5K1L

Dehaloperoxidase B from Amphitrite ornata: benzimidazole complex

• PDB DOI: https://doi.org/10.2210/pdb5K1L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amphitrite ornata
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-18 Released: 2017-06-07 
• Deposition Author(s): Moreno Chicano, T., Hough, M.A.
• Funding Organization(s): Leverhulme Trust, National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.177 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 

Literature

Dehaloperoxidase B from Amphitrite ornata: benzimidazole complex

Moreno Chicano, T., Hough, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.59 kDa 
• Atom Count: 2,734 
• Modelled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehaloperoxidase B	A, B	137	Amphitrite ornata	Mutation(s): 0
UniProt
Find proteins for Q9NAV7 (Amphitrite ornata) Explore Q9NAV7  Go to UniProtKB:  Q9NAV7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BZI	D [auth A], G [auth B]	BENZIMIDAZOLE C7 H6 N2 HYZJCKYKOHLVJF-UHFFFAOYSA-N
SO4	E [auth A], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
BZI	BindingDB:  5K1L	Kd: 1.10e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.177 
• R-Value Work: 0.151 
• R-Value Observed: 0.152 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.79	α = 90
b = 68.3	β = 90
c = 68.53	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Moreno Chicano, T., Hough, M.A.

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Funding Organization	Location	Grant Number
Leverhulme Trust	United Kingdom	RPG-2014-355
National Science Foundation	United States	CHE-1150709

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations
• Version 1.2: 2024-01-10
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description