) Query on PEP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain E [auth B] MOL2 format, chain H [auth A] MOL2 format, chain E [auth B] mmCIF format, chain H [auth A] mmCIF format, chain E [auth B]	E [auth B], H [auth A]	PHOSPHOENOLPYRUVATE C₃ H₅ O₆ P DTBNBXWJWCWCIK-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain H [auth A] Interactions & Density Focus chain E [auth B] Focus chain H [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth D] MOL2 format, chain F [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth D] mmCIF format, chain F [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth D]	F [auth B], I [auth A], J [auth A], M [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth D] Interactions & Density Focus chain F [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	G [auth A], K [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth D]