8ROS

human pyridoxine 5-phosphate oxidase in complex with Z isomer of pyridoxilidenrhodanine 5-phosphate

PDB DOI: https://doi.org/10.2210/pdb8ROS/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-12 Released: 2025-01-29
Deposition Author(s): Ilari, A., Fiorillo, A., Antonelli, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.200
R-Value Work: 0.163

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Pyridoxine 5-phosphate oxidase in complex with pyridoxilidenrhodanine 5-phosphate

Ilari, A., Fiorillo, A., Antonelli, L.

To be published.

Macromolecule Content

Total Structure Weight: 31.44 kDa
Atom Count: 2,004
Modelled Residue Count: 209
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxine-5'-phosphate oxidase	A [auth AAA]	264	Homo sapiens	Mutation(s): 0 Gene Names: PNPO EC: 1.4.3.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVS9 (Homo sapiens) Explore Q9NVS9 Go to UniProtKB: Q9NVS9
PHAROS: Q9NVS9 GTEx: ENSG00000108439
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NVS9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain B [auth AAA] MOL2 format, chain B [auth AAA] mmCIF format, chain B [auth AAA]	B [auth AAA]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth AAA] Interactions & Density Focus chain B [auth AAA]
A1H16 (Subject of Investigation/LOI) Query on A1H16 Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	[6-methyl-5-oxidanylidene-4-[(4-oxidanylidene-2-sulfanylidene-1,3-thiazol-5-yl)methyl]-4~{H}-pyridin-3-yl]methyl dihydrogen phosphate C₁₁ H₁₁ N₂ O₆ P S₂ WJDPAGLWZIPYMX-WAPJZHGLSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA]	D [auth AAA], E [auth AAA]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain F [auth AAA]	F [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Interactions & Density Focus chain F [auth AAA]