9R43 | pdb_00009r43

FAD-dependent oxidoreductase McrA

PDB DOI: https://doi.org/10.2210/pdb9R43/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces lavendulae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-07 Released: 2025-12-10
Deposition Author(s): Tjallinks, G., Mattevi, A.
Funding Organization(s): European Cooperation in Science and Technology (COST) action

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.247 (Depositor), 0.249 (DCC)
R-Value Work:
0.202 (Depositor), 0.211 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: in silico
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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

Characterization of the Mitomycin C Resistance Protein McrA

Tjallinks, G., Dunleavy, T., Jonker, T., Angeleri, N., Mattevi, A., Fraaije, M.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.11.28.691146

Macromolecule Content

Total Structure Weight: 101.03 kDa
Atom Count: 7,166
Modeled Residue Count: 882
Deposited Residue Count: 896
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitomycin radical oxidase	A, B	448	Streptomyces lavendulae	Mutation(s): 0 Gene Names: mcrA EC: 1.5.3
UniProt
Find proteins for P43485 (Streptomyces lavendulae) Explore P43485 Go to UniProtKB: P43485
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43485
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain C [auth A] MOL2 format, chain R [auth B] MOL2 format, chain C [auth A] mmCIF format, chain R [auth B] mmCIF format, chain C [auth A]	C [auth A], R [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain R [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain D [auth A] MOL2 format, chain V [auth B] MOL2 format, chain D [auth A] mmCIF format, chain V [auth B] mmCIF format, chain D [auth A]	D [auth A], V [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain V [auth B] Interactions & Density Focus chain D [auth A] Focus chain V [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain W [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain CA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] CA [auth B] E [auth A] F [auth A] G [auth A] AA [auth B], CA [auth B], E [auth A], F [auth A], G [auth A], J [auth A], K [auth A], L [auth A], N [auth A], O [auth A], Q [auth A], S [auth B], T [auth B], W [auth B], Y [auth B], Z [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain W [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain U [auth B] SDF format, chain P [auth A] SDF format, chain M [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain DA [auth B] SDF format, chain BA [auth B] MOL2 format, chain X [auth B] MOL2 format, chain U [auth B] MOL2 format, chain P [auth A] MOL2 format, chain M [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain X [auth B] mmCIF format, chain U [auth B] mmCIF format, chain P [auth A] mmCIF format, chain M [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain BA [auth B]	BA [auth B] DA [auth B] H [auth A] I [auth A] M [auth A] BA [auth B], DA [auth B], H [auth A], I [auth A], M [auth A], P [auth A], U [auth B], X [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Focus chain DA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain X [auth B] Interactions & Density Focus chain BA [auth B] Focus chain DA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain X [auth B]