8K1X | pdb_00008k1x

Biochemical and structural characterization of a multifunctional cytochrome P450 SpcN in staurosporine biosynthesis

PDB DOI: https://doi.org/10.2210/pdb8K1X/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces sanyensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-11 Released: 2024-10-16
Deposition Author(s): Xiao, F., Dong, S., Feng, Y., Li, W.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.234 (Depositor), 0.245 (DCC)
R-Value Work:
0.211 (Depositor), 0.223 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Molecular Basis for the P450-Catalyzed sp3 C-N Glycosidic Bond Formation in Staurosporine Biosynthesis.

Xiao, F., Dong, S., Feng, Y., Li, W.

(2024) ACS Catal 14: 14274-14284

DOI: https://doi.org/10.1021/acscatal.4c03875

Macromolecule Content

Total Structure Weight: 150.59 kDa
Atom Count: 9,344
Modeled Residue Count: 1,158
Deposited Residue Count: 1,320
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, C	440	Streptomyces sanyensis	Mutation(s): 0 Gene Names: spcN
UniProt
Find proteins for W5R4Y8 (Streptomyces sanyensis) Explore W5R4Y8 Go to UniProtKB: W5R4Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W5R4Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 K [auth C] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain K [auth C] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain K [auth C] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B], K [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain K [auth C]
VI4 (Subject of Investigation/LOI) Query on VI4 Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth B] E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], L [auth C]	13-(3-Amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranosyl)-6,7,12,13-tetrahydro-5H-indolo[2,3-a]pyrrolo[3,4-c]carbazol-5-one C₂₆ H₂₄ N₄ O₃ QNQXRLNOOGRQEB-FUJFFIKUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C]