9P3B | pdb_00009p3b

Structure of radical S-adenosylmethionine methyltransferase, NocN, from Nocardia with two SAM and [4Fe-4S] cluster bound

PDB DOI: https://doi.org/10.2210/pdb9P3B/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nocardia sp. ATCC 202099
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-06-13 Released: 2026-06-03
Deposition Author(s): Wang, B., Knox, H.L., York, N.J., Radle, M.I., Silakov, A., Booker, S.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.207 (Depositor), 0.207 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and Spectroscopic Basis for Catalysis by a Class C Radical S-Adenosylmethionine Methylase Involved in Nosiheptide/Nocathiacin Biosynthesis

Wang, B., Knox, H.L., York, N.J., Radle, M.I., Silakov, A., Booker, S.J.

(2026) J Am Chem Soc

DOI: https://doi.org/10.1021/jacs.6c03999

Macromolecule Content

Total Structure Weight: 95.59 kDa
Atom Count: 7,047
Modeled Residue Count: 789
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
radical S-adenosylmethionine methyltransferase NocN	A, B	420	Nocardia sp. ATCC 202099	Mutation(s): 0 Gene Names: nocN
UniProt
Find proteins for E5DUI5 (Nocardia sp. ATCC 202099) Explore E5DUI5 Go to UniProtKB: E5DUI5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E5DUI5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM (Subject of Investigation/LOI) Query on SAM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B]	E [auth A], I [auth A], K [auth B], M [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth B]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
HEZ Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	D [auth A], F [auth A], H [auth A], L [auth B]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain L [auth B]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]