8ROS | pdb_00008ros

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth AAA]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
A1H16 (Subject of Investigation/LOI)	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
PEG	D [auth AAA], E [auth AAA]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	F [auth AAA]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A [auth AAA]	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.163 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.15	α = 90
b = 83.15	β = 90
c = 59.17	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Ilari, A., Fiorillo, A., Antonelli, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release