9IFQ | pdb_00009ifq

Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with 5-hydroxymethylfurfural

PDB DOI: https://doi.org/10.2210/pdb9IFQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candolleomyces aberdarensis
Expression System: Komagataella phaffii CBS 7435
Mutation(s): No

Deposited: 2025-02-18 Released: 2025-08-06
Deposition Author(s): Fernandez-Garcia, A., Sanz-Aparicio, J.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.221 (Depositor), 0.228 (DCC)
R-Value Work:
0.195 (Depositor), 0.203 (DCC)
R-Value Observed:
0.197 (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

Unspecific peroxygenase from Psathyrella aberdarensis

Fernandez-Garcia, A., Sanz-Aparicio, J.

To be published.

Macromolecule Content

Total Structure Weight: 119.69 kDa
Atom Count: 9,217
Modeled Residue Count: 1,005
Deposited Residue Count: 1,005
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme-thiolate peroxidase	A, B, C	335	Candolleomyces aberdarensis	Mutation(s): 0 Gene Names: EST38_g8238 EC: 1.11.2.1
UniProt
Find proteins for A0A4V1Q376 (Candolleomyces aberdarensis) Explore A0A4V1Q376 Go to UniProtKB: A0A4V1Q376
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4V1Q376
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C
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)-[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	D, F	5		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	E	7		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	G	6		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 5
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	H	4		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 6
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	I	3		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain J [auth A] SDF format, chain U [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain U [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B]	CA [auth C], J [auth A], U [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain CA [auth C] Focus chain J [auth A] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain J [auth A] Focus chain U [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth B]	K [auth A], N [auth A], R [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth A] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain N [auth A] Focus chain R [auth B]
FUX (Subject of Investigation/LOI) Query on FUX Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	AA [auth C] BA [auth C] L [auth A] M [auth A] S [auth B] AA [auth C], BA [auth C], L [auth A], M [auth A], S [auth B], T [auth B]	5-HYDROXYMETHYL-FURFURAL C₆ H₆ O₃ NOEGNKMFWQHSLB-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth B] Focus chain T [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain Q [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	EA [auth C], FA [auth C], Q [auth A], W [auth B], X [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain Q [auth A] Focus chain W [auth B] Focus chain X [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain O [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	GA [auth C], HA [auth C], O [auth A], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain HA [auth C] Focus chain O [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain GA [auth C] Focus chain HA [auth C] Focus chain O [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain P [auth A] SDF format, chain V [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain V [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain V [auth B]	DA [auth C], P [auth A], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain P [auth A] Focus chain V [auth B] Interactions & Density Focus chain DA [auth C] Focus chain P [auth A] Focus chain V [auth B]