6HN8 | pdb_00006hn8

Structure of BM3 heme domain in complex with troglitazone

• PDB DOI: https://doi.org/10.2210/pdb6HN8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-09-14 Released: 2019-10-09 
• Deposition Author(s): Jeffreys, L., Munro, A.W.M., Leys, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.188 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Oxidation of antidiabetic compounds by cytochrome P450 BM3

Jeffreys, L., Leys, D., Munro, A.W.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 106.94 kDa 
• Atom Count: 8,304 
• Modeled Residue Count: 905 
• Deposited Residue Count: 914 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional cytochrome P450/NADPH--P450 reductase	A, B	457	Priestia megaterium	Mutation(s): 2  Gene Names: BTA37_15100 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779  Go to UniProtKB:  P14779

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
TDZ (Subject of Investigation/LOI)	D [auth A], F [auth B]	(5R)-5-(4-{[(2R)-6-HYDROXY-2,5,7,8-TETRAMETHYL-3,4-DIHYDRO-2H-CHROMEN-2-YL]METHOXY}BENZYL)-1,3-THIAZOLIDINE-2,4-DIONE C24 H27 N O5 S GXPHKUHSUJUWKP-NTKDMRAZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.188 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.905	α = 90
b = 120.375	β = 90
c = 145.951	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Jeffreys, L., Munro, A.W.M., Leys, D.

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary