8OO2

ChdA complex with amido-chelocardin

PDB DOI: https://doi.org/10.2210/pdb8OO2/pdb

Classification: TRANSCRIPTION
Organism(s): Amycolatopsis sulphurea
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-04-04 Released: 2023-08-02
Deposition Author(s): Koehnke, J., Sikandar, A.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.212
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Revision of the Absolute Configurations of Chelocardin and Amidochelocardin.

Sikandar, A., Popoff, A., Jumde, R.P., Mandi, A., Kaur, A., Elgaher, W.A.M., Rosenberger, L., Huttel, S., Jansen, R., Hunter, M., Kohnke, J., Hirsch, A.K.H., Kurtan, T., Muller, R.

(2023) Angew Chem Int Ed Engl 62: e202306437-e202306437

PubMed: 37466921 Search on PubMed
DOI: https://doi.org/10.1002/anie.202306437
Primary Citation of Related Structures:
8OO2

PubMed Abstract:
Even with the aid of the available methods, the configurational assignment of natural products can be a challenging task that is prone to errors, and it sometimes needs to be corrected after total synthesis or single-crystal X-ray diffraction (XRD) analysis. Herein, the absolute configuration of amidochelocardin is revised using a combination of XRD, NMR spectroscopy, experimental ECD spectra, and time-dependent density-functional theory (TDDFT)-ECD calculations. As amidochelocardin was obtained via biosynthetic engineering of chelocardin, we propose the same absolute configuration for chelocardin based on the similar biosynthetic origins of the two compounds and result of TDDFT-ECD calculations. The evaluation of spectral data of two closely related analogues, 6-desmethyl-chelocardin and its semisynthetic derivative 1, also supports this conclusion.

Organizational Affiliation

Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) -, Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany.

Macromolecule Content

Total Structure Weight: 42.88 kDa
Atom Count: 2,943
Modelled Residue Count: 349
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator	A, B	194	Amycolatopsis sulphurea	Mutation(s): 0 Gene Names: chdA, ATK36_5244
UniProt
Find proteins for V9XTV0 (Amycolatopsis sulphurea) Explore V9XTV0 Go to UniProtKB: V9XTV0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	V9XTV0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AV8 (Subject of Investigation/LOI) Query on AV8 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	2-carboxamido-2-deacetyl-chelocardin C₂₁ H₂₀ N₂ O₇ RKOLRLPHCAUUDK-JTWCOAEXSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B]	D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]