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- PDB-5olf: Ligand-Based NMR Study of C-X-C Chemokine Receptor Type 4 (CXCR4)... -

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Basic information

Entry
Database: PDB / ID: 5olf
TitleLigand-Based NMR Study of C-X-C Chemokine Receptor Type 4 (CXCR4)-Ligand Interactions in Living Cancer Cells
ComponentsGBA-ALA-CYS-ARG-PHE-PHE-CYS
KeywordsPEPTIDE BINDING PROTEIN / CXCR4 / IN-CELL NMR
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBrancaccio, D. / Carotenuto, A.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Ligand-Based NMR Study of C-X-C Chemokine Receptor Type 4 (CXCR4)-Ligand Interactions on Living Cancer Cells.
Authors: Brancaccio, D. / Diana, D. / Di Maro, S. / Di Leva, F.S. / Tomassi, S. / Fattorusso, R. / Russo, L. / Scala, S. / Trotta, A.M. / Portella, L. / Novellino, E. / Marinelli, L. / Carotenuto, A.
History
DepositionJul 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 2.0May 15, 2019Group: Atomic model / Data collection / Category: atom_site / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GBA-ALA-CYS-ARG-PHE-PHE-CYS


Theoretical massNumber of molelcules
Total (without water)9091
Polymers9091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1100 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide GBA-ALA-CYS-ARG-PHE-PHE-CYS


Mass: 909.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D 1H-1H NOESY
121anisotropic12D 1H-1H TOCSY
131anisotropic12D DQF-COSY

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Sample preparation

DetailsType: micelle
Contents: 2.0 mM NA peptide, 10 % [U-99% 2H] D2O, 90% H2O/10% D2O
Label: 1H_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMpeptideNA1
10 %D2O[U-99% 2H]1
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
XEASYBartels et al.chemical shift assignment
DYANAGuntert, Braun and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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