7PX0 | pdb_00007px0

Drosophila melanogaster Aldehyde Oxidase 1

PDB DOI: https://doi.org/10.2210/pdb7PX0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-10-07 Released: 2022-11-16
Deposition Author(s): Vilela-Alves, G., Mota, C., Romao, M.J.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.220 (Depositor), 0.230 (DCC)
R-Value Work:
0.175 (Depositor), 0.184 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Drosophila melanogaster's Aldehyde Oxidase 1: The First Invertebrate AOX structure

Vilela-Alves, G., Mota, C., Romao, M.J.

To be published.

Macromolecule Content

Total Structure Weight: 565.29 kDa
Atom Count: 41,321
Modeled Residue Count: 4,990
Deposited Residue Count: 5,092
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde oxidase 1	A, B, C, D	1,273	Drosophila melanogaster	Mutation(s): 0 Gene Names: AOX1, CT42272, DmAO1, Dmel\CG18522, LPO, PO, CG18522, Dmel_CG18522 EC: 1.2.3.8 (PDB Primary Data), 1.2.3.1 (UniProt), 1 (UniProt)
UniProt
Find proteins for Q9VF53 (Drosophila melanogaster) Explore Q9VF53 Go to UniProtKB: Q9VF53
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9VF53
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 Z [auth C] SDF format, chain Q [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D]	FA [auth D], G [auth A], Q [auth B], Z [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain FA [auth D] Focus chain G [auth A] Focus chain Q [auth B] Focus chain Z [auth C] Interactions & Density Focus chain FA [auth D] Focus chain G [auth A] Focus chain Q [auth B] Focus chain Z [auth C]
ZXF (Subject of Investigation/LOI) Query on ZXF Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain N [auth A] SDF format, chain JA [auth D] SDF format, chain CA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain N [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain CA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain N [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain CA [auth C]	CA [auth C], JA [auth D], N [auth A], W [auth B]	Molybdopterin hydoxy-oxo-thiol-molybdenum C₁₀ H₁₄ Mo N₅ O₈ P S₃ KIFQXVGEKPMGCB-BKZHXLINSA-J		Interactions Focus chain CA [auth C] Focus chain JA [auth D] Focus chain N [auth A] Focus chain W [auth B] Interactions & Density Focus chain CA [auth C] Focus chain JA [auth D] Focus chain N [auth A] Focus chain W [auth B]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth D] SDF format, chain E [auth A] SDF format, chain DA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth D]	DA [auth D] E [auth A] EA [auth D] F [auth A] O [auth B] DA [auth D], E [auth A], EA [auth D], F [auth A], O [auth B], P [auth B], X [auth C], Y [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain X [auth C] Focus chain Y [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth D] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] GA [auth D] H [auth A] HA [auth D] AA [auth C], BA [auth C], GA [auth D], H [auth A], HA [auth D], I [auth A], J [auth A], L [auth A], M [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain IA [auth D] MOL2 format, chain IA [auth D] mmCIF format, chain IA [auth D]	IA [auth D]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain IA [auth D] Interactions & Density Focus chain IA [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.220 (Depositor), 0.230 (DCC)
R-Value Work: 0.175 (Depositor), 0.184 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.663	α = 90
b = 127.914	β = 110.629
c = 152.547	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Vilela-Alves, G.

Mota, C.

Romao, M.J.

Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BBB-BEP/1185/2014

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 2.0: 2026-09-02
Type: Remediation
Reason: Metalloprotein remediation
Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary