6KW0 | pdb_00006kw0

The structure of EanB/Y353F-Cys412-persulfide in tetrahedral intermediate state with ergothioneine

PDB DOI: https://doi.org/10.2210/pdb6KW0/pdb

Classification: TRANSFERASE
Organism(s): Chlorobium limicola
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2019-09-05 Released: 2020-09-09
Deposition Author(s): Wu, L., Liu, P.H., Zhou, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.250 (Depositor), 0.256 (DCC)
R-Value Work:
0.196 (Depositor), 0.204 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The structure of EanB/Y353F-Cys412-persulfide in tetrahedral intermediate state with ergothioneine

Wu, L., Liu, P.H., Zhou, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 105.36 kDa
Atom Count: 6,857
Modeled Residue Count: 848
Deposited Residue Count: 920
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfurtransferase	A, B	460	Chlorobium limicola	Mutation(s): 1 Gene Names: Clim_1149
UniProt
Find proteins for B3ECE3 (Chlorobium limicola (strain DSM 245 / NBRC 103803 / 6330)) Explore B3ECE3 Go to UniProtKB: B3ECE3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3ECE3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LW8 (Subject of Investigation/LOI) Query on LW8 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	trimethyl-[(2S)-1-oxidanyl-1-oxidanylidene-3-(2-sulfanylidene-1,3-dihydroimidazol-4-yl)propan-2-yl]azanium C₉ H₁₆ N₃ O₂ S SSISHJJTAXXQAX-ZETCQYMHSA-O		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
PGE Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B] Focus chain I [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]