data_15218 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; 1H and 13C Chemical shifts for the ATWLPPR peptide. ; _BMRB_accession_number 15218 _BMRB_flat_file_name bmr15218.str _Entry_type new _Submission_date 2007-04-19 _Accession_date 2007-04-19 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'NMR chemical shifts and constraint files for the DYANA structure calculations of the ATWLPPR peptide' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 'Herve du Penhoat' Catherine L.M. . 2 Badache Sabah . . 3 Bouchemal Nadia C. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 45 "13C chemical shifts" 27 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-02-20 original author . 2008-02-20 update BMRB . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title ; Structure-function analysis of the antiangiogenic ATWLPPR peptide inhibiting VEGF(165) binding to neuropilin-1 and molecular dynamics simulations of the ATWLPPR/neuropilin-1 complex. ; _Citation_status published _Citation_type journal _PubMed_ID 17983687 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Starzec Anna . . 2 Vassy Roger . . 3 Badache Sabah . . 4 Bouchemal Nadia C. . 5 'Herve du Penhoat' Catherine L.M. . 6 Perret Gerard Y. . stop_ _Journal_abbreviation Peptides _Journal_volume 28 _Journal_issue 12 _Page_first 2397 _Page_last 2402 _Year 2007 loop_ _Keyword 'anti-angiogenic peptide' neuropilin-1 'vascular endothelial growth factor-165' 'binding inhibitor' ATWLPPR stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'ATWLPPR heptapeptide' loop_ _Mol_system_component_name _Mol_label 'subunit 1' $ATWLPPR stop_ _System_physical_state native _System_oligomer_state ? _System_paramagnetic no save_ ######################## # Monomeric polymers # ######################## save_ATWLPPR _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common ATWLPPR _Molecular_mass 843.014 _Mol_thiol_state 'not present' ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence ATWLPPR loop_ _Residue_seq_code _Residue_label 1 ALA 2 THR 3 TRP 4 LEU 5 PRO 6 PRO 7 ARG stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $ATWLPPR . . . . . . 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 $ATWLPPR 'chemical synthesis' . . . . ? stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '10 mM phosphate buffer containing 140 mM NaCl, 5 micromolar EDTA, and 2 micromolar NaN3 at pH 7.0' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $ATWLPPR 6 mM 'natural abundance' 'phosphate buffer' 10 mM 'natural abundance' NaCl 140 mM 'natural abundance' EDTA 5 uM 'natural abundance' NaN3 2 uM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '10 mM phosphate buffer containing 140 mM NaCl, 5 micromolar EDTA, and 2 micromolar NaN3' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $ATWLPPR 6 mM 'natural abundance' 'phosphate buffer' 10 mM 'natural abundance' NaCl 140 mM 'natural abundance' EDTA 5 uM 'natural abundance' NaN3 2 uM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_XEASY _Saveframe_category software _Name XEASY _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'data analysis' stop_ save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Vendor _Address _Electronic_address 'Guntert, Braun and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ save_ save_PROSA _Saveframe_category software _Name PROSA loop_ _Vendor _Address _Electronic_address Guntert . . stop_ loop_ _Task 'data analysis' stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UnityPlus _Field_strength 500 save_ ############################# # NMR applied experiments # ############################# save_2D_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_1D_proton_spectrum_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1D proton spectrum' _Sample_label $sample_1 save_ save_1D_proton_spectrum_8 _Saveframe_category NMR_applied_experiment _Experiment_name '1D proton spectrum' _Sample_label $sample_2 save_ save_1D_proton_spectrum_9 _Saveframe_category NMR_applied_experiment _Experiment_name '1D proton spectrum' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_11 _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 'pH 7.0, 25 degrees C' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 0.140 . M stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details 'pH 7.0, 5 degrees C' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 278 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 0.140 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference 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 DSS H 1 'methyl protons' ppm 0.00 internal direct ? ? ? 1.000000000 DSS C 13 'methyl protons' ppm 0.00 n/a indirect ? ? ? 0.251449530 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 loop_ _Software_label $XEASY stop_ loop_ _Experiment_label '2D DQF-COSY' '2D 1H-1H NOESY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'subunit 1' 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 ALA HA H 4.150 0.005 1 2 1 1 ALA HB H 1.482 0.005 1 3 1 1 ALA CA C 51.0 0.1 1 4 1 1 ALA CB C 18.7 0.1 1 5 2 2 THR HA H 4.352 0.005 1 6 2 2 THR HB H 4.122 0.005 1 7 2 2 THR HG2 H 1.220 0.005 1 8 2 2 THR CG2 C 21.0 0.1 1 9 3 3 TRP H H 8.390 0.005 1 10 3 3 TRP HA H 4.634 0.005 1 11 3 3 TRP HB2 H 3.250 0.005 1 12 3 3 TRP HB3 H 3.250 0.005 1 13 3 3 TRP HD1 H 7.259 0.005 1 14 3 3 TRP HE1 H 10.300 0.005 1 15 3 3 TRP HE3 H 7.580 0.005 1 16 3 3 TRP HZ2 H 7.488 0.005 1 17 3 3 TRP HZ3 H 7.136 0.005 1 18 3 3 TRP HH2 H 7.270 0.005 1 19 3 3 TRP CA C 57.1 0.1 1 20 3 3 TRP CB C 29.2 0.1 1 21 3 3 TRP CD1 C 124.1 0.1 1 22 3 3 TRP CE3 C 120.4 0.1 1 23 3 3 TRP CZ2 C 114.2 0.1 1 24 3 3 TRP CZ3 C 121.6 0.1 1 25 3 3 TRP CH2 C 126.7 0.1 1 26 4 4 LEU H H 7.770 0.005 1 27 4 4 LEU HA H 4.523 0.005 1 28 4 4 LEU HB2 H 1.395 0.005 1 29 4 4 LEU HB3 H 1.395 0.005 1 30 4 4 LEU HG H 1.485 0.005 1 31 4 4 LEU HD1 H 0.855 0.005 1 32 4 4 LEU HD2 H 0.891 0.005 1 33 4 4 LEU CA C 51.3 0.1 1 34 4 4 LEU CB C 42.2 0.1 1 35 4 4 LEU CG C 26.5 0.1 1 36 4 4 LEU CD1 C 23.1 0.1 1 37 4 4 LEU CD2 C 24.7 0.1 1 38 5 5 PRO HA H 4.272 0.005 1 39 5 5 PRO HB2 H 1.859 0.005 1 40 5 5 PRO HB3 H 2.308 0.005 1 41 5 5 PRO HG2 H 1.967 0.005 1 42 5 5 PRO HG3 H 1.967 0.005 1 43 5 5 PRO HD2 H 3.486 0.005 2 44 5 5 PRO HD3 H 3.528 0.005 2 45 5 5 PRO CA C 60.3 0.1 1 46 5 5 PRO CB C 30.4 0.1 1 47 5 5 PRO CG C 26.6 0.1 1 48 5 5 PRO CD C 49.6 0.1 1 49 6 6 PRO HA H 4.370 0.005 1 50 6 6 PRO HB2 H 1.978 0.005 1 51 6 6 PRO HB3 H 2.296 0.005 1 52 6 6 PRO HG2 H 2.078 0.005 1 53 6 6 PRO HG3 H 2.078 0.005 1 54 6 6 PRO HD2 H 3.716 0.005 2 55 6 6 PRO HD3 H 3.782 0.005 2 56 6 6 PRO CA C 61.8 0.1 1 57 6 6 PRO CB C 31.5 0.1 1 58 6 6 PRO CG C 26.3 0.1 1 59 6 6 PRO CD C 50.1 0.1 1 60 7 7 ARG H H 7.900 0.005 1 61 7 7 ARG HA H 4.216 0.005 1 62 7 7 ARG HB2 H 1.741 0.005 2 63 7 7 ARG HB3 H 1.872 0.005 2 64 7 7 ARG HG2 H 1.620 0.005 1 65 7 7 ARG HG3 H 1.620 0.005 1 66 7 7 ARG HD2 H 3.198 0.005 1 67 7 7 ARG HD3 H 3.198 0.005 1 68 7 7 ARG HE H 7.160 0.005 1 69 7 7 ARG CA C 55.9 0.1 1 70 7 7 ARG CB C 30.5 0.1 1 71 7 7 ARG CG C 26.3 0.1 1 72 7 7 ARG CD C 42.9 0.1 1 stop_ save_