8S02

BzdNO-benzoyl-CoA complex

PDB DOI: https://doi.org/10.2210/pdb8S02/pdb

Classification: OXIDOREDUCTASE
Organism(s): Azoarcus sp. CIB
Expression System: Escherichia coli K-12, Escherichia coli
Mutation(s): No

Deposited: 2024-02-13 Released: 2025-03-05
Deposition Author(s): Ermler, U., Boll, M., Fuchs, J., Demmer, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 ?
R-Value Free:
0.217 (Depositor), 0.218 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

X-ray structure of the BzdNO-benzoyl-CoA complex

Ermler, U., Boll, M., Fuchs, J., Demmer, U.

To be published.

Macromolecule Content

Total Structure Weight: 193.95 kDa
Atom Count: 14,359
Modelled Residue Count: 1,619
Deposited Residue Count: 1,652
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BzdO	A, C	447	Azoarcus sp. CIB	Mutation(s): 0 Gene Names: bzdO
UniProt
Find proteins for Q68VL9 (Aromatoleum sp. (strain CIB)) Explore Q68VL9 Go to UniProtKB: Q68VL9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q68VL9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BzdN	B, D	379	Azoarcus sp. CIB	Mutation(s): 0 Gene Names: bzdN
UniProt
Find proteins for Q68VM0 (Aromatoleum sp. (strain CIB)) Explore Q68VM0 Go to UniProtKB: Q68VM0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q68VM0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BYC Query on BYC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth C]	E [auth A], J [auth C]	benzoyl coenzyme A C₂₈ H₄₀ N₇ O₁₇ P₃ S VEVJTUNLALKRNO-TYHXJLICSA-N		Interactions Focus chain E [auth A] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth C]
BJ8 Query on BJ8 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain O [auth D] MOL2 format, chain H [auth B] MOL2 format, chain O [auth D] mmCIF format, chain H [auth B] mmCIF format, chain O [auth D]	H [auth B], O [auth D]	Double cubane cluster Fe₈ S₉ CSVVAMDLRWBOEA-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain O [auth D] Interactions & Density Focus chain H [auth B] Focus chain O [auth D]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C]	G [auth A], N [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C]	I [auth B], K [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain I [auth B] Focus chain K [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C]	F [auth A], L [auth C], M [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth C] Focus chain M [auth C]