9O5M | pdb_00009o5m

Prenylated-FMN maturase PhdC from Mycolicibacterium fortuitum bound to prenylated flavin mononucleotide in the P1 space group

PDB DOI: https://doi.org/10.2210/pdb9O5M/pdb

Classification: FLAVOPROTEIN
Organism(s): Mycolicibacterium fortuitum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-10 Released: 2026-02-18
Deposition Author(s): Kilde, I.R., Koutmos, M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.168 (Depositor), 0.168 (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

Structure and Mechanism of the Prenylated-FMN Maturase, PhdC

DiRocco, D.J., Kilde, I., Langford, D.P., Roy, P., Bhaumik, S., Mendoza, J., Koutmos, M., Marsh, E.N.G.

(2026) ACS Catal 16: 1773-1782

DOI: https://doi.org/10.1021/acscatal.5c08793

Macromolecule Content

Total Structure Weight: 77.03 kDa
Atom Count: 5,613
Modeled Residue Count: 619
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxamine 5'-phosphate oxidase putative domain-containing protein	A, B, C, D	168	Mycolicibacterium fortuitum	Mutation(s): 0 Gene Names: XA26_16660
UniProt
Find proteins for A0A0N9XAG5 (Mycolicibacterium fortuitum) Explore A0A0N9XAG5 Go to UniProtKB: A0A0N9XAG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0N9XAG5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4LU (Subject of Investigation/LOI) Query on 4LU Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain K [auth D] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C]	E [auth A], G [auth B], I [auth C], K [auth D]	1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol C₂₂ H₃₀ N₄ O₉ P KOUJZPGFPGLHCZ-IYOUNJFTSA-O		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B]	F [auth A], H [auth B], J [auth C], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]