9JKZ | pdb_00009jkz

CYP105A1 R84A complexed with simvastatin

• PDB DOI: https://doi.org/10.2210/pdb9JKZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces griseolus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-09-17 Released: 2025-09-24 
• Deposition Author(s): Mikami, B., Takita, T., Sakaki, T., Yasuda, K., Yasukawa, K., Yoneda, S., Yamagata, M.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Structure analysis of Streptomyces griseolus CYP105A1 R84A complex with statins

Takita, T., Yoneda, S., Yasuda, K., Mikami, B., Sakaki, T., Yasukawa, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.16 kDa 
• Atom Count: 3,391 
• Modeled Residue Count: 404 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 dihydroxylase	A	412	Streptomyces griseolus	Mutation(s): 2  Gene Names: cyp105A1, suaC EC: 1.14.15 (PDB Primary Data), 1.14.15.22 (UniProt)
UniProt
Find proteins for P18326 (Streptomyces griseolus) Explore P18326  Go to UniProtKB:  P18326

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SIM (Subject of Investigation/LOI)	C [auth A]	Simvastatin acid C25 H40 O6 XWLXKKNPFMNSFA-HGQWONQESA-N
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.489	α = 90
b = 53.982	β = 90
c = 141.081	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Mikami, B., Takita, T., Sakaki, T., Yasuda, K., Yasukawa, K., Yoneda, S., Yamagata, M.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22K05441
Japan Society for the Promotion of Science (JSPS)	Japan	25292062

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release