5AG1

DyP-type peroxidase of Auricularia auricula-judae (AauDyPI) with meso- nitrated heme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystallographic Trapping of a Covalently Modified Heme in a Dye-Decolorizing Peroxidase

Strittmatter, E.Piontek, K.Plattner, D.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DYE-DECOLORIZING PEROXIDASE
A, B
446Auricularia auricula-judaeMutation(s): 0 
Gene Names: dyp1
EC: 1.11.1.19, 1.11.1.7
Find proteins for I2DBY1 (Auricularia auricula-judae)
Go to UniProtKB:  I2DBY1
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NO2
Query on NO2

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Download CCD File 
A, B
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
 Ligand Interaction
N7H
Query on N7H

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Download CCD File 
A, B
DELTA-MESO NITROHEME
C34 H29 Fe N5 O6
KYBKYUQKNYQUQX-GYHFSKQYSA-J
 Ligand Interaction
CAC
Query on CAC

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Download CCD File 
A, B
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.000α = 90.00
b = 46.780β = 100.53
c = 148.150γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release