7VZS | pdb_00007vzs

FAD-dpendent Glucose Dehydrogenase complexed with an inhibitor at pH7.56

PDB DOI: https://doi.org/10.2210/pdb7VZS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aspergillus oryzae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-11-16 Released: 2022-11-16
Deposition Author(s): Nakajima, Y.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.190 (Depositor), 0.200 (DCC)
R-Value Work:
0.152 (Depositor), 0.160 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Conformational change of catalytic residue in reduced enzyme of FAD-dependent Glucose Dehydrogenase at pH6.5

Nakajima, Y.

To be published.

Macromolecule Content

Total Structure Weight: 127.24 kDa
Atom Count: 9,682
Modeled Residue Count: 1,134
Deposited Residue Count: 1,144
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMC oxidoreductase	A, B	572	Aspergillus oryzae	Mutation(s): 0 Gene Names: OAory_01010120 EC: 1.1.3.4
UniProt
Find proteins for A0A1S9DW10 (Aspergillus oryzae) Explore A0A1S9DW10 Go to UniProtKB: A0A1S9DW10
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1S9DW10
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B]	J [auth A], R [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]
DGO (Subject of Investigation/LOI) Query on DGO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	D [auth A] E [auth A] F [auth A] L [auth B] M [auth B] D [auth A], E [auth A], F [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	D-glucal C₆ H₁₀ O₄ YVECGMZCTULTIS-PBXRRBTRSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B]	I [auth A], Q [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain Q [auth B]