7SJG

Structure of Dehaloperoxidase B in Complex with Thymoquinone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.142 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The Multifunctional Globin Dehaloperoxidase as a Biocatalyst in the Oxidation of Monoterpenes

Malewschick, T.Yun, D.de Serrano, V.Ghiladi, R.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehaloperoxidase B
A, B
137Amphitrite ornataMutation(s): 0 
UniProt
Find proteins for Q9NAV7 (Amphitrite ornata)
Explore Q9NAV7 
Go to UniProtKB:  Q9NAV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NAV7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
9IX (Subject of Investigation/LOI)
Query on 9IX

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H [auth A],
R [auth B]
2-methyl-5-(propan-2-yl)benzene-1,4-diol
C10 H14 O2
OQIOHYHRGZNZCW-UHFFFAOYSA-N
9J9 (Subject of Investigation/LOI)
Query on 9J9

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G [auth A],
I [auth A],
J [auth A],
Q [auth B]
(6R)-4-hydroxy-6-methyl-3-(propan-2-yl)cyclohexa-2,4-dien-1-one
C10 H14 O2
QZGDYXFNICWHLG-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

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K [auth A],
L [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
N [auth B]
O [auth B]
D [auth A],
E [auth A],
F [auth A],
N [auth B],
O [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.358α = 90
b = 67.565β = 90
c = 67.825γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary