9EBM | pdb_00009ebm

Piperazate synthase (PipS) in complex with haem and N5-OH-L-ornithine

PDB DOI: https://doi.org/10.2210/pdb9EBM/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces griseus subsp. griseus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-12 Released: 2025-01-22
Deposition Author(s): Higgins, M.A., Ryan, K.S.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.212 (Depositor), 0.213 (DCC)
R-Value Work:
0.174 (Depositor), 0.176 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure and mechanism of haem-dependent nitrogen-nitrogen bond formation in piperazate synthase

Higgins, M.A., Shi, X., Soler, J., Harland, J.B., Parkkila, T., Lehnert, N., Garcia-Borras, M., Du, Y.L., Ryan, K.S.

(2025) Nat Catal

DOI: https://doi.org/10.1038/s41929-024-01280-8

Macromolecule Content

Total Structure Weight: 52.02 kDa
Atom Count: 3,703
Modeled Residue Count: 431
Deposited Residue Count: 452
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Piperazate synthase	A [auth B], B [auth A]	226	Streptomyces griseus subsp. griseus	Mutation(s): 0
UniProt
Find proteins for A0A7K2YFL1 (Streptomyces sp. SID3343) Explore A0A7K2YFL1 Go to UniProtKB: A0A7K2YFL1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7K2YFL1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth B] mmCIF format, chain E [auth A]	C [auth B], E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain E [auth A]
ONH (Subject of Investigation/LOI) Query on ONH Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain H [auth A] MOL2 format, chain D [auth B] MOL2 format, chain H [auth A] mmCIF format, chain D [auth B] mmCIF format, chain H [auth A]	D [auth B], H [auth A]	N~5~-hydroxy-L-ornithine C₅ H₁₂ N₂ O₃ OZMJDTPATROLQC-BYPYZUCNSA-N		Interactions Focus chain D [auth B] Focus chain H [auth A] Interactions & Density Focus chain D [auth B] Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]