7T9E

Crystal structure of dehaloperoxidase B in complex with +(-)-limonene oxide

PDB DOI: https://doi.org/10.2210/pdb7T9E/pdb

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

Deposited: 2021-12-18 Released: 2023-01-25
Deposition Author(s): de Serrano, V.S., Ghiladi, R.A., Malewschik, T., Yun, D.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.218
R-Value Work: 0.143

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Malewschik, T., de Serrano, V.S., Yun, D., Ghiladi, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 32.84 kDa
Atom Count: 2,833
Modelled Residue Count: 274
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehaloperoxidase B	A [auth AAA], B [auth BBB]	137	Amphitrite ornata	Mutation(s): 0
UniProt
Find proteins for Q9NAV7 (Amphitrite ornata) Explore Q9NAV7 Go to UniProtKB: Q9NAV7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NAV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain I [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain I [auth BBB]	C [auth AAA], I [auth BBB]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth AAA] Focus chain I [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain I [auth BBB]
GH9 (Subject of Investigation/LOI) Query on GH9 Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain J [auth BBB] MOL2 format, chain D [auth AAA] MOL2 format, chain J [auth BBB]	D [auth AAA], J [auth BBB]	(1R,4R,6S)-1-methyl-4-(prop-1-en-2-yl)-7-oxabicyclo[4.1.0]heptane C₁₀ H₁₆ O CCEFMUBVSUDRLG-KXUCPTDWSA-N		Interactions Focus chain D [auth AAA] Focus chain J [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain J [auth BBB]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain G [auth AAA] SDF format, chain K [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain G [auth AAA] MOL2 format, chain K [auth BBB]	F [auth AAA], G [auth AAA], K [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain K [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain G [auth AAA] Focus chain K [auth BBB]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain H [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain H [auth BBB]	E [auth AAA], H [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain H [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain H [auth BBB]