9VL0 | pdb_00009vl0

CYP105A1 complexed with simvastatin (cryogenic data collection)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.202 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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Literature

Room-temperature X-ray data collection enabled the structural determination of statin-bound CYP105A1.

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

(2025) Acta Crystallogr D Struct Biol 81: 573-583

  • DOI: https://doi.org/10.1107/S2059798325007673
  • Primary Citation of Related Structures:  
    9JKW, 9JKZ, 9JL5, 9VL0

  • PubMed Abstract: 

    Streptomyces griseolus CYP105A1 exhibits monooxygenase activity towards a wide variety of structurally diverse substrates with regiospecificity and stereospecificity, making it suitable for broad applications. Our previous studies have demonstrated that both wild-type CYP105A1 and its mutants metabolize vitamin D 3 and its derivatives, as well as 12 types of nonsteroidal anti-inflammatory drugs (NSAIDs) and statins. Notably, the R84A mutant displayed high activity against vitamin D 3 , numerous NSAIDs and statins. Although we were unable to obtain CYP105A1-statin complex structures through co-crystallization and standard cryo data collection, we successfully acquired complex structures with mevastatin and simvastatin using room-temperature data collection with a conventional capillary method. We observed that the reduced unit-cell dimensions of the cryo crystals resulted in increased symmetry interactions, which induced cis-trans conversion of the peptide bond between Pro142 and Thr143 and conformational changes in the residues critical for statin binding. It is suggested that these increased symmetry interactions in the cryo crystals lead to dissociation of the statins from the active site of the enzyme.


  • Organizational Affiliation
    • Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Sakyou-ku, Kyoto 606-8502, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin D3 dihydroxylase412Streptomyces griseolusMutation(s): 2 
Gene Names: cyp105A1suaC
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18326
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
TRS
Query on TRS

Download Ideal Coordinates CCD File 
E [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD (Subject of Investigation/LOI)
Query on MPD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52α = 90
b = 53.202β = 90
c = 138.801γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan22K05441
Japan Society for the Promotion of Science (JSPS)Japan23K24590
Japan Society for the Promotion of Science (JSPS)Japan21380067

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release