BMRB Entry 34017

Name: NMR structure of peptide 10 targeting CXCR4
Published: 2016-09-02

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PDB ID: 5lfh
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34017
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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:

NMR structure of peptide 10 targeting CXCR4

Deposition date:

2016-07-01

Original release date:

2016-09-02

Authors:

Di Maro, S.; Trotta, A.; Brancaccio, D.; Di Leva, F.; La Pietra, V.; Ierano, C.; Napolitano, M.; Portella, L.; D'Alterio, C.; Siciliano, R.; Sementa, D.; Tomassi, S.; Carotenuto, A.; Novellino, E.; Scala, S.; Marinelli, L.

Citation:

Citation: Di Maro, S.; Trotta, A.; Brancaccio, D.; Di Leva, F.; La Pietra, V.; Ierano, C.; Napolitano, M.; Portella, L.; D'Alterio, C.; Siciliano, R.; Sementa, D.; Tomassi, S.; Carotenuto, A.; Novellino, E.; Scala, S.; Marinelli, L.. "Exploring the N-terminal region of C-X-C motif chemokine 12 (CXCL12): Identification of plasma-stable cyclic peptides as novel, potent C-X-C chemokine receptor type 4 (CXCR4) antagonists." J. Med. Chem. 59, 8369-8380 (2016).
PubMed: 27571038

Assembly members:

Assembly members:
entity_1, polymer, 8 residues, 930.152 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XRAXRFFC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
1H chemical shifts	50

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 - 930.152 Da.

1

ACE

ARG

ALA

DCY

ARG

PHE

CYS

Samples:

sample_1: H2O, deuterated, 10%; PEPTIDE 10 2 mM; SDS, deuterated, 200 mM

sample_conditions_1: ionic strength: 0 mM; pH: 5.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D 1H	sample_1	anisotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	anisotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	anisotropic	sample_conditions_1
2D DQF-COSY	sample_1	anisotropic	sample_conditions_1

Software:

DISCOVER, Accelrys Software Inc. - refinement

DYANA, Guntert, Braun and Wuthrich - structure calculation

XEASY, Bartels et al. - chemical shift assignment

NMR spectrometers:

Varian INOVA 700 MHz