BMRB Entry 19175

Name: [Asp2]RTD-1
Published: 2014-02-03

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PDB ID: 2m77
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19175
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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:

[Asp2]RTD-1

Deposition date:

2013-04-18

Original release date:

2014-02-03

Authors:

Conibear, Anne; Bochen, Alexander; Rosengren, K. Johan; Kessler, Horst; Craik, David

Citation:

Citation: Conibear, Anne; Bochen, Alexander; Rosengren, K. Johan; Stupar, Petar; Wang, Conan; Kessler, Horst; Craik, David. "The Cyclic Cystine Ladder of Theta-Defensins as a Stable, Bifunctional Scaffold: A Proof-of-Concept Study Using the Integrin-Binding RGD Motif" ChemBioChem 15, 451-459 (2014).
PubMed: 24382674

Assembly members:

Assembly members:
[Asp2]RTD-1, polymer, 18 residues, 2078.569 Da.

Natural source:

Natural source: Common Name: Rhesus monkey Taxonomy ID: 9544 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Macaca mulatta

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
[Asp2]RTD-1: GDCRCLCRRGVCRCICTR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	52
1H chemical shifts	116

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	[Asp2]RTD-1	1

Entities:

Entity 1, [Asp2]RTD-1 18 residues - 2078.569 Da.

Head-to-tail (Arg-Gly) cyclic peptide with disulfide bonds between cystine residues 3-16, 5-14, and 7-12.

1

GLY

ASP

CYS

ARG

CYS

LEU

CYS

ARG

GLY

2

VAL

CYS

ARG

CYS

ILE

CYS

THR

ARG

Samples:

sample_1: [Asp2]RTD-1 0.7 mM; DSS 10 ug; H2O 90%; D2O 10%

sample_2: [Asp2]RTD-1 0.6 mM; DSS 10 ug; D2O 100%

sample_conditions_1: pH: 3; pressure: 1 atm; temperature: 298 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-13C HSQC	sample_2	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H ECOSY	sample_2	isotropic	sample_conditions_1

Software:

CcpNMR v2.1, CCPN - chemical shift assignment, data analysis, peak picking

TOPSPIN v2.1, Bruker Biospin - collection, processing

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v2.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz