data_20020 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of a V3 (LAI isolate) peptide ; _BMRB_accession_number 20020 _BMRB_flat_file_name bmr20020.str _Entry_type new _Submission_date 2008-04-10 _Accession_date 2008-04-10 _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 Galanakis Petros A. . 2 Kandias Nikolaos G. . 3 Rizos Apostolos . . 4 Morikis Dimitrios . . 5 Krambovitis Elias . . 6 Spyroulias Georgios A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 99 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-06-03 update BMRB 'edit assembly name' 2009-04-03 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR evidence of charge-dependent interaction between various PND V3 and CCR5 N-terminal peptides' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19117029 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Galanakis Petros A. . 2 Kandias Nikolaos G. . 3 Rizos Apostolos K. . 4 Morikis Dimitrios . . 5 Krambovitis Elias . . 6 Spyroulias Georgios A. . stop_ _Journal_abbreviation Biopolymers _Journal_volume 92 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 94 _Page_last 109 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name PND_LAI _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label PND_LAI $PND_LAI PND $PND stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_PND_LAI _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common PND_LAI _Molecular_mass 1746.110 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence RKSIRIQRGPGRAFV loop_ _Residue_seq_code _Residue_label 1 ARG 2 LYS 3 SER 4 ILE 5 ARG 6 ILE 7 GLN 8 ARG 9 GLY 10 PRO 11 GLY 12 ARG 13 ALA 14 PHE 15 VAL 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 PDB 1QNZ "Nmr Structure Of The 0.5b Anti-hiv Antibody Complex With The Gp120 V3 Peptide" 100.00 18 100.00 100.00 3.86e+00 DBJ BAA11444 "env, partial [Human immunodeficiency virus 1]" 100.00 35 100.00 100.00 2.10e+00 DBJ BAA11445 "env [Human immunodeficiency virus 1]" 100.00 35 100.00 100.00 2.10e+00 DBJ BAC02630 "envelope glycoprotein [Human immunodeficiency virus 1]" 100.00 253 100.00 100.00 4.64e-01 DBJ BAC02631 "envelope glycoprotein [Human immunodeficiency virus 1]" 100.00 253 100.00 100.00 4.64e-01 DBJ BAC02633 "envelope glycoprotein, partial [Human immunodeficiency virus 1]" 100.00 253 100.00 100.00 4.64e-01 EMBL CAA25903 "unnamed protein product [Human immunodeficiency virus 1]" 100.00 833 100.00 100.00 7.12e-01 GB AAA44205 "envelope polyprotein [Human immunodeficiency virus 1]" 100.00 856 100.00 100.00 7.86e-01 GB AAA44244 "env, partial [Human immunodeficiency virus 1]" 100.00 42 100.00 100.00 1.90e+00 GB AAA44249 "env, partial [Human immunodeficiency virus 1]" 100.00 41 100.00 100.00 1.75e+00 GB AAA44281 "env, partial [Human immunodeficiency virus 1]" 100.00 42 100.00 100.00 1.65e+00 GB AAA44741 "envelope protein, partial [Human immunodeficiency virus 1]" 100.00 36 100.00 100.00 1.92e+00 PRF 1102247A "protein env-lor" 100.00 863 100.00 100.00 7.95e-01 PRF 1103299B "env gene" 100.00 856 100.00 100.00 6.82e-01 PRF 1923361A "gp41 protein" 100.00 746 100.00 100.00 6.65e-01 SP P03375 "RecName: Full=Envelope glycoprotein gp160; AltName: Full=Env polyprotein; Contains: RecName: Full=Surface protein gp120; Short=" 100.00 856 100.00 100.00 7.86e-01 SP P03377 "RecName: Full=Envelope glycoprotein gp160; AltName: Full=Env polyprotein; Contains: RecName: Full=Surface protein gp120; Short=" 100.00 861 100.00 100.00 7.23e-01 SP P19551 "RecName: Full=Envelope glycoprotein gp160; AltName: Full=Env polyprotein; Contains: RecName: Full=Surface protein gp120; Short=" 100.00 853 100.00 100.00 8.01e-01 stop_ save_ ############# # Ligands # ############# save_PND _Saveframe_category ligand _Mol_type non-polymer _Name_common "PND (P-NITROPHENYLHYDRAZINE)" _BMRB_code . _PDB_code PND _Molecular_mass 153.139 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Fri Feb 15 20:30:47 2008 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N N 0 . ? C1 C1 C N 0 . ? N2 N2 N N 0 . ? C2 C2 C N 0 . ? C3 C3 C N 0 . ? C4 C4 C N 0 . ? N4 N4 N N 1 . ? O3 O3 O N -1 . ? O4 O4 O N 0 . ? C5 C5 C N 0 . ? C6 C6 C N 0 . ? HN11 HN11 H N 0 . ? HN12 HN12 H N 0 . ? HN2 HN2 H N 0 . ? H2 H2 H N 0 . ? H3 H3 H N 0 . ? H5 H5 H N 0 . ? H6 H6 H N 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 N1 N2 ? ? SING N1 HN11 ? ? SING N1 HN12 ? ? SING C1 N2 ? ? DOUB C1 C2 ? ? SING C1 C6 ? ? SING N2 HN2 ? ? SING C2 C3 ? ? SING C2 H2 ? ? DOUB C3 C4 ? ? SING C3 H3 ? ? SING C4 N4 ? ? SING C4 C5 ? ? SING N4 O3 ? ? DOUB N4 O4 ? ? DOUB C5 C6 ? ? SING C5 H5 ? ? SING C6 H6 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $PND_LAI . . . . . . 'HUMAN IMMUNODEFICIENCY VIRUS TYPE 1' 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 $PND_LAI 'recombinant technology' . . . . . 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $PND_LAI . mM 2 2.5 'natural abundance' $PND . mM 2 2.5 'natural abundance' D2O 10 % . . . H2O 90 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 5.0 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_DYANA _Saveframe_category software _Name DYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_XEASY _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 278 . K pH 7.85 . pH stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 286 . K pH 7.85 . pH stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _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 water H 1 protons ppm 5.05 internal indirect . . . 1 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $XEASY stop_ loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name PND_LAI _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 1 ARG HA H 4.077 0.003 1 2 1 1 ARG HB2 H 1.960 0.003 1 3 1 1 ARG HB3 H 1.960 0.003 1 4 1 1 ARG HD2 H 3.279 0.003 1 5 1 1 ARG HD3 H 3.279 0.003 1 6 1 1 ARG HG2 H 1.699 0.003 1 7 1 1 ARG HG3 H 1.699 0.003 1 8 2 2 LYS HA H 4.447 0.001 1 9 2 2 LYS HB2 H 1.909 0.003 2 10 2 2 LYS HB3 H 1.822 0.003 2 11 2 2 LYS HD2 H 1.749 0.003 1 12 2 2 LYS HD3 H 1.749 0.003 1 13 2 2 LYS HE2 H 3.058 0.003 1 14 2 2 LYS HE3 H 3.058 0.003 1 15 2 2 LYS HG2 H 1.503 0.003 1 16 2 2 LYS HG3 H 1.503 0.003 1 17 3 3 SER H H 8.720 0.003 1 18 3 3 SER HA H 4.530 0.003 1 19 3 3 SER HB2 H 3.898 0.001 1 20 3 3 SER HB3 H 3.898 0.001 1 21 4 4 ILE H H 8.481 0.002 1 22 4 4 ILE HA H 4.259 0.003 1 23 4 4 ILE HB H 1.919 0.003 1 24 4 4 ILE HD1 H 0.918 0.003 1 25 4 4 ILE HG12 H 1.505 0.001 2 26 4 4 ILE HG13 H 1.247 0.003 2 27 4 4 ILE HG2 H 0.957 0.003 1 28 5 5 ARG H H 8.584 0.003 1 29 5 5 ARG HA H 4.419 0.003 1 30 5 5 ARG HB2 H 1.841 0.003 2 31 5 5 ARG HB3 H 1.789 0.003 2 32 5 5 ARG HD2 H 3.231 0.003 1 33 5 5 ARG HD3 H 3.231 0.003 1 34 5 5 ARG HE H 7.307 0.003 1 35 5 5 ARG HG2 H 1.675 0.003 2 36 5 5 ARG HG3 H 1.598 0.003 2 37 6 6 ILE H H 8.504 0.002 1 38 6 6 ILE HA H 4.185 0.003 1 39 6 6 ILE HB H 1.874 0.003 1 40 6 6 ILE HD1 H 0.903 0.003 1 41 6 6 ILE HG12 H 1.537 0.003 2 42 6 6 ILE HG13 H 1.244 0.001 2 43 6 6 ILE HG2 H 0.930 0.003 1 44 7 7 GLN H H 8.721 0.001 1 45 7 7 GLN HA H 4.413 0.003 1 46 7 7 GLN HB2 H 2.116 0.002 2 47 7 7 GLN HB3 H 2.014 0.001 2 48 7 7 GLN HE21 H 7.026 0.003 2 49 7 7 GLN HE22 H 7.699 0.001 2 50 7 7 GLN HG2 H 2.389 0.003 1 51 7 7 GLN HG3 H 2.389 0.003 1 52 8 8 ARG H H 8.685 0.003 1 53 8 8 ARG HA H 4.447 0.003 1 54 8 8 ARG HB2 H 1.913 0.003 2 55 8 8 ARG HB3 H 1.805 0.003 2 56 8 8 ARG HD2 H 3.224 0.003 1 57 8 8 ARG HD3 H 3.224 0.003 1 58 8 8 ARG HE H 7.307 0.002 1 59 8 8 ARG HG2 H 1.678 0.003 1 60 8 8 ARG HG3 H 1.678 0.003 1 61 9 9 GLY H H 8.509 0.003 1 62 9 9 GLY HA2 H 4.188 0.002 2 63 9 9 GLY HA3 H 4.126 0.001 2 64 10 10 PRO HA H 4.498 0.003 1 65 10 10 PRO HB2 H 2.333 0.003 2 66 10 10 PRO HB3 H 2.082 0.003 2 67 10 10 PRO HD2 H 3.683 0.003 1 68 10 10 PRO HD3 H 3.683 0.003 1 69 10 10 PRO HG2 H 2.033 0.003 1 70 10 10 PRO HG3 H 2.033 0.003 1 71 11 11 GLY H H 8.709 0.003 1 72 11 11 GLY HA2 H 3.992 0.001 1 73 11 11 GLY HA3 H 3.992 0.001 1 74 12 12 ARG H H 8.257 0.003 1 75 12 12 ARG HA H 4.350 0.003 1 76 12 12 ARG HB2 H 1.839 0.002 2 77 12 12 ARG HB3 H 1.752 0.003 2 78 12 12 ARG HD2 H 3.194 0.001 1 79 12 12 ARG HD3 H 3.194 0.001 1 80 12 12 ARG HE H 7.255 0.003 1 81 12 12 ARG HG2 H 1.596 0.001 1 82 12 12 ARG HG3 H 1.596 0.001 1 83 13 13 ALA H H 8.478 0.001 1 84 13 13 ALA HA H 4.323 0.002 1 85 13 13 ALA HB H 1.349 0.003 1 86 14 14 PHE H H 8.357 0.003 1 87 14 14 PHE HA H 4.708 0.003 1 88 14 14 PHE HB2 H 3.223 0.003 2 89 14 14 PHE HB3 H 3.056 0.003 2 90 14 14 PHE HD1 H 7.305 0.003 1 91 14 14 PHE HD2 H 7.305 0.003 1 92 14 14 PHE HE1 H 7.391 0.003 1 93 14 14 PHE HE2 H 7.391 0.003 1 94 14 14 PHE HZ H 7.346 0.003 1 95 15 15 VAL H H 7.787 0.003 1 96 15 15 VAL HA H 4.050 0.003 1 97 15 15 VAL HB H 2.093 0.003 1 98 15 15 VAL HG1 H 0.940 0.003 1 99 15 15 VAL HG2 H 0.940 0.003 1 stop_ save_ save_constraint_statistics _Saveframe_category constraint_statistics _Text_data_format . _Text_data . _NOE_interproton_distance_evaluation . _NOE_pseudoatom_corrections . _Details . save_