8VQU | pdb_00008vqu

Crystal Structure of Dehaloperoxidase B in complex with substrate 1,4-cyclohexadiene

PDB DOI: https://doi.org/10.2210/pdb8VQU/pdb

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

Deposited: 2024-01-19 Released: 2025-08-13
Deposition Author(s): de Seerano, V.S., Yun, D., Ghiladi, R.A.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.220 (Depositor), 0.224 (DCC)
R-Value Work:
0.185 (Depositor), 0.194 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Dehaloperoxidase B in complex with substrate 1,4-cyclohexadiene

de Seerano, V.S., Yun, D., Ghiladi, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 32.93 kDa
Atom Count: 2,879
Modeled Residue Count: 274
Deposited Residue Count: 274
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NAV7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 L [auth B] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain C [auth A]	C [auth A], L [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], K [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
A1ADJ (Subject of Investigation/LOI) Query on A1ADJ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	cyclohexa-1,4-diene C₆ H₈ UVJHQYIOXKWHFD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]