8RTP | pdb_00008rtp

Bilirubin oxidase from Myrothecium verrucaria in complex with NAD+

PDB DOI: https://doi.org/10.2210/pdb8RTP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Albifimbria verrucaria
Expression System: Aspergillus oryzae
Mutation(s): No

Deposited: 2024-01-27 Released: 2025-08-06
Deposition Author(s): Svecova, L., Koval, T., Kolenko, P., Ostergaard, L.H., Dohnalek, J.
Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, European Regional Development Fund, Czech Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.215 (Depositor), 0.188 (DCC)
R-Value Work:
0.169 (Depositor), 0.176 (DCC)
R-Value Observed:
0.169 (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

Bilirubin oxidase - answers to questions on ligand binding and Trp-His covalent link formation

Svecova, L., Koval, T., Kolenko, P., Ostergaard, L.H., Dohnalek, J.

To be published.

Macromolecule Content

Total Structure Weight: 124.85 kDa
Atom Count: 9,877
Modeled Residue Count: 1,067
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bilirubin oxidase	A [auth AAA], B [auth BBB]	534	Albifimbria verrucaria	Mutation(s): 0 EC: 1.3.3.5
UniProt
Find proteins for Q12737 (Albifimbria verrucaria) Explore Q12737 Go to UniProtKB: Q12737
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12737
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A [auth AAA] Focus chain B [auth BBB]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth AeA]	4		N-Glycosylation	Interactions Focus chain C [auth AeA] Interactions & Density Focus chain C [auth AeA]

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth AiA], E [auth BeB], F [auth BgB]	2		N-Glycosylation	Interactions Focus chain D [auth AiA] Focus chain E [auth BeB] Focus chain F [auth BgB] Interactions & Density Focus chain D [auth AiA] Focus chain E [auth BeB] Focus chain F [auth BgB]

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain P [auth AAA] SDF format, chain Y [auth BBB] MOL2 format, chain P [auth AAA] MOL2 format, chain Y [auth BBB] mmCIF format, chain P [auth AAA] mmCIF format, chain Y [auth BBB]	P [auth AAA], Y [auth BBB]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain P [auth AAA] Focus chain Y [auth BBB] Interactions & Density Focus chain P [auth AAA] Focus chain Y [auth BBB]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain N [auth AAA] SDF format, chain W [auth BBB] MOL2 format, chain N [auth AAA] MOL2 format, chain W [auth BBB] mmCIF format, chain N [auth AAA] mmCIF format, chain W [auth BBB]	N [auth AAA], W [auth BBB]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain N [auth AAA] Focus chain W [auth BBB] Interactions & Density Focus chain N [auth AAA] Focus chain W [auth BBB]
SIN Query on SIN Download Ideal Coordinates CCD File SDF format, chain K [auth AAA] SDF format, chain L [auth AAA] SDF format, chain U [auth BBB] MOL2 format, chain K [auth AAA] MOL2 format, chain L [auth AAA] MOL2 format, chain U [auth BBB] mmCIF format, chain K [auth AAA] mmCIF format, chain L [auth AAA] mmCIF format, chain U [auth BBB]	K [auth AAA], L [auth AAA], U [auth BBB]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain U [auth BBB] Interactions & Density Focus chain K [auth AAA] Focus chain L [auth AAA] Focus chain U [auth BBB]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain X [auth BBB] MOL2 format, chain X [auth BBB] mmCIF format, chain X [auth BBB]	X [auth BBB]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain X [auth BBB] Interactions & Density Focus chain X [auth BBB]
PGR Query on PGR Download Ideal Coordinates CCD File SDF format, chain O [auth AAA] MOL2 format, chain O [auth AAA] mmCIF format, chain O [auth AAA]	O [auth AAA]	R-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-GSVOUGTGSA-N		Interactions Focus chain O [auth AAA] Interactions & Density Focus chain O [auth AAA]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] SDF format, chain Q [auth BBB] SDF format, chain R [auth BBB] SDF format, chain S [auth BBB] SDF format, chain T [auth BBB] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] MOL2 format, chain J [auth AAA] MOL2 format, chain Q [auth BBB] MOL2 format, chain R [auth BBB] MOL2 format, chain S [auth BBB] MOL2 format, chain T [auth BBB] mmCIF format, chain G [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA] mmCIF format, chain J [auth AAA] mmCIF format, chain Q [auth BBB] mmCIF format, chain R [auth BBB] mmCIF format, chain S [auth BBB] mmCIF format, chain T [auth BBB]	G [auth AAA] H [auth AAA] I [auth AAA] J [auth AAA] Q [auth BBB] G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], Q [auth BBB], R [auth BBB], S [auth BBB], T [auth BBB]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB] Interactions & Density Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Focus chain Q [auth BBB] Focus chain R [auth BBB] Focus chain S [auth BBB] Focus chain T [auth BBB]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain M [auth AAA] SDF format, chain V [auth BBB] MOL2 format, chain M [auth AAA] MOL2 format, chain V [auth BBB] mmCIF format, chain M [auth AAA] mmCIF format, chain V [auth BBB]	M [auth AAA], V [auth BBB]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain M [auth AAA] Focus chain V [auth BBB] Interactions & Density Focus chain M [auth AAA] Focus chain V [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.215 (Depositor), 0.188 (DCC)
R-Value Work: 0.169 (Depositor), 0.176 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.727	α = 90
b = 202.441	β = 90
c = 224.762	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	LM2018127
European Regional Development Fund	European Union	CZ.02.1.01/0.0/0.0/15_003/0000447
Czech Academy of Sciences	Czech Republic	86652036