8Q6Y

Crystal structure of Cytochrome P450 GymB5 from Streptomyces katrae in complex with cYY and Hypoxanthine

PDB DOI: https://doi.org/10.2210/pdb8Q6Y/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces katrae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-15 Released: 2024-06-26
Deposition Author(s): Freytag, J., Mueller, J.M., Stehle, T., Zocher, G.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.216
R-Value Work: 0.185
R-Value Observed: 0.186

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

Intramolecular Coupling and Nucleobase Transfer - How Cytochrome P450 Enzymes GymBx Establish Their Chemoselectivity

Freytag, J., Martin, A., Muller, J.C., Kelm, T., Stehle, T., Li, S.M., Zocher, G.

(2024) ChemCatChem 16

DOI: https://doi.org/10.1002/cctc.202481002

Macromolecule Content

Total Structure Weight: 92.3 kDa
Atom Count: 6,664
Modelled Residue Count: 777
Deposited Residue Count: 820
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450	A, B	410	Streptomyces katrae	Mutation(s): 0 Gene Names: VR44_17910
UniProt
Find proteins for A0A0F4JF04 (Streptomyces katrae) Explore A0A0F4JF04 Go to UniProtKB: A0A0F4JF04
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F4JF04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
YTT (Subject of Investigation/LOI) Query on YTT Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(3S,6S)-3,6-bis(4-hydroxybenzyl)piperazine-2,5-dione C₁₈ H₁₈ N₂ O₄ NGPCLOGFGKJCBP-HOTGVXAUSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
HPA (Subject of Investigation/LOI) Query on HPA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	E [auth A], J [auth B], K [auth B]	HYPOXANTHINE C₅ H₄ N₄ O FDGQSTZJBFJUBT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	F [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]