9WK1 | pdb_00009wk1

Cryo-EM structure of DONepi, a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5

PDB DOI: https://doi.org/10.2210/pdb9WK1/pdb
EM Map EMD-66036: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Nocardioides sp. S5-5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-09-01 Released: 2026-09-09
Deposition Author(s): He, W.J., Wu, A.B., Xiong, R.Y.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation

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

Literature

Cryo-EM structure of DONepi, a deoxynivalenol 3-epimerase from Nocardioides sp. S5-5

He, W.J., Wu, A.B., Xiong, R.Y.

To be published.

Macromolecule Content

Total Structure Weight: 311.1 kDa
Atom Count: 20,724
Modeled Residue Count: 2,626
Deposited Residue Count: 2,768
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DON 3-epimerase chain D	A [auth D] B [auth A] C [auth B] D [auth C] E A [auth D], B [auth A], C [auth B], D [auth C], E, F, G, H	346	Nocardioides sp. S5-5	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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 I [auth D] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth G] SDF format, chain P [auth H] MOL2 format, chain I [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth G] MOL2 format, chain P [auth H] mmCIF format, chain I [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth G] mmCIF format, chain P [auth H]	I [auth D] J [auth A] K [auth B] L [auth C] M [auth E] I [auth D], J [auth A], K [auth B], L [auth C], M [auth E], N [auth F], O [auth G], P [auth H]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain I [auth D] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth D] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]