9RG4 | pdb_00009rg4

Unspecific peroxygenase from Psathyrella aberdarensis, Grogu variant, in complex with 5-formyl-2-furoic acid

PDB DOI: https://doi.org/10.2210/pdb9RG4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candolleomyces aberdarensis
Expression System: Komagataella phaffii CBS 7435
Mutation(s): Yes

Deposited: 2025-06-05 Released: 2026-04-01
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: 1.70 Å
R-Value Free:
0.180 (Depositor), 0.188 (DCC)
R-Value Work:
0.153 (Depositor), 0.163 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

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: 80.23 kDa
Atom Count: 6,606
Modeled Residue Count: 668
Deposited Residue Count: 668
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	334	Candolleomyces aberdarensis	Mutation(s): 3 Gene Names: EST38_g7491 EC: 1.11.2.1
UniProt
Find proteins for A0A4Q2DF39 (Candolleomyces aberdarensis) Explore A0A4Q2DF39 Go to UniProtKB: A0A4Q2DF39
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4Q2DF39
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MH0 (Subject of Investigation/LOI) Query on MH0 Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B]	P [auth A], PA [auth B]	Mesoheme C₃₄ H₃₆ Fe N₄ O₄ CKMCSMAXNUVLQI-RGGAHWMASA-N		Interactions Focus chain P [auth A] Focus chain PA [auth B] Interactions & Density Focus chain P [auth A] Focus chain PA [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain OA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain OA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain OA [auth B]	E [auth A] EA [auth B] HA [auth B] IA [auth B] K [auth A] E [auth A], EA [auth B], HA [auth B], IA [auth B], K [auth A], KA [auth B], LA [auth B], OA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain EA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain OA [auth B] Interactions & Density Focus chain E [auth A] Focus chain EA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain OA [auth B]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B]	F [auth A], FA [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain FA [auth B] Interactions & Density Focus chain F [auth A] Focus chain FA [auth B]
BMA Query on BMA Download Ideal Coordinates CCD File SDF format, chain QA [auth B] MOL2 format, chain QA [auth B] mmCIF format, chain QA [auth B]	QA [auth B]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain QA [auth B] Interactions & Density Focus chain QA [auth B]
A1JHS (Subject of Investigation/LOI) Query on A1JHS Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B]	CA [auth B], DA [auth B]	5-Formyl-2-furancarboxylic Acid C₆ H₄ O₄ SHNRXUWGUKDPMA-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A]	G [auth A], J [auth A], M [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Focus chain M [auth A] Interactions & Density Focus chain G [auth A] Focus chain J [auth A] Focus chain M [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain YA [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain YA [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain YA [auth B]	BA [auth A], YA [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth A] Focus chain YA [auth B] Interactions & Density Focus chain BA [auth A] Focus chain YA [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain JA [auth B] SDF format, chain L [auth A] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain O [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A]	GA [auth B] H [auth A] I [auth A] JA [auth B] L [auth A] GA [auth B], H [auth A], I [auth A], JA [auth B], L [auth A], MA [auth B], NA [auth B], O [auth A]	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 JA [auth B] Focus chain L [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain O [auth A] Interactions & Density Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain JA [auth B] Focus chain L [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain O [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] R [auth A] S [auth A] T [auth A] TA [auth B] AA [auth A], R [auth A], S [auth A], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], Z [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain Z [auth A]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain SA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain SA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain SA [auth B]	N [auth A], SA [auth B]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain SA [auth B] Interactions & Density Focus chain N [auth A] Focus chain SA [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain RA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain RA [auth B]	Q [auth A], RA [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain RA [auth B] Interactions & Density Focus chain Q [auth A] Focus chain RA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.180 (Depositor), 0.188 (DCC)
R-Value Work: 0.153 (Depositor), 0.163 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.496	α = 90
b = 76.496	β = 90
c = 273.21	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-04-01

Deposition Author(s):

Fernandez-Garcia, A.

Sanz-Aparicio, J.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	Y2018/BIO-4738-EVOQUIMERA-CM
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2019-105838RB-C33