8GY3

Cryo-EM Structure of Membrane-Bound Aldehyde Dehydrogenase from Gluconobacter oxydans

PDB DOI: https://doi.org/10.2210/pdb8GY3/pdb
EM Map EMD-34369: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Gluconobacter oxydans
Expression System: Gluconobacter oxydans
Mutation(s): No

Deposited: 2022-09-21 Released: 2023-08-02
Deposition Author(s): Adachi, T., Miyata, T., Makino, F., Tanaka, H., Namba, K., Sowa, K., Kitazumi, Y., Shirai, O.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Experimental and Theoretical Insights into Bienzymatic Cascade for Mediatorless Bioelectrochemical Ethanol Oxidation with Alcohol and Aldehyde Dehydrogenases

Adachi, T., Miyata, T., Makino, F., Tanaka, H., Namba, K., Kano, K., Sowa, K., Kitazumi, Y., Shirai, O.

(2023) ACS Catal 13: 7955-7965

DOI: https://doi.org/10.1021/acscatal.3c01962

Macromolecule Content

Total Structure Weight: 152.54 kDa
Atom Count: 10,320
Modelled Residue Count: 1,326
Deposited Residue Count: 1,373
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c subunit of aldehyde dehydrogenase	A	444	Gluconobacter oxydans	Mutation(s): 0 EC: 1.2.99.7
UniProt
Find proteins for Q5DW50 (Gluconobacter oxydans) Explore Q5DW50 Go to UniProtKB: Q5DW50
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5DW50
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small subunit of aldehyde dehydrogenase	B	158	Gluconobacter oxydans	Mutation(s): 0 EC: 1.2.99.7
UniProt
Find proteins for Q5FTD2 (Gluconobacter oxydans (strain 621H)) Explore Q5FTD2 Go to UniProtKB: Q5FTD2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5FTD2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Large subunit of aldehyde dehydrogenase	C	771	Gluconobacter oxydans	Mutation(s): 0 EC: 1.2.99.7
UniProt
Find proteins for Q5FTD1 (Gluconobacter oxydans (strain 621H)) Explore Q5FTD1 Go to UniProtKB: Q5FTD1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5FTD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U10 Query on U10 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PCD Query on PCD Download Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C]	J [auth C]	(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V) C₁₉ H₂₆ Mo N₈ O₁₆ P₂ S₂ YEBYDVFRFUQMER-MQPNXHJTSA-L		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	H [auth B], I [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain H [auth B] Focus chain I [auth B]