8U78 | pdb_00008u78

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.183 (Depositor), 0.183 (DCC)
R-Value Work:
0.154 (Depositor), 0.154 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.joc.3c02617
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-Methyl-D-Gln4,Lys10-teixobactin	A, B, C, D, E 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	3D Interactions
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain V [auth G] MOL2 format, chain V [auth G] mmCIF format, chain V [auth G]	V [auth G]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain V [auth G] Interactions & Density Focus chain V [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain T [auth F] SDF format, chain U [auth G] SDF format, chain W [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H]	I [auth A] J [auth A] K [auth A] L [auth B] M [auth B] 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		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain W [auth H]

Biologically Interesting Molecules (External Reference)

1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.183 (Depositor), 0.183 (DCC)
R-Value Work: 0.154 (Depositor), 0.154 (DCC)
R-Value Observed: 0.157 (Depositor)

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-06

Deposition Author(s):

Nowick, J.S.

Yang, H.

Kreutzer, A.G.

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