8U78

Structure of a N-Me-D-Gln4,Lys10-teixobactin analogue

• PDB DOI: https://doi.org/10.2210/pdb8U78/pdb

• Classification: ANTIBIOTIC
• Organism(s): Eleftheria terrae
• Mutation(s): No 


• Deposited: 2023-09-14 Released: 2024-03-06 
• Deposition Author(s): Nowick, J.S., Yang, H., Kreutzer, A.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.183 
• R-Value Work: 0.154 
• R-Value Observed: 0.157 

Literature

Supramolecular Interactions of Teixobactin Analogues in the Crystal State.

Yang, H., Kreutzer, A.G., Nowick, J.S.

(2024) J Org Chem 89: 5104-5108

• PubMed: 38506062 
• DOI: https://doi.org/10.1021/acs.joc.3c02617
• Primary Citation of Related Structures:  
  8U78


• PubMed Abstract: 
  

  This Note presents the X-ray crystallographic structure of the N -methylated teixobactin analogue N -Me-d-Gln ₄ ,Lys ₁₀ -teixobactin ( 1 ). Eight peptide molecules comprise the asymmetric unit, with each peptide molecule binding a chloride anion through hydrogen bonding with the amide NH group of residues 7, 8, 10, and 11. The peptide molecules form hydrogen-bonded antiparallel β-sheet dimers in the crystal lattice, with residues 1-3 comprising the dimerization interface. The dimers further assemble end-to-end in the crystal lattice.

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Organizational Affiliation: 

Department of Chemistry, University of California Irvine, Irvine, California 92697, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.76 kDa 
• Atom Count: 802 
• Modelled Residue Count: 88 
• Deposited Residue Count: 88 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-Methyl-D-Gln4,Lys10-teixobactin	A, B, C, D, E, F, G, H	11	Eleftheria terrae	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG6	V [auth G]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C12 H26 O6 DMDPGPKXQDIQQG-UHFFFAOYSA-N
CL	I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth C], O [auth C], P [auth D], Q [auth D], R [auth E], S [auth E], T [auth F], U [auth G], W [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002532	A, B, C, D, E, F, G, H	N-Methyl-D-Gln4,Lys10-teixobactin	Peptide-like / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.183 
• R-Value Work: 0.154 
• R-Value Observed: 0.157 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.88	α = 90
b = 24.88	β = 90
c = 106.315	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
BOS	data collection
XDS	data reduction
pointless	data scaling
Aimless	data scaling
PHENIX	phasing
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Nowick, J.S., Yang, H., Kreutzer, A.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI121548
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI137258

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Database references
• Version 1.2: 2024-04-17
  Changes: Database references