8RID | pdb_00008rid

Crystallographic structure of oligosaccharide dehydrogenase from Pycnoporus cinnabarinus bound to Sinapic Acid, orthorhombic crystal

PDB DOI: https://doi.org/10.2210/pdb8RID/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trametes cinnabarina
Expression System: Aspergillus niger
Mutation(s): No

Deposited: 2023-12-18 Released: 2025-07-02
Deposition Author(s): Savino, C., Sciara, G., Gugole, E., Vallone, B., Fata, F., Bulfaro, G., Costanzo, A., Montemiglio, L.C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.178 (Depositor), 0.180 (DCC)
R-Value Work:
0.143 (Depositor), 0.145 (DCC)
R-Value Observed:
0.144 (Depositor)

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

Towards an understanding of microbial lignin breakdown: fungal flavoenzymes prevent laccase-mediated polymerization of phenolic compounds

Savino, C., Sciara, G., Gugole, E., Vallone, B., Fata, F., Bulfaro, G., Costanzo, A., Montemiglio, L.C., Record, E.

To be published.

Macromolecule Content

Total Structure Weight: 65.56 kDa
Atom Count: 5,745
Modeled Residue Count: 591
Deposited Residue Count: 591
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose oxidase	A	591	Trametes cinnabarina	Mutation(s): 0 Gene Names: BN946_scf184803.g17
UniProt
Find proteins for A0A060SC37 (Pycnoporus cinnabarinus) Explore A0A060SC37 Go to UniProtKB: A0A060SC37
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A060SC37
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 4 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] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SXX (Subject of Investigation/LOI) Query on SXX Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth A] MOL2 format, chain D [auth A] MOL2 format, chain M [auth A] mmCIF format, chain D [auth A] mmCIF format, chain M [auth A]	D [auth A], M [auth A]	SINAPINATE C₁₁ H₁₂ O₅ PCMORTLOPMLEFB-ONEGZZNKSA-N		Interactions Focus chain D [auth A] Focus chain M [auth A] Interactions & Density Focus chain D [auth A] Focus chain M [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]