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- PDB-1b03: SOLUTION STRUCTURE OF THE ANTIBODY-BOUND HIV-1IIIB V3 PEPTIDE -

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Entry
Database: PDB / ID: 1b03
TitleSOLUTION STRUCTURE OF THE ANTIBODY-BOUND HIV-1IIIB V3 PEPTIDE
ComponentsPROTEIN (P1053 PEPTIDE)
KeywordsVIRAL PROTEIN / P1053 STRUCTURE
Function / homologyGp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / Glycoprotein 120
Function and homology information
MethodSOLUTION NMR / HYBRID DG-SA
AuthorsTugarinov, V. / Zvi, A. / Levy, R. / Anglister, J.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: A cis proline turn linking two beta-hairpin strands in the solution structure of an antibody-bound HIV-1IIIB V3 peptide.
Authors: Tugarinov, V. / Zvi, A. / Levy, R. / Anglister, J.
#1: Journal: Biochemistry / Year: 1997
Title: Conformation of the Principal Neutralizing Determinant of Human Immunodeficiency Virus Type 1 in Complex with an Anti-GP120 Virus Neutralizing Antibody Studied by Two-dimensional Nuclear ...Title: Conformation of the Principal Neutralizing Determinant of Human Immunodeficiency Virus Type 1 in Complex with an Anti-GP120 Virus Neutralizing Antibody Studied by Two-dimensional Nuclear Magnetic Resonance Difference Spectroscopy.
Authors: Zvi, A. / Feigelson, D.J. / Hayek, Y. / Anglister, J.
History
DepositionNov 17, 1998Processing site: RCSB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (P1053 PEPTIDE)


Theoretical massNumber of molelcules
Total (without water)2,0171
Polymers2,0171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / -LEAST RESTRAINT VIOLATIONS
Representative

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Components

#1: Protein/peptide PROTEIN (P1053 PEPTIDE)


Mass: 2017.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / References: UniProt: Q79428

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N
12113C FILTERED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED IN COMPLEX WITH THE FV ANTIBODY FRAGMENT USING ISOTOPE-FILTERED AND ISOTOPE-EDITED NMR WITH EITHER THE FV OR THE PEPTIDE LABELLED WITH 15N AND 13C.

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Sample preparation

Sample conditionspH: 7.1 / Temperature: 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX600 / Manufacturer: Bruker / Model: DMX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
NMRPipestructure solution
RefinementMethod: HYBRID DG-SA / Software ordinal: 1
Details: AFTER INITIAL SIMULATED ANNEALING CALCULATIONS THE STRUCTURES WERE MINIMIZED USING A FULL L-J POTENTIAL REPRESENTATION. THE CIS PEPTIDE BOND BETWEEN GLY 12 AND PRO 13 WAS PATHED CIS IN THE ...Details: AFTER INITIAL SIMULATED ANNEALING CALCULATIONS THE STRUCTURES WERE MINIMIZED USING A FULL L-J POTENTIAL REPRESENTATION. THE CIS PEPTIDE BOND BETWEEN GLY 12 AND PRO 13 WAS PATHED CIS IN THE PROCESS OF STRUCTURE GENERATION.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS / Conformers submitted total number: 35

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