9QS1 | pdb_00009qs1

Tetrapodal ancestor of L-amino acid oxidases

PDB DOI: https://doi.org/10.2210/pdb9QS1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Tetrapoda
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2025-04-04 Released: 2026-04-15
Deposition Author(s): Massari, M., Mattevi, A.
Funding Organization(s): Italian Association for Cancer Research, Italian Ministry of Education

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.246 (Depositor), 0.247 (DCC)
R-Value Work:
0.205 (Depositor), 0.212 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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

Literature

Evolution of Human IL4i1 Preference for Aromatic Amino Acids from a Broad-Specificity L-Amino Acid Oxidase Ancestor

Massari, M., Mattevi, A.

To be published.

Macromolecule Content

Total Structure Weight: 56.31 kDa
Atom Count: 3,997
Modeled Residue Count: 483
Deposited Residue Count: 488
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrapodal ancestor of L-amino acis oxidases	A	488	Tetrapoda	Mutation(s): 0

Small Molecules

Ligands 3 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.246 (Depositor), 0.247 (DCC)
R-Value Work: 0.205 (Depositor), 0.212 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.515	α = 90
b = 94.515	β = 90
c = 190.062	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Italian Association for Cancer Research	Italy	26648
Italian Ministry of Education	Italy	P2022FESRR

Revision History (Full details and data files)

Version 1.0: 2026-04-15
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.