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 1.0 of the entry. See complete history.

Literature

Crosslinking Reveals the Molecular Details of Intermodular Condensation and Epimerization in Nonribosomal Peptide Biosynthesis

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

To be published.

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]	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]
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]	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]
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]	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]
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]	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]