2MIJ | pdb_00002mij

NMR structure of the S-linked glycopeptide sublancin 168

• PDB DOI: https://doi.org/10.2210/pdb2MIJ/pdb
• BMRB: 19683

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Bacillus subtilis
• Mutation(s): No 


• Deposited: 2013-12-13 Released: 2014-03-12 
• Deposition Author(s): Garcia De Gonzalo, C.V., Zhu, L., Oman, T.J., van der Donk, W.A.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

NMR structure of the s-linked glycopeptide sublancin 168.

Garcia De Gonzalo, C.V., Zhu, L., Oman, T.J., van der Donk, W.A.

(2014) ACS Chem Biol 9: 796-801

• PubMed: 24405370 
• DOI: https://doi.org/10.1021/cb4008106
• Primary Citation Related Structures: 
  2MIJ


• PubMed Abstract: 
  

  Sublancin 168 is a member of a small group of glycosylated antimicrobial peptides known as glycocins. The solution structure of sublancin 168, a 37-amino-acid peptide produced by Bacillus subtilis 168, has been solved by nuclear magnetic resonance (NMR) spectroscopy. Sublancin comprises two α-helices and a well-defined interhelical loop. The two helices span residues 6-16 and 26-35, and the loop region encompasses residues 17-25. The 9-amino-acid loop region contains a β-S-linked glucose moiety attached to Cys22. Hydrophobic interactions as well as hydrogen bonding are responsible for the well-structured loop region. The three-dimensional structure provides an explanation for the previously reported extraordinary high stability of sublancin 168.

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Organizational Affiliation: 
• Howard Hughes Medical Institute and Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.9 kDa 
• Atom Count: 268 
• Modeled Residue Count: 37 
• Deposited Residue Count: 37 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPBc2 prophage-derived bacteriocin sublancin-168	A	37	Bacillus subtilis	Mutation(s): 0
UniProt
Find proteins for P68577 (Bacillus subtilis (strain 168)) Explore P68577  Go to UniProtKB:  P68577
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	B [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 150 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Garcia De Gonzalo, C.V., Zhu, L., Oman, T.J., van der Donk, W.A.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2014-04-02
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-06-14
  Changes: Database references, Other, Structure summary
• Version 2.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary