8RTR | pdb_00008rtr

Bilirubin oxidase from Myrothecium verrucaria with R356S mutation

PDB DOI: https://doi.org/10.2210/pdb8RTR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Albifimbria verrucaria
Expression System: Aspergillus oryzae
Mutation(s): Yes

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: 2.05 Å
R-Value Free:
0.203 (Depositor), 0.180 (DCC)
R-Value Work:
0.158 (Depositor), 0.169 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 124.3 kDa
Atom Count: 9,994
Modeled Residue Count: 1,067
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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): 1 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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth AeA], E [auth BeB]	3		N-Glycosylation	Interactions Focus chain C [auth AeA] Focus chain E [auth BeB] Interactions & Density Focus chain C [auth AeA] Focus chain E [auth BeB]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 AhA], F [auth BhB]	2		N-Glycosylation	Interactions Focus chain D [auth AhA] Focus chain F [auth BhB] Interactions & Density Focus chain D [auth AhA] Focus chain F [auth BhB]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain HA [auth BBB] SDF format, chain Q [auth AAA] SDF format, chain R [auth AAA] MOL2 format, chain HA [auth BBB] MOL2 format, chain Q [auth AAA] MOL2 format, chain R [auth AAA] mmCIF format, chain HA [auth BBB] mmCIF format, chain Q [auth AAA] mmCIF format, chain R [auth AAA]	HA [auth BBB], Q [auth AAA], R [auth AAA]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain HA [auth BBB] Focus chain Q [auth AAA] Focus chain R [auth AAA] Interactions & Density Focus chain HA [auth BBB] Focus chain Q [auth AAA] Focus chain R [auth AAA]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain IA [auth BBB] SDF format, chain S [auth AAA] SDF format, chain T [auth AAA] SDF format, chain U [auth AAA] MOL2 format, chain IA [auth BBB] MOL2 format, chain S [auth AAA] MOL2 format, chain T [auth AAA] MOL2 format, chain U [auth AAA] mmCIF format, chain IA [auth BBB] mmCIF format, chain S [auth AAA] mmCIF format, chain T [auth AAA] mmCIF format, chain U [auth AAA]	IA [auth BBB], S [auth AAA], T [auth AAA], U [auth AAA]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain IA [auth BBB] Focus chain S [auth AAA] Focus chain T [auth AAA] Focus chain U [auth AAA] Interactions & Density Focus chain IA [auth BBB] Focus chain S [auth AAA] Focus chain T [auth AAA] Focus chain U [auth AAA]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth BBB] SDF format, chain GA [auth BBB] SDF format, chain L [auth AAA] SDF format, chain M [auth AAA] SDF format, chain N [auth AAA] SDF format, chain P [auth AAA] SDF format, chain O [auth AAA] MOL2 format, chain FA [auth BBB] MOL2 format, chain GA [auth BBB] MOL2 format, chain L [auth AAA] MOL2 format, chain M [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain P [auth AAA] MOL2 format, chain O [auth AAA] mmCIF format, chain FA [auth BBB] mmCIF format, chain GA [auth BBB] mmCIF format, chain L [auth AAA] mmCIF format, chain M [auth AAA] mmCIF format, chain N [auth AAA] mmCIF format, chain P [auth AAA] mmCIF format, chain O [auth AAA]	FA [auth BBB] GA [auth BBB] L [auth AAA] M [auth AAA] N [auth AAA] FA [auth BBB], GA [auth BBB], L [auth AAA], M [auth AAA], N [auth AAA], O [auth AAA], P [auth AAA]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth BBB] Focus chain GA [auth BBB] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Interactions & Density Focus chain FA [auth BBB] Focus chain GA [auth BBB] Focus chain L [auth AAA] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain AA [auth BBB] SDF format, chain BA [auth BBB] SDF format, chain CA [auth BBB] SDF format, chain DA [auth BBB] SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] SDF format, chain J [auth AAA] MOL2 format, chain AA [auth BBB] MOL2 format, chain BA [auth BBB] MOL2 format, chain CA [auth BBB] MOL2 format, chain DA [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] mmCIF format, chain AA [auth BBB] mmCIF format, chain BA [auth BBB] mmCIF format, chain CA [auth BBB] mmCIF format, chain DA [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]	AA [auth BBB] BA [auth BBB] CA [auth BBB] DA [auth BBB] G [auth AAA] AA [auth BBB], BA [auth BBB], CA [auth BBB], DA [auth BBB], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth BBB] Focus chain BA [auth BBB] Focus chain CA [auth BBB] Focus chain DA [auth BBB] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA] Interactions & Density Focus chain AA [auth BBB] Focus chain BA [auth BBB] Focus chain CA [auth BBB] Focus chain DA [auth BBB] Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain I [auth AAA] Focus chain J [auth AAA]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain KA [auth BBB] SDF format, chain LA [auth BBB] SDF format, chain MA [auth BBB] SDF format, chain V [auth AAA] SDF format, chain W [auth AAA] SDF format, chain Y [auth AAA] SDF format, chain Z [auth AAA] SDF format, chain JA [auth BBB] SDF format, chain X [auth AAA] MOL2 format, chain KA [auth BBB] MOL2 format, chain LA [auth BBB] MOL2 format, chain MA [auth BBB] MOL2 format, chain V [auth AAA] MOL2 format, chain W [auth AAA] MOL2 format, chain Y [auth AAA] MOL2 format, chain Z [auth AAA] MOL2 format, chain JA [auth BBB] MOL2 format, chain X [auth AAA] mmCIF format, chain KA [auth BBB] mmCIF format, chain LA [auth BBB] mmCIF format, chain MA [auth BBB] mmCIF format, chain V [auth AAA] mmCIF format, chain W [auth AAA] mmCIF format, chain Y [auth AAA] mmCIF format, chain Z [auth AAA] mmCIF format, chain JA [auth BBB] mmCIF format, chain X [auth AAA]	JA [auth BBB] KA [auth BBB] LA [auth BBB] MA [auth BBB] V [auth AAA] JA [auth BBB], KA [auth BBB], LA [auth BBB], MA [auth BBB], V [auth AAA], W [auth AAA], X [auth AAA], Y [auth AAA], Z [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain JA [auth BBB] Focus chain KA [auth BBB] Focus chain LA [auth BBB] Focus chain MA [auth BBB] Focus chain V [auth AAA] Focus chain W [auth AAA] Focus chain X [auth AAA] Focus chain Y [auth AAA] Focus chain Z [auth AAA] Interactions & Density Focus chain JA [auth BBB] Focus chain KA [auth BBB] Focus chain LA [auth BBB] Focus chain MA [auth BBB] Focus chain V [auth AAA] Focus chain W [auth AAA] Focus chain X [auth AAA] Focus chain Y [auth AAA] Focus chain Z [auth AAA]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain EA [auth BBB] SDF format, chain K [auth AAA] MOL2 format, chain EA [auth BBB] MOL2 format, chain K [auth AAA] mmCIF format, chain EA [auth BBB] mmCIF format, chain K [auth AAA]	EA [auth BBB], K [auth AAA]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain EA [auth BBB] Focus chain K [auth AAA] Interactions & Density Focus chain EA [auth BBB] Focus chain K [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.203 (Depositor), 0.180 (DCC)
R-Value Work: 0.158 (Depositor), 0.169 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.072	α = 90
b = 200.888	β = 90
c = 217.306	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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