9P3C | pdb_00009p3c

Structure of radical S-adenosylmethionine methyltransferase, NocN, from Nocardia with SAH and side-ring closed product analog bound

PDB DOI: https://doi.org/10.2210/pdb9P3C/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: 1.78 Å
R-Value Free:
0.194 (Depositor), 0.194 (DCC)
R-Value Work:
0.161 (Depositor), 0.162 (DCC)
R-Value Observed:
0.162 (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

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: 99.24 kDa
Atom Count: 7,374
Modeled Residue Count: 783
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
radical S-adenosylmethionine methyltransferase NocN	A [auth B], B [auth A]	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CG2( Subject of Investigation/LOI) Query on A1CG2 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	F [auth B], G [auth B], L [auth A], M [auth A]	2-[(6S,13S)-6-[(2-{(1S,2R)-1-[(N-{2-[(1S)-1-amino-2-hydroxyethyl]-1,3-thiazole-4-carbonyl}-L-threonyl)amino]-2-hydroxypropyl}-1,3-thiazole-4-carbonyl)amino]-18-methyl-3,11,16-trioxo-1,3,4,5,6,11,12,13,14,16-decahydro-10,7-(azeno)-17,19-epimino-2,15,8,12-benzodioxathiazacycloicosin-13-yl]-1,3-thiazole-4-carboxylic acid C₄₂ H₄₄ N₁₀ O₁₃ S₄ HVBCZPGWEUXHNE-BPOZVCBLSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain L [auth A] Focus chain M [auth A]
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	D [auth B], E [auth B], J [auth A], K [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain J [auth A] Focus chain K [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain I [auth A] MOL2 format, chain C [auth B] MOL2 format, chain I [auth A] mmCIF format, chain C [auth B] mmCIF format, chain I [auth A]	C [auth B], I [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain I [auth A] Interactions & Density Focus chain C [auth B] Focus chain I [auth A]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain N [auth A] MOL2 format, chain H [auth B] MOL2 format, chain N [auth A] mmCIF format, chain H [auth B] mmCIF format, chain N [auth A]	H [auth B], N [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain N [auth A] Interactions & Density Focus chain H [auth B] Focus chain N [auth A]