BMRB Entry 34850

Name: Conformations of macrocyclic peptides sampled by exact NOEs: models for cell-permeability. NMR structure of Omphalotin A in methanol / water indoleOut conformation.
Published: 2023-12-12

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PDB ID: 8qbp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34850
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Conformations of macrocyclic peptides sampled by exact NOEs: models for cell-permeability. NMR structure of Omphalotin A in methanol / water indoleOut conformation.

Deposition date:

2023-08-25

Original release date:

2023-12-12

Authors:

Ruedisser, S.; Matabaro, E.; Sonderegger, L.; Guentert, P.; Kuenzler, M.; Gossert, A.

Citation:

Citation: Rudisser, S.; Matabaro, E.; Sonderegger, L.; Guntert, P.; Kunzler, M.; Gossert, A.. "Conformations of Macrocyclic Peptides Sampled by Nuclear Magnetic Resonance: Models for Cell-Permeability." J. Am. Chem. Soc. 145, 27601-27615 (2023).
PubMed: 38062770

Assembly members:

Assembly members:
entity_1, polymer, 12 residues, 1336.746 Da.

Natural source:

Natural source: Common Name: Omphalotus olearius Taxonomy ID: 72120 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Omphalotus olearius

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Komagataella pastoris

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: WXIXXXXXXVXX

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
1H chemical shifts	93

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 12 residues - 1336.746 Da.

1

TRP

MVA

ILE

MVA

SAR

MVA

IML

SAR

VAL

2

IML

SAR

Samples:

sample_1: omphalotin A 20 ± 2 uM

sample_conditions_1: ionic strength: 0 M; pH: 7; pressure: 1 bar; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

TopSpin v4.0.7, Bruker Biospin - processing

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

Amber v22, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - peak picking

CcpNmr Analysis, CCPN - chemical shift assignment

NMR spectrometers:

Bruker AVANCE III HD 900 MHz