9BFG

Structure of the crosslinked PCP-E didomain of tyrocidine synthetase A

PDB DOI: https://doi.org/10.2210/pdb9BFG/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Brevibacillus parabrevis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-04-17 Released: 2024-10-09
Deposition Author(s): Heberlig, G.W., Burkart, M.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.228
R-Value Work: 0.188

Starting Model: experimental
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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

Crosslinking intermodular condensation in non-ribosomal peptide biosynthesis

Heberlig, G.W., La Clair, J.J., Burkart, M.D.

(2024) Nature

DOI: https://doi.org/10.1038/s41586-024-08306-y

Macromolecule Content

Total Structure Weight: 128.79 kDa
Atom Count: 8,996
Modelled Residue Count: 1,065
Deposited Residue Count: 1,110
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrocidine synthase 1	A, B	555	Brevibacillus parabrevis	Mutation(s): 1 Gene Names: tycA EC: 5.1.1.11
UniProt
Find proteins for P09095 (Brevibacillus parabrevis) Explore P09095 Go to UniProtKB: P09095
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09095
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2GH (Subject of Investigation/LOI) Query on 2GH Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain V [auth B] MOL2 format, chain L [auth A] MOL2 format, chain V [auth B] mmCIF format, chain L [auth A] mmCIF format, chain V [auth B]	L [auth A], V [auth B]	N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-pentyl-beta-alaninamide C₁₄ H₂₉ N₂ O₇ P YNPRWOBMMGRKHD-LBPRGKRZSA-N		Interactions Focus chain L [auth A] Focus chain V [auth B] Interactions & Density Focus chain L [auth A] Focus chain V [auth B]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] mmCIF format, chain E [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B]	E [auth A], Q [auth B], S [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain Q [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain Q [auth B] Focus chain S [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain U [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain U [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain U [auth B]	C [auth A] D [auth A] F [auth A] H [auth A] I [auth A] C [auth A], D [auth A], F [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth A], O [auth B], P [auth B], R [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth B] Focus chain U [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth B] Focus chain U [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth A] SDF format, chain T [auth B] SDF format, chain W [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth B] MOL2 format, chain W [auth B] mmCIF format, chain G [auth A] mmCIF format, chain N [auth A] mmCIF format, chain T [auth B] mmCIF format, chain W [auth B]	G [auth A], N [auth A], T [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain W [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain W [auth B]