5K1L

Dehaloperoxidase B from Amphitrite ornata: benzimidazole complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Dehaloperoxidase B from Amphitrite ornata: benzimidazole complex

Moreno Chicano, T.Hough, M.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dehaloperoxidase B
A, B
137Amphitrite ornataMutation(s): 0 
Find proteins for Q9NAV7 (Amphitrite ornata)
Go to UniProtKB:  Q9NAV7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BZI
Query on BZI

Download SDF File 
Download CCD File 
A, B
BENZIMIDAZOLE
C7 H6 N2
HYZJCKYKOHLVJF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.790α = 90.00
b = 68.300β = 90.00
c = 68.530γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Leverhulme TrustUnited KingdomRPG-2014-355
National Science FoundationUnited StatesCHE-1150709

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2018-12-19
    Type: Author supporting evidence, Data collection, Database references, Derived calculations