8RZ6

SeMet derivative structure of the condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase

PDB DOI: https://doi.org/10.2210/pdb8RZ6/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces regensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-12 Released: 2024-06-26
Deposition Author(s): Karanth, M., Schmelz, S., Kirkpatrick, J., Krausze, J., Scrima, A., Carlomagno, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.216
R-Value Work: 0.172
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

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

Literature

The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain

Karanth, M.N., Kirkpatrick, J.P., Krausze, J., Schmelz, S., Scrima, A., Carlomagno, T.

(2024) Sci Adv 10

DOI: https://doi.org/10.1126/sciadv.adm9404

Macromolecule Content

Total Structure Weight: 120.04 kDa
Atom Count: 7,521
Modelled Residue Count: 881
Deposited Residue Count: 1,074
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tomaymycin non-ribosomal peptide synthetase	A, B	537	Streptomyces regensis	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	G [auth A], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	E [auth A], F [auth A], J [auth B], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]