9BE3

The pre-condensation state of the dimodular NRPS protein LgrA

PDB DOI: https://doi.org/10.2210/pdb9BE3/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Brevibacillus parabrevis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-13 Released: 2024-11-20
Deposition Author(s): Pistofidis, A., Schmeing, T.M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.258
R-Value Work: 0.216
R-Value Observed: 0.217

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

To be determined and updated

Pistofidis, A., Ma, P., Houk, K.N., Schmeing, T.M.

To be published.

Macromolecule Content

Total Structure Weight: 413.64 kDa
Atom Count: 28,355
Modelled Residue Count: 3,520
Deposited Residue Count: 3,628
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Linear gramicidin synthase subunit A	A, B	1,814	Brevibacillus parabrevis	Mutation(s): 0 Gene Names: lgrA
UniProt
Find proteins for Q70LM7 (Brevibacillus parabrevis) Explore Q70LM7 Go to UniProtKB: Q70LM7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q70LM7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JQG (Subject of Investigation/LOI) Query on JQG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	(2~{R})-~{N}-[3-[2-[[(2~{S})-2-formamido-3-methyl-butanoyl]amino]ethylamino]-3-oxidanylidene-propyl]-3,3-dimethyl-2-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-butanamide C₁₇ H₃₂ N₄ O₉ P SZJRFDKIBVCSLN-KBPBESRZSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
A1AMO (Subject of Investigation/LOI) Query on A1AMO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	N-[2-(glycylamino)ethyl]-N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide C₁₃ H₂₇ N₄ O₈ P ZCWBBGZAVLIBIM-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	C [auth A], D [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	G [auth A], J [auth B], K [auth B], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]