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- PDB-1jdk: solution structure of lactam analogue (EDap) of HIV gp41 600-612 loop. -

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Basic information

Entry
Database: PDB / ID: 1jdk
Titlesolution structure of lactam analogue (EDap) of HIV gp41 600-612 loop.
ComponentsACETYL GROUP
KeywordsVIRAL PROTEIN / cyclic peptide / peptidomimetics / HIV / gp41 / lactam bond
MethodSOLUTION NMR / torsion angle dynamics, energy minimization, molecular dynamics
AuthorsPhan Chan Du, A. / Limal, D. / Semetey, V. / Dali, H. / Jolivet, M. / Desgranges, C. / Cung, M.T. / Briand, J.P. / Petit, M.C. / Muller, S.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural and immunological characterisation of heteroclitic peptide analogues corresponding to the 600-612 region of the HIV envelope gp41 glycoprotein.
Authors: Du, A.P. / Limal, D. / Semetey, V. / Dali, H. / Jolivet, M. / Desgranges, C. / Cung, M.T. / Briand, J.P. / Petit, M.C. / Muller, S.
History
DepositionJun 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: ACETYL GROUP


Theoretical massNumber of molelcules
Total (without water)1,4031
Polymers1,4031
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)25 / 50target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ACETYL GROUP


Mass: 1402.615 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the parent peptide IWGCSGKLICTTA occurs naturally in HIV gp41 glycoprotein
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
NMR detailsText: Typical 2D ho;onuclear techniques were applied. Different NOESY experiment with different mixing times (from 80ms to 800ms) were recorded in order to determine the best conditions without spin diffusion.

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Sample preparation

DetailsContents: 3mMpeptide in 500ul solvent / Solvent system: 100% DMSO-D6
Sample conditionsPressure: atmospheric atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE4001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker GMBHcollection
XwinNMR2.6Bruker GMBHprocessing
XEASY1.2Bartels C., Xia T., Billeter M., Guentert P and Wuethrich K. (1995) J. Biomol.NMR, 5, 1-10data analysis
DYANA1.5Guentert P., Mumenthaler C. and Wuethrich K. (1997) J.Mol.Biol., 273,283-298refinement
Discover3MSI, San Diegorefinement
RefinementMethod: torsion angle dynamics, energy minimization, molecular dynamics
Software ordinal: 1
Details: 50 initial random strucutre were generated using DYANA software, followed by 500 steps energy minimization. Then using DISCOVER 3 35 ps MD in vacuo at 300K, 200 steps energy minimization ...Details: 50 initial random strucutre were generated using DYANA software, followed by 500 steps energy minimization. Then using DISCOVER 3 35 ps MD in vacuo at 300K, 200 steps energy minimization under NMR restraints and 750 steps conjugate gradient EM.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 25

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