data_5109 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of a lactam analogue (DabD) of HIV gp41 600-612 loop ; _BMRB_accession_number 5109 _BMRB_flat_file_name bmr5109.str _Entry_type original _Submission_date 2001-08-15 _Accession_date 2001-08-15 _Entry_origination author _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 'Phan Chan Du' A. . . 2 Limal D. . . 3 Semetey V. . . 4 Dali H. . . 5 Jolivet M. . . 6 Desgranges C. . . 7 Cung M. T. . 8 Briand J. P. . 9 Petit M. C. . 10 Muller S. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 73 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-16 update BMRB 'Updating non=standard residue' 2008-03-24 update BMRB . 2003-01-28 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 5108 'DapE (Ace)IWG(Dap)SGKLIETTA analogue of HIV GP41' 5110 'HCYS (ACE)IWG(BCX)SGKLICTTA analogue of HIV GP41' 5111 'HSER (ACE)IWGC(BSE)GKLICTTA analogue of HIV GP41' 5136 'EDap (Ace)IWGESGKLI(DAB)TTA analogue of HIV GP41' 5137 'DapD (Ace)IWG(DAP)SGKLIDTTA analogue of HIV GP41' 5138 'EDap (Ace)IWGESGKLI(DNP)TTA analogue of HIV GP41' 5139 'DDap (Ace)IWGDSGKLI(DNP)TTA analogue of HIV GP41' 5140 'DDab (Ace)IWGDSGKLI(Dab)TTA analogue of HIV GP41' stop_ _Original_release_date 2015-04-16 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural and Immunological Characterization of Heteroclitic Peptide Analogues Corresponding to the 600-612 Region of the HIV Envelope gp41 Glycoprotein ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22269625 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Du Angelique P.C. . 2 Limal David . . 3 Semetey Vincent . . 4 Dali Hayet . . 5 Jolivet Michel . . 6 Desgranges Claude . . 7 Cung Manh T. . 8 Briand Jean P. . 9 Petit Marie C. . 10 Muller Sylviane . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 323 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 503 _Page_last 521 _Year 2002 _Details . loop_ _Keyword HIV 'cyclic peptide' gp41 'lactam bond' 'lactam peptide' stop_ save_ ################################## # Molecular system description # ################################## save_system_DabD _Saveframe_category molecular_system _Mol_system_name 'DabD (Ace)IWG(DAB)SGKLIDTTA ANALOGUE OF HIV GP41' _Abbreviation_common DabD _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DabD (Ace)IWG(DAB)SGKLIDTTA ANALOGUE OF HIV GP41' $DabD stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DabD _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common DabD _Abbreviation_common DabD _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence ; XIWGXSGKLIDTTA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 2 ACE 2 2 ILE 3 3 TRP 4 4 GLY 5 5 DAB 6 6 SER 7 7 GLY 8 8 LYS 9 9 LEU 10 10 ILE 11 11 ASP 12 12 THR 13 13 THR 14 14 ALA stop_ _Sequence_homology_query_date 2005-11-24 _Sequence_homology_query_revised_last_date 2003-02-02 save_ ###################### # Polymer residues # ###################### save_chem_comp_ACE _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'ACETYL GROUP' _BMRB_code ACE _PDB_code ACE _Standard_residue_derivative . _Molecular_mass 44.053 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? O O O . 0 . ? CH3 CH3 C . 0 . ? H H H . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 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 DOUB C O ? ? SING C CH3 ? ? SING C H ? ? SING CH3 H1 ? ? SING CH3 H2 ? ? SING CH3 H3 ? ? stop_ save_ save_chem_comp_DAB _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common '2,4-DIAMINOBUTYRIC ACID' _BMRB_code . _PDB_code DAB _Standard_residue_derivative . _Molecular_mass 118.134 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jul 21 09:57:51 2011 ; 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 . ? CG CG C . 0 . ? ND ND N . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 H . 0 . ? HXT HXT 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 OXT ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG ND ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING ND HD1 ? ? SING ND HD2 ? ? SING OXT HXT ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DabD HIV 12721 Virus . Lentivirus 'human immunodeficiency virus' 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 $DabD 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DabD 3.5 mM . DMSO 100 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 2.6 loop_ _Task collection processing stop_ _Details 'Bruker GMBH' save_ save_XEASY _Saveframe_category software _Name XEASY _Version 1.2 loop_ _Task 'data analysis' stop_ _Details ; Bartels C., Xia T., Billeter M., Guentert P. and Wuethrich K. (1995) J. Biomol. NMR, 5, 1-10. ; save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task refinement stop_ _Details ; Guentert P., Mumethaler C.and Wuethrich K. (1997) J. Mol. Biol., 273, 283-298. ; save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 3 loop_ _Task refinement stop_ _Details 'Molecular Simulation Inc. San Diego' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_1 save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_2D_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 TMS H 1 'methyl protons' ppm 0.0 internal direct cylindrical internal parallel 1.0 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_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label TOCSY DQF-COSY '2D NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'DabD (Ace)IWG(DAB)SGKLIDTTA ANALOGUE OF HIV GP41' _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 . 2 ILE H H 7.85 . . 2 . 2 ILE HA H 4.11 . . 3 . 2 ILE HB H 1.63 . . 4 . 2 ILE HG12 H 1.29 . . 5 . 2 ILE HG13 H 1.29 . . 6 . 2 ILE HG2 H 1.02 . . 7 . 2 ILE HD1 H 0.73 . . 8 . 3 TRP H H 8.03 . . 9 . 3 TRP HA H 4.50 . . 10 . 3 TRP HB2 H 2.97 . . 11 . 3 TRP HB3 H 3.12 . . 12 . 3 TRP HD1 H 7.14 . . 13 . 3 TRP HE1 H 10.81 . . 14 . 3 TRP HE3 H 7.54 . . 15 . 3 TRP HZ2 H 6.95 . . 16 . 3 TRP HZ3 H 7.04 . . 17 . 3 TRP HH2 H 7.30 . . 18 . 4 GLY H H 8.19 . . 19 . 4 GLY HA2 H 3.71 . . 20 . 4 GLY HA3 H 3.71 . . 21 . 5 DAB H H 8.06 . . 22 . 5 DAB HA H 4.33 . . 23 . 5 DAB HB2 H 1.62 . . 24 . 5 DAB HB3 H 1.90 . . 25 . 5 DAB HG2 H 3.05 . . 26 . 5 DAB HG3 H 3.05 . . 27 . 5 DAB HD2 H 7.93 . . 28 . 6 SER H H 8.00 . . 29 . 6 SER HA H 4.14 . . 30 . 6 SER HB2 H 3.62 . . 31 . 6 SER HB3 H 3.62 . . 32 . 7 GLY H H 8.52 . . 33 . 7 GLY HA2 H 3.62 . . 34 . 7 GLY HA3 H 3.78 . . 35 . 8 LYS H H 7.69 . . 36 . 8 LYS HA H 4.18 . . 37 . 8 LYS HB2 H 1.53 . . 38 . 8 LYS HB3 H 1.69 . . 39 . 8 LYS HG2 H 1.22 . . 40 . 8 LYS HG3 H 1.22 . . 41 . 8 LYS HD2 H 1.34 . . 42 . 8 LYS HD3 H 1.34 . . 43 . 8 LYS HE2 H 2.78 . . 44 . 8 LYS HE3 H 2.86 . . 45 . 9 LEU H H 8.04 . . 46 . 9 LEU HA H 4.16 . . 47 . 9 LEU HB2 H 1.54 . . 48 . 9 LEU HB3 H 1.54 . . 49 . 9 LEU HG H 1.45 . . 50 . 9 LEU HD1 H 0.81 . . 51 . 9 LEU HD2 H 1.04 . . 52 . 10 ILE H H 7.42 . . 53 . 10 ILE HA H 4.12 . . 54 . 10 ILE HB H 1.69 . . 55 . 10 ILE HG12 H 1.44 . . 56 . 10 ILE HG13 H 1.44 . . 57 . 10 ILE HG2 H 1.02 . . 58 . 10 ILE HD1 H 0.80 . . 59 . 11 ASP H H 8.27 . . 60 . 11 ASP HA H 4.76 . . 61 . 11 ASP HB2 H 2.43 . . 62 . 11 ASP HB3 H 2.55 . . 63 . 12 THR H H 7.58 . . 64 . 12 THR HA H 4.36 . . 65 . 12 THR HB H 4.04 . . 66 . 12 THR HG2 H 1.03 . . 67 . 13 THR H H 7.88 . . 68 . 13 THR HA H 4.16 . . 69 . 13 THR HB H 4.06 . . 70 . 13 THR HG2 H 1.24 . . 71 . 14 ALA H H 7.78 . . 72 . 14 ALA HA H 4.16 . . 73 . 14 ALA HB H 1.03 . . stop_ save_