9IUV | pdb_00009iuv

Crystal Structure of a PtOYE Mutant (ADes-5)

PDB DOI: https://doi.org/10.2210/pdb9IUV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Parageobacillus thermantarcticus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-07-22 Released: 2025-08-27
Deposition Author(s): Zheng, S., Liu, Z., Yu, F., Yin, H.
Funding Organization(s): National Science Foundation (NSF, China), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)
R-Value Observed:
0.177 (Depositor)

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

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Molecular-dynamics-simulation-guided directed evolution of flavoenzymes for atroposelective desaturation

Yin, H.N., Chen, Z., Zhao, X., Liu, Z., Yu, F., Zheng, S., Huang, N., Liu, Z.

(2025) Nat Synth 4: 1621-1629

DOI: https://doi.org/10.1038/s44160-025-00882-9

Macromolecule Content

Total Structure Weight: 154.05 kDa
Atom Count: 12,135
Modeled Residue Count: 1,360
Deposited Residue Count: 1,360
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH dehydrogenase	A, B, C, D	340	Parageobacillus thermantarcticus	Mutation(s): 0 Gene Names: namA, SAMN05192569_10087 EC: 1.6.99.1
UniProt
Find proteins for A0A1I0SYV3 (Parageobacillus thermantarcticus) Explore A0A1I0SYV3 Go to UniProtKB: A0A1I0SYV3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1I0SYV3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]