8RTO | pdb_00008rto

Bilirubin oxidase from Myrothecium verrucaria in complex with ATP

PDB DOI: https://doi.org/10.2210/pdb8RTO/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: 2.40 Å
R-Value Free:
0.224 (Depositor), 0.188 (DCC)
R-Value Work:
0.170 (Depositor), 0.176 (DCC)
R-Value Observed:
0.170 (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: 247.07 kDa
Atom Count: 18,922
Modeled Residue Count: 2,135
Deposited Residue Count: 2,136
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], C [auth CCC], D [auth DDD]	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] Focus chain C [auth CCC] Focus chain D [auth DDD]
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	E [auth AeA], G [auth BeB]	3		N-Glycosylation	Interactions Focus chain E [auth AeA] Focus chain G [auth BeB] Interactions & Density Focus chain E [auth AeA] Focus chain G [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	F [auth AhA], H [auth BhB], I [auth CeC], J [auth CgC], K [auth DeD], F [auth AhA], H [auth BhB], I [auth CeC], J [auth CgC], K [auth DeD], L [auth DgD]	2		N-Glycosylation	Interactions Focus chain F [auth AhA] Focus chain H [auth BhB] Focus chain I [auth CeC] Focus chain J [auth CgC] Focus chain K [auth DeD] Focus chain L [auth DgD] Interactions & Density Focus chain F [auth AhA] Focus chain H [auth BhB] Focus chain I [auth CeC] Focus chain J [auth CgC] Focus chain K [auth DeD] Focus chain L [auth DgD]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain EA [auth CCC] SDF format, chain MA [auth DDD] SDF format, chain Q [auth AAA] SDF format, chain Y [auth BBB] MOL2 format, chain EA [auth CCC] MOL2 format, chain MA [auth DDD] MOL2 format, chain Q [auth AAA] MOL2 format, chain Y [auth BBB] mmCIF format, chain EA [auth CCC] mmCIF format, chain MA [auth DDD] mmCIF format, chain Q [auth AAA] mmCIF format, chain Y [auth BBB]	EA [auth CCC], MA [auth DDD], Q [auth AAA], Y [auth BBB]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain EA [auth CCC] Focus chain MA [auth DDD] Focus chain Q [auth AAA] Focus chain Y [auth BBB] Interactions & Density Focus chain EA [auth CCC] Focus chain MA [auth DDD] Focus chain Q [auth AAA] Focus chain Y [auth BBB]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain AA [auth CCC] SDF format, chain BA [auth CCC] SDF format, chain CA [auth CCC] SDF format, chain DA [auth CCC] SDF format, chain IA [auth DDD] SDF format, chain JA [auth DDD] SDF format, chain KA [auth DDD] SDF format, chain LA [auth DDD] SDF format, chain M [auth AAA] SDF format, chain N [auth AAA] SDF format, chain O [auth AAA] SDF format, chain P [auth AAA] SDF format, chain U [auth BBB] SDF format, chain V [auth BBB] SDF format, chain W [auth BBB] SDF format, chain X [auth BBB] MOL2 format, chain AA [auth CCC] MOL2 format, chain BA [auth CCC] MOL2 format, chain CA [auth CCC] MOL2 format, chain DA [auth CCC] MOL2 format, chain IA [auth DDD] MOL2 format, chain JA [auth DDD] MOL2 format, chain KA [auth DDD] MOL2 format, chain LA [auth DDD] MOL2 format, chain M [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain O [auth AAA] MOL2 format, chain P [auth AAA] MOL2 format, chain U [auth BBB] MOL2 format, chain V [auth BBB] MOL2 format, chain W [auth BBB] MOL2 format, chain X [auth BBB] mmCIF format, chain AA [auth CCC] mmCIF format, chain BA [auth CCC] mmCIF format, chain CA [auth CCC] mmCIF format, chain DA [auth CCC] mmCIF format, chain IA [auth DDD] mmCIF format, chain JA [auth DDD] mmCIF format, chain KA [auth DDD] mmCIF format, chain LA [auth DDD] mmCIF format, chain M [auth AAA] mmCIF format, chain N [auth AAA] mmCIF format, chain O [auth AAA] mmCIF format, chain P [auth AAA] mmCIF format, chain U [auth BBB] mmCIF format, chain V [auth BBB] mmCIF format, chain W [auth BBB] mmCIF format, chain X [auth BBB]	AA [auth CCC] BA [auth CCC] CA [auth CCC] DA [auth CCC] IA [auth DDD] AA [auth CCC], BA [auth CCC], CA [auth CCC], DA [auth CCC], IA [auth DDD], JA [auth DDD], KA [auth DDD], LA [auth DDD], M [auth AAA], N [auth AAA], O [auth AAA], P [auth AAA], U [auth BBB], V [auth BBB], W [auth BBB], X [auth BBB]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth CCC] Focus chain BA [auth CCC] Focus chain CA [auth CCC] Focus chain DA [auth CCC] Focus chain IA [auth DDD] Focus chain JA [auth DDD] Focus chain KA [auth DDD] Focus chain LA [auth DDD] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain U [auth BBB] Focus chain V [auth BBB] Focus chain W [auth BBB] Focus chain X [auth BBB] Interactions & Density Focus chain AA [auth CCC] Focus chain BA [auth CCC] Focus chain CA [auth CCC] Focus chain DA [auth CCC] Focus chain IA [auth DDD] Focus chain JA [auth DDD] Focus chain KA [auth DDD] Focus chain LA [auth DDD] Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain O [auth AAA] Focus chain P [auth AAA] Focus chain U [auth BBB] Focus chain V [auth BBB] Focus chain W [auth BBB] Focus chain X [auth BBB]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain GA [auth CCC] SDF format, chain HA [auth CCC] SDF format, chain S [auth AAA] SDF format, chain T [auth AAA] MOL2 format, chain GA [auth CCC] MOL2 format, chain HA [auth CCC] MOL2 format, chain S [auth AAA] MOL2 format, chain T [auth AAA] mmCIF format, chain GA [auth CCC] mmCIF format, chain HA [auth CCC] mmCIF format, chain S [auth AAA] mmCIF format, chain T [auth AAA]	GA [auth CCC], HA [auth CCC], S [auth AAA], T [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain GA [auth CCC] Focus chain HA [auth CCC] Focus chain S [auth AAA] Focus chain T [auth AAA] Interactions & Density Focus chain GA [auth CCC] Focus chain HA [auth CCC] Focus chain S [auth AAA] Focus chain T [auth AAA]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain FA [auth CCC] SDF format, chain NA [auth DDD] SDF format, chain R [auth AAA] SDF format, chain Z [auth BBB] MOL2 format, chain FA [auth CCC] MOL2 format, chain NA [auth DDD] MOL2 format, chain R [auth AAA] MOL2 format, chain Z [auth BBB] mmCIF format, chain FA [auth CCC] mmCIF format, chain NA [auth DDD] mmCIF format, chain R [auth AAA] mmCIF format, chain Z [auth BBB]	FA [auth CCC], NA [auth DDD], R [auth AAA], Z [auth BBB]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain FA [auth CCC] Focus chain NA [auth DDD] Focus chain R [auth AAA] Focus chain Z [auth BBB] Interactions & Density Focus chain FA [auth CCC] Focus chain NA [auth DDD] Focus chain R [auth AAA] Focus chain Z [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.224 (Depositor), 0.188 (DCC)
R-Value Work: 0.170 (Depositor), 0.176 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.468	α = 90
b = 204.726	β = 90
c = 221.388	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