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- PDB-2l6t: Efficacy of an HIV-1 entry inhibitor targeting the GP41 fusion peptide -

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Basic information

Entry
Database: PDB / ID: 2l6t
TitleEfficacy of an HIV-1 entry inhibitor targeting the GP41 fusion peptide
ComponentsVIR-576
KeywordsANTIVIRAL PROTEIN / anti-viral polypeptide / gp41 Fusion Peptide / FP1-24
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 3
AuthorsForssmann, W. / The, Y. / Stoll, M. / Adermann, K. / Albrecht, U. / Barlos, K. / Busmann, A. / Can les-Mayordomo, A. / Gimenez-Gallego, G. / Hirsch, J. ...Forssmann, W. / The, Y. / Stoll, M. / Adermann, K. / Albrecht, U. / Barlos, K. / Busmann, A. / Can les-Mayordomo, A. / Gimenez-Gallego, G. / Hirsch, J. / Jimenez-Barbero, J. / Meyer-Olson, D. / Muench, J. / Perez-Castells, J. / Staendker, L. / Kirchhoff, F. / Schmidt, R.E.
Citation
Journal: Sci Transl Med / Year: 2010
Title: Short-term monotherapy in HIV-infected patients with a virus entry inhibitor against the gp41 fusion peptide.
Authors: Forssmann, W.G. / The, Y.H. / Stoll, M. / Adermann, K. / Albrecht, U. / Barlos, K. / Busmann, A. / Canales-Mayordomo, A. / Gimenez-Gallego, G. / Hirsch, J. / Jimenez-Barbero, J. / Meyer- ...Authors: Forssmann, W.G. / The, Y.H. / Stoll, M. / Adermann, K. / Albrecht, U. / Barlos, K. / Busmann, A. / Canales-Mayordomo, A. / Gimenez-Gallego, G. / Hirsch, J. / Jimenez-Barbero, J. / Meyer-Olson, D. / Munch, J. / Perez-Castells, J. / Standker, L. / Kirchhoff, F. / Schmidt, R.E.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2007
Title: Discovery and optimization of a natural HIV-1 entry inhibitor targeting the GP41 fusion peptide.
Authors: Muench, J. / Staendker, L. / Adermann, K. / Schulz, A. / Schindler, M. / Chinnadurai, R. / Pohlmann, S. / Chaipan, C. / BieT, T. / Peters, T. / Meyer, B. / Wilhelm, D. / Lu, H. / Jing, W. / ...Authors: Muench, J. / Staendker, L. / Adermann, K. / Schulz, A. / Schindler, M. / Chinnadurai, R. / Pohlmann, S. / Chaipan, C. / BieT, T. / Peters, T. / Meyer, B. / Wilhelm, D. / Lu, H. / Jing, W. / Jiang, S. / Forssmann, W. / Kirchhoff, F.
History
DepositionNov 24, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VIR-576


Theoretical massNumber of molelcules
Total (without water)2,2531
Polymers2,2531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide VIR-576


Mass: 2252.689 Da / Num. of mol.: 1 / Source method: obtained synthetically
Sequence detailsVIR-576 IS A NEW POLYPEPTIDE DESIGNED ON THE BASIS OF VIRIP [CELL 129 (2007) 263], A NATURAL ...VIR-576 IS A NEW POLYPEPTIDE DESIGNED ON THE BASIS OF VIRIP [CELL 129 (2007) 263], A NATURAL POLYPEPTIDE THAT BINDS TO THE GP41 FUSION PEPTIDE OF HIV-1 PREVENTS THE VIRUS FROM ENTERING TARGET CELLS. VIR-576 WAS SELECTED AFTER A LONG SCREENING PROCESS BECAUSE IT SHOWS A CONSIDERABLE ENHANCED ACTIVITY.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY

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Sample preparation

DetailsContents: 0.05 mM VIR-576, 0.1 mM FP1-24, 8 % [U-100% 2H] DMSO, 20 mM [U-100% 2H] SODIUM ACETATE, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.05 mMVIR-576-11
0.1 mMFP1-24-21
8 %DMSO-3[U-100% 2H]1
20 mMSODIUM ACETATE-4[U-100% 2H]1
Sample conditionsIonic strength: 20 SODIUM ACETATE-D3 / pH: 2.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XEASYBartels et al.chemical shift assignment
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 14

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