9P2U | pdb_00009p2u

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

PDB DOI: https://doi.org/10.2210/pdb9P2U/pdb

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

Deposited: 2025-06-12 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: 1.40 Å
R-Value Free:
0.163 (Depositor), 0.162 (DCC)
R-Value Work:
0.133 (Depositor), 0.135 (DCC)
R-Value Observed:
0.134 (Depositor)

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Ligand Structure Quality Assessment

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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: 47.49 kDa
Atom Count: 3,828
Modeled Residue Count: 400
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Radical S-adenosylmethionine methyltransferase NocN	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SA8 (Subject of Investigation/LOI) Query on SA8 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE C₁₅ H₂₃ N₇ O₅ JISVTSUBJCPLSV-TWBCTODHSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.163 (Depositor), 0.162 (DCC)
R-Value Work: 0.133 (Depositor), 0.135 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.551	α = 90
b = 70.506	β = 97.8
c = 54.672	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-122595

Revision History (Full details and data files)

Version 1.0: 2026-06-03
Type: Initial release

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