8WVR | pdb_00008wvr

Complex structure of the azoxy synthase VlmB and its substrate

PDB DOI: https://doi.org/10.2210/pdb8WVR/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Kitasatospora setae KM-6054
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-24 Released: 2024-10-30
Deposition Author(s): Zang, X., Zhou, J.H., Yiling, D., Jingkun, S., Zhijie, Z., Zhuanglin, S., Guiyun, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.240 (Depositor), 0.241 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.198 (Depositor)

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

A conserved enzymatic route for azoxy bond formation in natural product biosynthesis

Zang, X., Zhou, J.H., Yiling, D., Jingkun, S., Zhijie, Z., Zhuanglin, S., Guiyun, Z.

To be published.

Macromolecule Content

Total Structure Weight: 148.61 kDa
Atom Count: 10,691
Modeled Residue Count: 1,286
Deposited Residue Count: 1,328
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative VlmB homolog	A, B, C, D	332	Kitasatospora setae KM-6054	Mutation(s): 0 Gene Names: vlmB
UniProt
Find proteins for E4N6B3 (Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054)) Explore E4N6B3 Go to UniProtKB: E4N6B3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E4N6B3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XBN (Subject of Investigation/LOI) Query on XBN Download:Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	(2~{S})-2-(2-hexylhydrazinyl)-3-oxidanyl-propanoic acid C₉ H₂₀ N₂ O₃ HIBZWEWQIZJYRX-QMMMGPOBSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], O [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] J [auth B] M [auth C] F [auth A], G [auth A], I [auth B], J [auth B], M [auth C], N [auth C], P [auth D], Q [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth D]