9IFP | pdb_00009ifp

Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with 2,6-dimethoxyphenol

PDB DOI: https://doi.org/10.2210/pdb9IFP/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: 1.90 Å
R-Value Free:
0.219 (Depositor), 0.226 (DCC)
R-Value Work:
0.200 (Depositor), 0.208 (DCC)
R-Value Observed:
0.201 (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: 120.68 kDa
Atom Count: 9,232
Modeled Residue Count: 1,005
Deposited Residue Count: 1,005
Unique protein chains: 1

Macromolecules

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(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	5		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
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

Small Molecules

Ligands 9 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 F [auth A] SDF format, chain U [auth B] SDF format, chain WA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain U [auth B] MOL2 format, chain WA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain U [auth B] mmCIF format, chain WA [auth C]	F [auth A], U [auth B], WA [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain F [auth A] Focus chain U [auth B] Focus chain WA [auth C] Interactions & Density Focus chain F [auth A] Focus chain U [auth B] Focus chain WA [auth C]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B]	CA [auth B], DA [auth B], FA [auth B], G [auth A], M [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth B] Focus chain G [auth A] Focus chain M [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth B] Focus chain G [auth A] Focus chain M [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain HA [auth B] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain HA [auth B]	HA [auth B] OA [auth C] PA [auth C] QA [auth C] RA [auth C] HA [auth B], OA [auth C], PA [auth C], QA [auth C], RA [auth C], V [auth B], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain HA [auth B] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain HA [auth B] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain UA [auth C] SDF format, chain Z [auth B] SDF format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain AA [auth B]	AA [auth B], BA [auth B], UA [auth C], Z [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain UA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain UA [auth C] Focus chain Z [auth B]
BMA Query on BMA Download Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain Y [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain Y [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain Y [auth B]	IA [auth B], SA [auth C], TA [auth C], Y [auth B]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain IA [auth B] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain Y [auth B] Interactions & Density Focus chain IA [auth B] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain Y [auth B]
3DM (Subject of Investigation/LOI) Query on 3DM Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain LA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain YA [auth C] SDF format, chain Q [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain Q [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain Q [auth A]	EA [auth B] LA [auth B] O [auth A] P [auth A] Q [auth A] EA [auth B], LA [auth B], O [auth A], P [auth A], Q [auth A], YA [auth C]	2,6-dimethoxyphenol C₈ H₁₀ O₃ KLIDCXVFHGNTTM-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain LA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain YA [auth C] Interactions & Density Focus chain EA [auth B] Focus chain LA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain YA [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain ZA [auth C] SDF format, chain S [auth A] SDF format, chain MA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain ZA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain MA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain ZA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain MA [auth B]	MA [auth B], R [auth A], S [auth A], ZA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain MA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain MA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain ZA [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain VA [auth C] SDF format, chain XA [auth C] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain H [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain H [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain H [auth A]	GA [auth B] H [auth A] I [auth A] J [auth A] JA [auth B] GA [auth B], H [auth A], I [auth A], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], N [auth A], VA [auth C], XA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain N [auth A] Focus chain VA [auth C] Focus chain XA [auth C] Interactions & Density Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain N [auth A] Focus chain VA [auth C] Focus chain XA [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain NA [auth B] SDF format, chain T [auth A] SDF format, chain AB [auth C] MOL2 format, chain NA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain AB [auth C] mmCIF format, chain NA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain AB [auth C]	AB [auth C], NA [auth B], T [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth C] Focus chain NA [auth B] Focus chain T [auth A] Interactions & Density Focus chain AB [auth C] Focus chain NA [auth B] Focus chain T [auth A]