9J0E | pdb_00009j0e

A Chemoenzymatic Strategy for Efficient Synthesis of Aporphine Alkaloids

PDB DOI: https://doi.org/10.2210/pdb9J0E/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces aurantiacus JA 4570
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-02 Released: 2025-08-13
Deposition Author(s): Yang, L., Qu, X.D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.191 (Depositor), 0.191 (DCC)
R-Value Work:
0.175 (Depositor), 0.175 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Catalyst-free photoinitiated intramolecular carbon-carbon coupling enables the efficient synthesis of pharmaceutically important biaryls

Yang, L., Qu, X.D.

To be published.

Macromolecule Content

Total Structure Weight: 61.33 kDa
Atom Count: 5,144
Modeled Residue Count: 577
Deposited Residue Count: 578
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase GLYR1 like protein	A, B	289	Streptomyces aurantiacus JA 4570	Mutation(s): 0 Gene Names: STRAU_4331
UniProt
Find proteins for S3ZG23 (Streptomyces aurantiacus JA 4570) Explore S3ZG23 Go to UniProtKB: S3ZG23
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S3ZG23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.191 (Depositor), 0.191 (DCC)
R-Value Work: 0.175 (Depositor), 0.175 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.49	α = 90
b = 133.76	β = 90
c = 43.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22XD1421300
National Natural Science Foundation of China (NSFC)	China	23ZR1432800

Revision History (Full details and data files)

Version 1.0: 2025-08-13
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.