9KG5 | pdb_00009kg5

Crystal structure of the CYP154C5 F92A/R114A/T248D/E282A variant from Nocardia farcinica

PDB DOI: https://doi.org/10.2210/pdb9KG5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nocardia farcinica IFM 10152
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-11-07 Released: 2025-11-05
Deposition Author(s): Qin, M.M., Fan, S.X., Cong, Z.Q., Jiang, Y.P.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.202 (Depositor), 0.203 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (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

Semirationally Engineering an Efficient P450 Peroxygenase for Regio- and Enantioselective Hydroxylation of Steroids

Fan, S., Qin, M., Wang, Q., Jiang, Y., Cong, Z.

(2025) ACS Catal 15: 2977-2986

DOI: https://doi.org/10.1021/acscatal.4c06342

Macromolecule Content

Total Structure Weight: 96.98 kDa
Atom Count: 7,083
Modeled Residue Count: 810
Deposited Residue Count: 858
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 monooxygenase	A [auth B], B [auth A]	429	Nocardia farcinica IFM 10152	Mutation(s): 4 Gene Names: NFA_53110
UniProt
Find proteins for Q5YNS8 (Nocardia farcinica (strain IFM 10152)) Explore Q5YNS8 Go to UniProtKB: Q5YNS8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5YNS8
Sequence Annotations Expand
Reference Sequence

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 D [auth B] SDF format, chain L [auth A] MOL2 format, chain D [auth B] MOL2 format, chain L [auth A] mmCIF format, chain D [auth B] mmCIF format, chain L [auth A]	D [auth B], L [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth B] Focus chain L [auth A] Interactions & Density Focus chain D [auth B] Focus chain L [auth A]
TES (Subject of Investigation/LOI) Query on TES Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain K [auth A] MOL2 format, chain C [auth B] MOL2 format, chain K [auth A] mmCIF format, chain C [auth B] mmCIF format, chain K [auth A]	C [auth B], K [auth A]	TESTOSTERONE C₁₉ H₂₈ O₂ MUMGGOZAMZWBJJ-DYKIIFRCSA-N		Interactions Focus chain C [auth B] Focus chain K [auth A] Interactions & Density Focus chain C [auth B] Focus chain K [auth A]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	E [auth B], F [auth B], G [auth B], N [auth A], O [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain N [auth A] Focus chain O [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	I [auth B], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain P [auth A] MOL2 format, chain H [auth B] MOL2 format, chain P [auth A] mmCIF format, chain H [auth B] mmCIF format, chain P [auth A]	H [auth B], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Focus chain P [auth A] Interactions & Density Focus chain H [auth B] Focus chain P [auth A]