9SI5 | pdb_00009si5

Crystal structure of DoxA in complex with reaction intermediate DHD

• PDB DOI: https://doi.org/10.2210/pdb9SI5/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces peucetius
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-28 Released: 2025-12-24 
• Deposition Author(s): Kim, R.Q., Metsa-Ketela, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.281 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.232 (DCC) 

Starting Model: experimental

Literature

Metabolic Engineering of Doxorubicin Biosynthesis: Advancing P450 Catalysis through Redox Partner Optimization and Structural Analysis of DoxA

Koroleva, A., Artukka, E., Yamada, K., Newmister, S.A., Sherman, D.H., Kim, R.Q., Metsa-Ketela, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 101.69 kDa 
• Atom Count: 6,585 
• Modeled Residue Count: 814 
• Deposited Residue Count: 914 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P-450 monooxygenase DoxA	A, B [auth D]	457	Streptomyces peucetius	Mutation(s): 0  Gene Names: doxA EC: 1.14.13.181
UniProt
Find proteins for Q9ZAU3 (Streptomyces peucetius) Explore Q9ZAU3  Go to UniProtKB:  Q9ZAU3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A], E [auth D]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
A1JN3 (Subject of Investigation/LOI)	D [auth A], F [auth D]	(7~{S},9~{S})-7-[(2~{R},4~{S},5~{S},6~{S})-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-4-methoxy-6,9,11-tris(oxidanyl)-9-[(1~{R})-1-oxidanylethyl]-8,10-dihydro-7~{H}-tetracene-5,12-dione C27 H31 N O10 HJEZFVLKJYFNQW-OXCIRTNUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.281 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.232 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.873	α = 90
b = 108.058	β = 90
c = 179.772	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Kim, R.Q., Metsa-Ketela, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release