BMRB Entry 30357

Name: Solution structure of de novo macrocycle design8.2
Published: 2017-12-26

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PDB ID: 6ben
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30357
MolProbity Validation Chart

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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: Solution structure of de novo macrocycle design8.2 PubMed: 29242347

Deposition date: 2017-10-25 Original release date: 2017-12-26

Authors: Shortridge, M.; Hosseinzadeh, P.; Pardo-Avila, F.; Varani, G.; Baker, B.

Citation: Hosseinzadeh, P.; Bhardwaj, G.; Mulligan, V.; Shortridge, M.; Craven, T.; Pardo-Avila, F.; Rettie, S.; Kim, D.; Silva, D.; Ibrahim, Y.; Webb, I.; Cort, J.; Adkins, J.; Varani, G.; Baker, D.. "Comprehensive computational design of ordered peptide macrocycles." Science 358, 1461-1466 (2017).

Assembly members:
entity_1, polymer, 8 residues, 1040.133 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):
entity_1: XQXXRXPQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
15N chemical shifts	9
1H chemical shifts	56

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 8 residues - 1040.133 Da.

1

DAR

GLN

DPR

DGN

ARG

DGL

PRO

GLN

Samples:

sample_1: Design8.2 5 mg/mL; glycerol, [U-2H], 5%

sample_conditions_1: ionic strength: 0 Not defined; pH: 5.5; pressure: 1 atm; temperature: 278 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

gromacs v2016.1, Abraham - refinement

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker DRX 500 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts