5GTF | pdb_00005gtf

Crystal structure of onion lachrymatory factor synthase (LFS) containing glycerol

PDB DOI: https://doi.org/10.2210/pdb5GTF/pdb

Classification: ISOMERASE
Organism(s): Allium cepa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-20 Released: 2017-08-23
Deposition Author(s): Takabe, J., Arakawa, T., Masamura, N., Tsuge, N., Imai, S., Fushinobu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.199 (Depositor), 0.210 (DCC)
R-Value Work:
0.170 (Depositor), 0.180 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Dissecting the Stereocontrolled Conversion of Short-Lived Sulfenic Acid by Lachrymatory Factor Synthase

Arakawa, T., Sato, Y., Yamada, M., Takabe, J., Moriwaki, Y., Masamura, N., Kato, M., Aoyagi, M., Kamoi, T., Terada, T., Shimizu, K., Tsuge, N., Imai, S., Fushinobu, S.

(2020) ACS Catal 10: 9-19

DOI: https://doi.org/10.1021/acscatal.9b03720

Macromolecule Content

Total Structure Weight: 81.03 kDa
Atom Count: 5,626
Modelled Residue Count: 604
Deposited Residue Count: 700
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lachrymatory-factor synthase	A, B, C, D	175	Allium cepa	Mutation(s): 0 Gene Names: LFS EC: 5.3 (PDB Primary Data), 5.3.99.12 (UniProt)
UniProt
Find proteins for P59082 (Allium cepa) Explore P59082 Go to UniProtKB: P59082
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59082
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D] mmCIF format, chain R [auth D]	R [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain P [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth C]	G [auth A], K [auth B], L [auth B], M [auth C], P [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain P [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain P [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D]	E [auth A] F [auth A] H [auth B] I [auth B] J [auth B] E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], N [auth C], O [auth C], Q [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D]