9GIA | pdb_00009gia

Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Bacillus cereus Apo-form

PDB DOI: https://doi.org/10.2210/pdb9GIA/pdb

Classification: TRANSFERASE
Organism(s): Bacillus cereus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-19 Released: 2025-09-03
Deposition Author(s): Saleem-Batcha, R., Keppler, M., Kuge, M., Andexer, J.N.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.273 (Depositor), 0.272 (DCC)
R-Value Work:
0.210 (Depositor), 0.217 (DCC)

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

Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Bacillus cereus Apo-form

Saleem-Batcha, R., Keppler, M., Kuge, M., Andexer, J.N.

To be published.

Macromolecule Content

Total Structure Weight: 69.88 kDa
Atom Count: 4,394
Modeled Residue Count: 502
Deposited Residue Count: 574
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyphosphate-AMP phosphotransferase	A, B	287	Bacillus cereus	Mutation(s): 0 Gene Names: pap, BC_1755 EC: 2
UniProt
Find proteins for Q81F46 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q81F46 Go to UniProtKB: Q81F46
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q81F46
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POP (Subject of Investigation/LOI) Query on POP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	D [auth A] E [auth A] F [auth A] G [auth B] I [auth B] D [auth A], E [auth A], F [auth A], G [auth B], I [auth B], J [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth B] Focus chain J [auth B]