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Yorodumi- PDB-1jdk: solution structure of lactam analogue (EDap) of HIV gp41 600-612 loop. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jdk | ||||||
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Title | solution structure of lactam analogue (EDap) of HIV gp41 600-612 loop. | ||||||
Components | ACETYL GROUP | ||||||
Keywords | VIRAL PROTEIN / cyclic peptide / peptidomimetics / HIV / gp41 / lactam bond | ||||||
Method | SOLUTION NMR / torsion angle dynamics, energy minimization, molecular dynamics | ||||||
Authors | Phan Chan Du, A. / Limal, D. / Semetey, V. / Dali, H. / Jolivet, M. / Desgranges, C. / Cung, M.T. / Briand, J.P. / Petit, M.C. / Muller, S. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jdk.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jdk.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jdk_validation.pdf.gz | 353.3 KB | Display | wwPDB validaton report |
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Full document | 1jdk_full_validation.pdf.gz | 453.7 KB | Display | |
Data in XML | 1jdk_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1jdk_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jdk ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jdk | HTTPS FTP |
-Related structure data
Related structure data | 1im7C 1j8nC 1j8zC 1j9vC 1jaaC 1jarC 1jc8C 1jcpC 1jd8C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 1402.615 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: the parent peptide IWGCSGKLICTTA occurs naturally in HIV gp41 glycoprotein |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: 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. |
-Sample preparation
Details | Contents: 3mMpeptide in 500ul solvent / Solvent system: 100% DMSO-D6 |
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Sample conditions | Pressure: atmospheric atm / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 25 |