9HE9 | pdb_00009he9

Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with lauric acid

PDB DOI: https://doi.org/10.2210/pdb9HE9/pdb

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

Deposited: 2024-11-13 Released: 2025-02-26
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: 2.15 Å
R-Value Free:
0.227 (Depositor), 0.234 (DCC)
R-Value Work:
0.199 (Depositor), 0.205 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Characterization of Recombinant Unspecific Peroxygenase from Candolleomyces aberdarensis through Crystallographic and Substrate Selectivity Studies

Menes-Rubio, A., Fernandez-Garcia, A., Monterrey, D.T., de Santos, P.G., Sanchez-Moreno, I., Sanz-Aparicio, J., Alcalde, M.

(2025) ChemCatChem

DOI: https://doi.org/10.1002/cctc.202402015

Macromolecule Content

Total Structure Weight: 118.83 kDa
Atom Count: 9,241
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

Help

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 [auth G]	5		N-Glycosylation	Interactions Focus chain D [auth G] Interactions & Density Focus chain D [auth G]
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 [auth H]	7		N-Glycosylation	Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 4
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	F [auth X], H [auth l]	4		N-Glycosylation	Interactions Focus chain F [auth X] Focus chain H [auth l] Interactions & Density Focus chain F [auth X] Focus chain H [auth l]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 5
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 [auth Y]	6		N-Glycosylation	Interactions Focus chain G [auth Y] Interactions & Density Focus chain G [auth Y]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth n]	2		N-Glycosylation	Interactions Focus chain I [auth n] Interactions & Density Focus chain I [auth n]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 N [auth A] SDF format, chain U [auth B] SDF format, chain Y [auth C] MOL2 format, chain N [auth A] MOL2 format, chain U [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain N [auth A] mmCIF format, chain U [auth B] mmCIF format, chain Y [auth C]	N [auth A], U [auth B], Y [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain N [auth A] Focus chain U [auth B] Focus chain Y [auth C] Interactions & Density Focus chain N [auth A] Focus chain U [auth B] Focus chain Y [auth C]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain S [auth B] SDF format, chain X [auth C] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] mmCIF format, chain K [auth A] mmCIF format, chain S [auth B] mmCIF format, chain X [auth C]	K [auth A], S [auth B], X [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain S [auth B] Focus chain X [auth C] Interactions & Density Focus chain K [auth A] Focus chain S [auth B] Focus chain X [auth C]
DAO (Subject of Investigation/LOI) Query on DAO Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B]	J [auth A], R [auth B]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain V [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth C]	AA [auth C], O [auth A], P [auth A], V [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain V [auth B] Focus chain Z [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain T [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B]	L [auth A], M [auth A], T [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain Q [auth A] SDF format, chain W [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain W [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain W [auth B]	BA [auth C], Q [auth A], W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain Q [auth A] Focus chain W [auth B] Interactions & Density Focus chain BA [auth C] Focus chain Q [auth A] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.227 (Depositor), 0.234 (DCC)
R-Value Work: 0.199 (Depositor), 0.205 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 271.878	α = 90
b = 75.001	β = 111.74
c = 105.446	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-02-26

Deposition Author(s):

Fernandez-Garcia, A.

Sanz-Aparicio, J.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	Synergy CAM Project Y2018/BIO-4738-EVOQUIMERA-CM
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2022-136367OB-C33

Revision History (Full details and data files)

Version 1.0: 2025-02-26
Type: Initial release
Version 1.1: 2025-03-05
Changes: Source and taxonomy

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9HE9 | pdb_00009he9

Unspecific peroxygenase from Psathyrella aberdarensis (PabUPO-II) in complex with lauric acid

Characterization of Recombinant Unspecific Peroxygenase from Candolleomyces aberdarensis through Crystallographic and Substrate Selectivity Studies

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

9HE9 | pdb_00009he9