8WKO

Crystal structure of O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum in the closed form

PDB DOI: https://doi.org/10.2210/pdb8WKO/pdb

Classification: LYASE
Organism(s): Lactiplantibacillus plantarum JDM1
Expression System: Escherichia coli B
Mutation(s): No

Deposited: 2023-09-28 Released: 2024-02-14
Deposition Author(s): Oda, K., Matoba, Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.262
R-Value Work: 0.203
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Allosteric regulation of an acidophilic O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum

Matoba, Y., Oda, K., Wataeda, M., Matsuo, K.

To be published.

Macromolecule Content

Total Structure Weight: 97.37 kDa
Atom Count: 6,514
Modelled Residue Count: 849
Deposited Residue Count: 896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-methionine gamma-lyase	A, B	448	Lactiplantibacillus plantarum JDM1	Mutation(s): 0 Gene Names: mgl
UniProt
Find proteins for A0A0G9F7S9 (Lactiplantibacillus plantarum) Explore A0A0G9F7S9 Go to UniProtKB: A0A0G9F7S9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0G9F7S9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LLP (Subject of Investigation/LOI) Query on LLP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B]	E [auth A], J [auth B]	(2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid C₁₄ H₂₂ N₃ O₇ P YQSOQJORMNSDJL-QFULYMJESA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
PRO Query on PRO Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	PROLINE C₅ H₉ N O₂ ONIBWKKTOPOVIA-BYPYZUCNSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [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 B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B]	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]