data_1886 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Conformational Preferences of Immunogenic Peptides Derived from the Principal Neutralizing Determinant of the HIV-1 Envelope Glycoprotein gp120 ; _BMRB_accession_number 1886 _BMRB_flat_file_name bmr1886.str _Entry_type update _Submission_date 1995-07-31 _Accession_date 1996-04-12 _Entry_origination BMRB _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chandrasekhar Kasibhatla . . 2 Profy Albert T. . 3 Dyson H. Jane . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 153 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-16 revision BMRB 'Complete natural source information' 2008-07-10 revision BMRB 'Updated non-standard residue' 1999-06-14 revision BMRB 'Converted to BMRB NMR-STAR V 2.1 format' 1996-04-12 revision BMRB 'Error corrected in abrreviations given to non-polymers' 1996-03-25 reformat BMRB 'Converted to the BMRB 1996-03-01 STAR flat-file format' 1995-07-31 original BMRB 'Last release in original BMRB flat-file format' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full ; Chandrasekhar, Kasibhatla, Profy, Albert T., Dyson, H. Jane, "Solution Conformational Preferences of Immunogenic Peptides Derived from the Principal Neutralizing Determinant of the HIV-1 Envelope Glycoprotein gp120," Biochemistry 30, 9187-9194 (1991). ; _Citation_title ; Solution Conformational Preferences of Immunogenic Peptides Derived from the Principal Neutralizing Determinant of the HIV-1 Envelope Glycoprotein gp120 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chandrasekhar Kasibhatla . . 2 Profy Albert T. . 3 Dyson H. Jane . stop_ _Journal_abbreviation Biochemistry _Journal_volume 30 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9187 _Page_last 9194 _Year 1991 _Details . save_ ################################## # Molecular system description # ################################## save_system_gp120 _Saveframe_category molecular_system _Mol_system_name gp120 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label gp120 $gp120 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic ? _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_gp120 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common gp120 _Name_variant RP142 _Molecular_mass . _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 24 _Mol_residue_sequence ; YNKRKRIHIGPGRAFYTTKN IIGX ; loop_ _Residue_seq_code _Residue_label 1 TYR 2 ASN 3 LYS 4 ARG 5 LYS 6 ARG 7 ILE 8 HIS 9 ILE 10 GLY 11 PRO 12 GLY 13 ARG 14 ALA 15 PHE 16 TYR 17 THR 18 THR 19 LYS 20 ASN 21 ILE 22 ILE 23 GLY 24 CY3 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-03-16 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 1885 gp120 95.83 40 100.00 100.00 1.85e-06 PDB 1ACY "Crystal Structure Of The Principal Neutralizing Site Of Hiv- 1" 95.83 24 100.00 100.00 1.98e-06 PDB 1GGI "Crystal Structure Of An Hiv-1 Neutralizing Antibody 50.1 In Complex With Its V3 Loop Peptide Antigen" 58.33 16 100.00 100.00 2.64e+00 PDB 1NAK "Igg1 Fab Fragment (83.1) Complex With 16-residue Peptide (residues 304-321 Of Hiv-1 Gp120 (mn Isolate))" 58.33 16 100.00 100.00 2.64e+00 PDB 1NIZ "Nmr Structure Of A V3 (Mn Isolate) Peptide Bound To 447-52d, A Human Hiv-1 Neutralizing Antibody" 66.67 16 100.00 100.00 2.02e-01 PDB 1NJ0 "Nmr Structure Of A V3 (Mn Isolate) Peptide Bound To 447-52d, A Human Hiv-1 Neutralizing Antibody" 66.67 16 100.00 100.00 2.02e-01 PDB 1Q1J "Crystal Structure Analysis Of Anti-Hiv-1 Fab 447-52d In Complex With V3 Peptide" 58.33 16 100.00 100.00 2.64e+00 PDB 2B0S "Crystal Structure Analysis Of Anti-Hiv-1 V3 Fab 2219 In Complex With Mn Peptide" 75.00 19 100.00 100.00 6.74e-03 PDB 2QSC "Crystal Structure Analysis Of Anti-Hiv-1 V3-Fab F425-B4e8 In Complex With A V3-Peptide" 62.50 15 100.00 100.00 8.08e-01 PDB 3GO1 "Crystal Structure Of Anti-Hiv-1 Fab 268-D In Complex With V3 Peptide Mn" 58.33 14 100.00 100.00 3.89e+00 PDB 3MLW "Crystal Structure Of Anti-Hiv-1 V3 Fab 1006-15d In Complex With An Mn V3 Peptide" 95.83 23 100.00 100.00 2.18e-06 PDB 3MLX "Crystal Structure Of Anti-Hiv-1 V3 Fab 3074 In Complex With An Mn V3 Peptide" 95.83 23 100.00 100.00 2.18e-06 PDB 3UJI "Crystal Structure Of Anti-Hiv-1 V3 Fab 2558 In Complex With Mn Peptide" 95.83 23 100.00 100.00 2.18e-06 GB AAA44857 "envelope polyprotein [Human immunodeficiency virus 1]" 95.83 856 100.00 100.00 2.91e-07 GB AAC21502 "envelope glycoprotein [Human immunodeficiency virus 1]" 95.83 205 100.00 100.00 2.29e-06 GB AAT67509 "envelope glycoprotein [Human immunodeficiency virus 1]" 95.83 857 100.00 100.00 2.91e-07 GB AAW72244 "envelope glycoprotein [Human immunodeficiency virus 1]" 95.83 857 100.00 100.00 3.27e-07 GB ABO85035 "envelope glylcoprotein, partial [Human immunodeficiency virus 1]" 95.83 263 100.00 100.00 3.94e-06 PIR VCLJMN "env polyprotein precursor - human immunodeficiency virus type 1 (isolate MN)" 95.83 859 100.00 100.00 3.09e-07 SP P05877 "RecName: Full=Envelope glycoprotein gp160; AltName: Full=Env polyprotein; Contains: RecName: Full=Surface protein gp120; Short=" 95.83 856 100.00 100.00 2.91e-07 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_CY3 _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 2-AMINO-3-MERCAPTO-PROPIONAMIDE _BMRB_code CY3 _PDB_code CY3 _Standard_residue_derivative . _Molecular_mass 120.173 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? C C C . 0 . ? O O O . 0 . ? CB CB C . 0 . ? SG SG S . 0 . ? N1 N1 N . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG HG H . 0 . ? HN11 HN11 H . 0 . ? HN12 HN12 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N H2 ? ? SING CA C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C N1 ? ? SING CB SG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING SG HG ? ? SING N1 HN11 ? ? SING N1 HN12 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain $gp120 HIV 12721 Virus . HIV . generic stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $gp120 'not available' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_list _Saveframe_category NMR_spectrometer _Manufacturer unknown _Model unknown _Field_strength 0 _Details 'spectrometer information not available' save_ ############################# # NMR applied experiments # ############################# save__1 _Saveframe_category NMR_applied_experiment _Sample_label $sample_one save_ ####################### # Sample conditions # ####################### save_sample_condition_set_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.34 . n/a temperature 278 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_par_set_one _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio_citation_label _Correction_value_citation_label p-dioxane H . . ppm 3.75 . . . . . $entry_citation $entry_citation stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_assignment_data_set_one _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_condition_set_one _Chem_shift_reference_set_label $chem_shift_reference_par_set_one _Mol_system_component_name gp120 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 TYR HA H 4.21 . 1 2 . 1 TYR HB2 H 3.09 . 1 3 . 1 TYR HB3 H 3.09 . 1 4 . 1 TYR HD1 H 7.08 . 1 5 . 1 TYR HD2 H 7.08 . 1 6 . 1 TYR HE1 H 6.83 . 1 7 . 1 TYR HE2 H 6.83 . 1 8 . 2 ASN H H 8.82 . 1 9 . 2 ASN HA H 4.72 . 1 10 . 2 ASN HB2 H 2.68 . 2 11 . 2 ASN HB3 H 2.76 . 2 12 . 3 LYS H H 8.61 . 1 13 . 3 LYS HA H 4.23 . 1 14 . 3 LYS HB2 H 1.73 . 2 15 . 3 LYS HB3 H 1.83 . 2 16 . 3 LYS HG2 H 1.43 . 1 17 . 3 LYS HG3 H 1.43 . 1 18 . 3 LYS HD2 H 1.7 . 1 19 . 3 LYS HD3 H 1.7 . 1 20 . 3 LYS HE2 H 2.97 . 1 21 . 3 LYS HE3 H 2.97 . 1 22 . 4 ARG H H 8.44 . 1 23 . 4 ARG HA H 4.26 . 1 24 . 4 ARG HB2 H 1.82 . 1 25 . 4 ARG HB3 H 1.82 . 1 26 . 4 ARG HG2 H 1.6 . 2 27 . 4 ARG HG3 H 1.65 . 2 28 . 4 ARG HD2 H 3.17 . 1 29 . 4 ARG HD3 H 3.17 . 1 30 . 4 ARG HE H 7.24 . 1 31 . 5 LYS H H 8.43 . 1 32 . 5 LYS HA H 4.28 . 1 33 . 5 LYS HB2 H 1.8 . 1 34 . 5 LYS HB3 H 1.8 . 1 35 . 5 LYS HG2 H 1.4 . 1 36 . 5 LYS HG3 H 1.4 . 1 37 . 5 LYS HD2 H 1.6 . 1 38 . 5 LYS HD3 H 1.6 . 1 39 . 5 LYS HE2 H 2.95 . 1 40 . 5 LYS HE3 H 2.95 . 1 41 . 6 ARG H H 8.57 . 1 42 . 6 ARG HA H 4.35 . 1 43 . 6 ARG HB2 H 1.75 . 1 44 . 6 ARG HB3 H 1.75 . 1 45 . 6 ARG HG2 H 1.54 . 2 46 . 6 ARG HG3 H 1.61 . 2 47 . 6 ARG HD2 H 3.16 . 1 48 . 6 ARG HD3 H 3.16 . 1 49 . 6 ARG HE H 7.23 . 1 50 . 7 ILE H H 8.4 . 1 51 . 7 ILE HA H 4.15 . 1 52 . 7 ILE HB H 1.78 . 1 53 . 7 ILE HG12 H 1.38 . 2 54 . 7 ILE HG13 H 1.13 . 2 55 . 7 ILE HG2 H .83 . 1 56 . 7 ILE HD1 H .82 . 1 57 . 8 HIS H H 8.83 . 1 58 . 8 HIS HA H 4.71 . 1 59 . 8 HIS HB2 H 3.13 . 1 60 . 8 HIS HB3 H 3.13 . 1 61 . 8 HIS HD2 H 7.22 . 1 62 . 8 HIS HE1 H 8.55 . 1 63 . 9 ILE H H 8.44 . 1 64 . 9 ILE HA H 4.19 . 1 65 . 9 ILE HB H 1.79 . 1 66 . 9 ILE HG12 H 1.43 . 2 67 . 9 ILE HG13 H 1.12 . 2 68 . 9 ILE HG2 H .87 . 1 69 . 9 ILE HD1 H .81 . 1 70 . 10 GLY H H 8.52 . 1 71 . 10 GLY HA2 H 4.07 . 2 72 . 10 GLY HA3 H 4.14 . 2 73 . 11 PRO HA H 4.46 . 1 74 . 11 PRO HB2 H 2.23 . 2 75 . 11 PRO HB3 H 1.96 . 2 76 . 11 PRO HG2 H 1.96 . 1 77 . 11 PRO HG3 H 1.96 . 1 78 . 11 PRO HD2 H 3.62 . 1 79 . 11 PRO HD3 H 3.62 . 1 80 . 12 GLY H H 8.66 . 1 81 . 12 GLY HA2 H 3.96 . 1 82 . 12 GLY HA3 H 3.96 . 1 83 . 13 ARG H H 8.32 . 1 84 . 13 ARG HA H 4.26 . 1 85 . 13 ARG HB2 H 1.68 . 2 86 . 13 ARG HB3 H 1.75 . 2 87 . 13 ARG HG2 H 1.55 . 1 88 . 13 ARG HG3 H 1.55 . 1 89 . 13 ARG HD2 H 3.13 . 1 90 . 13 ARG HD3 H 3.13 . 1 91 . 14 ALA H H 8.42 . 1 92 . 14 ALA HA H 4.22 . 1 93 . 14 ALA HB H 1.24 . 1 94 . 15 PHE H H 8.25 . 1 95 . 15 PHE HA H 4.54 . 1 96 . 15 PHE HB2 H 2.98 . 2 97 . 15 PHE HB3 H 3.09 . 2 98 . 15 PHE HD1 H 7.09 . 1 99 . 15 PHE HD2 H 7.09 . 1 100 . 15 PHE HE1 H 7.27 . 1 101 . 15 PHE HE2 H 7.27 . 1 102 . 15 PHE HZ H 7.25 . 1 103 . 16 TYR H H 8.18 . 1 104 . 16 TYR HA H 4.62 . 1 105 . 16 TYR HB2 H 2.88 . 2 106 . 16 TYR HB3 H 3.02 . 2 107 . 16 TYR HD1 H 7.06 . 1 108 . 16 TYR HD2 H 7.06 . 1 109 . 16 TYR HE1 H 6.77 . 1 110 . 16 TYR HE2 H 6.77 . 1 111 . 17 THR H H 8.19 . 1 112 . 17 THR HA H 4.38 . 1 113 . 17 THR HB H 4.18 . 1 114 . 17 THR HG2 H 1.17 . 1 115 . 18 THR H H 8.26 . 1 116 . 18 THR HA H 4.32 . 1 117 . 18 THR HB H 4.21 . 1 118 . 18 THR HG2 H 1.21 . 1 119 . 19 LYS H H 8.45 . 1 120 . 19 LYS HA H 4.29 . 1 121 . 19 LYS HB2 H 1.8 . 1 122 . 19 LYS HB3 H 1.8 . 1 123 . 19 LYS HG2 H 1.4 . 1 124 . 19 LYS HG3 H 1.4 . 1 125 . 19 LYS HD2 H 1.6 . 1 126 . 19 LYS HD3 H 1.6 . 1 127 . 19 LYS HE2 H 2.95 . 1 128 . 19 LYS HE3 H 2.95 . 1 129 . 20 ASN H H 8.58 . 1 130 . 20 ASN HA H 4.68 . 1 131 . 20 ASN HB2 H 2.69 . 2 132 . 20 ASN HB3 H 2.78 . 2 133 . 21 ILE H H 8.3 . 1 134 . 21 ILE HA H 4.18 . 1 135 . 21 ILE HB H 1.86 . 1 136 . 21 ILE HG12 H 1.41 . 2 137 . 21 ILE HG13 H 1.15 . 2 138 . 21 ILE HG2 H .85 . 1 139 . 21 ILE HD1 H .83 . 1 140 . 22 ILE H H 8.42 . 1 141 . 22 ILE HA H 4.5 . 1 142 . 22 ILE HB H 1.85 . 1 143 . 22 ILE HG12 H 1.2 . 2 144 . 22 ILE HG13 H 1.49 . 2 145 . 22 ILE HG2 H .9 . 1 146 . 22 ILE HD1 H .85 . 1 147 . 23 GLY H H 8.69 . 1 148 . 23 GLY HA2 H 3.99 . 1 149 . 23 GLY HA3 H 3.99 . 1 150 . 24 CY3 H H 8.41 . 1 151 . 24 CY3 HA H 4.53 . 1 152 . 24 CY3 HB2 H 2.92 . 1 153 . 24 CY3 HB3 H 2.92 . 1 stop_ save_