6KU2 | pdb_00006ku2

The structure of EanB/Y353A complex with ergothioneine covalent linked with persulfide Cys412

PDB DOI: https://doi.org/10.2210/pdb6KU2/pdb

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

Deposited: 2019-08-30 Released: 2020-08-26
Deposition Author(s): Wu, L., Liu, P.H., Zhou, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.228 (Depositor), 0.227 (DCC)
R-Value Work:
0.171 (Depositor), 0.177 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Single-Step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source in the Anaerobic Ergothioneine Biosynthesis

Cheng, R., Wu, L., Lai, R., Peng, C., Naowarojna, N., Hu, W., Li, X., Whelan, S.A., Lee, N., Lopez, J., Zhao, C., Yong, Y., Xue, J., Jiang, X., Grinstaff, M.W., Deng, Z., Chen, J., Cui, Q., Zhou, J.H., Liu, P.

(2020) ACS Catal 10: 8981-8994

DOI: https://doi.org/10.1021/acscatal.0c01809

Macromolecule Content

Total Structure Weight: 105.72 kDa
Atom Count: 7,222
Modeled Residue Count: 854
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 [auth E]	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 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DV6 (Subject of Investigation/LOI) Query on DV6 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth E] MOL2 format, chain C [auth A] MOL2 format, chain K [auth E] mmCIF format, chain C [auth A] mmCIF format, chain K [auth E]	C [auth A], K [auth E]	[(2S)-3-[(2S)-2-(disulfanyl)-2,3-dihydro-1H-imidazol-4-yl]-1-oxidanyl-1-oxidanylidene-propan-2-yl]-trimethyl-azanium C₉ H₁₈ N₃ O₂ S₂ XGMLHKDWXWTLLL-CBAPKCEASA-O		Interactions Focus chain C [auth A] Focus chain K [auth E] Interactions & Density Focus chain C [auth A] Focus chain K [auth E]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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 I [auth A] SDF format, chain S [auth E] MOL2 format, chain I [auth A] MOL2 format, chain S [auth E] mmCIF format, chain I [auth A] mmCIF format, chain S [auth E]	I [auth A], S [auth E]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain S [auth E] Interactions & Density Focus chain I [auth A] Focus chain S [auth E]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth E] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth E] mmCIF format, chain G [auth A] mmCIF format, chain Q [auth E]	G [auth A], Q [auth E]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain Q [auth E] Interactions & Density Focus chain G [auth A] Focus chain Q [auth E]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain R [auth E] MOL2 format, chain H [auth A] MOL2 format, chain R [auth E] mmCIF format, chain H [auth A] mmCIF format, chain R [auth E]	H [auth A], R [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain R [auth E] Interactions & Density Focus chain H [auth A] Focus chain R [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E]	O [auth E], P [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth E] Focus chain P [auth E] Interactions & Density Focus chain O [auth E] Focus chain P [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth E] SDF format, chain L [auth E] MOL2 format, chain E [auth A] MOL2 format, chain N [auth E] MOL2 format, chain L [auth E] mmCIF format, chain E [auth A] mmCIF format, chain N [auth E] mmCIF format, chain L [auth E]	E [auth A], L [auth E], N [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain L [auth E] Focus chain N [auth E] Interactions & Density Focus chain E [auth A] Focus chain L [auth E] Focus chain N [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth E] MOL2 format, chain D [auth A] MOL2 format, chain M [auth E] mmCIF format, chain D [auth A] mmCIF format, chain M [auth E]	D [auth A], M [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth E] Interactions & Density Focus chain D [auth A] Focus chain M [auth E]