9O35 | pdb_00009o35

Crystal structure of DoxA in complex with daunorubicin

• PDB DOI: https://doi.org/10.2210/pdb9O35/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces peucetius subsp. caesius ATCC 27952
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-04 Released: 2025-12-24 
• Deposition Author(s): Newmister, S.A., Harte, R.J., Kim, R.Q., Metsa-Ketela, M., Sherman, D.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Metabolic Engineering of Doxorubicin Biosynthesis: Advancing P450 Catalysis through Redox Partner2 Optimization and Structural Analysis of DoxA

Koroleva, A., Artukka, E., Yamada, K., Newmister, S.A., Harte, R.J., Boesger, H., Londen, M., Sanders, J.N., Tirkkonen, H., Kannisto, M., Kuin, R.C.M., Hulst, M., Wang, R., Barillec, M., Niemi, J., van Wezel, G.P., Neefjes, J., Nybo, S.E., Houk, K.N., 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: 94.51 kDa 
• Atom Count: 6,702 
• Modeled Residue Count: 801 
• Deposited Residue Count: 850 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P-450 monooxygenase DoxA	A, B	425	Streptomyces peucetius subsp. caesius ATCC 27952	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DM1 (Subject of Investigation/LOI)	D [auth A], F [auth B]	DAUNOMYCIN C27 H29 N O10 STQGQHZAVUOBTE-VGBVRHCVSA-N
SO4	G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.253 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.773	α = 90
b = 108.956	β = 90
c = 181.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Newmister, S.A., Harte, R.J., Kim, R.Q., Metsa-Ketela, M., Sherman, D.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM118101

Revision History  

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