data_34470 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of PD-i6 peptide inhibitor of the human PD-1 extracellular domain ; _BMRB_accession_number 34470 _BMRB_flat_file_name bmr34470.str _Entry_type original _Submission_date 2019-12-23 _Accession_date 2019-12-23 _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 Guardiola S. . . 2 Varese M. . . 3 Garcia J. . . 4 Giralt E. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 50 "13C chemical shifts" 34 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2021-01-06 original BMRB . stop_ _Original_release_date 2020-01-10 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution structure of PD-i6 peptide targeting the human PD-1 extracellular domain ; _Citation_status 'in preparation' _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 Guardiola S. . . 2 Varese M. . . 3 Garcia J. . . 4 Giralt E. . . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name TRP-DTR-VAL-DPR-GLU-ALA-DLY-ASP _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 1030.133 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence ; WXVXEAXD ; loop_ _Residue_seq_code _Residue_label 1 TRP 2 DTR 3 VAL 4 DPR 5 GLU 6 ALA 7 DLY 8 ASP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DLY _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-LYSINE _BMRB_code DLY _PDB_code DLY _Standard_residue_derivative . _Molecular_mass 146.188 _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 . ? CG CG C . 0 . ? CD CD C . 0 . ? CE CE C . 0 . ? NZ NZ 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 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE2 HE2 H . 0 . ? HE3 HE3 H . 0 . ? HZ1 HZ1 H . 0 . ? HZ2 HZ2 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 CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD CE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING CE NZ ? ? SING CE HE2 ? ? SING CE HE3 ? ? SING NZ HZ1 ? ? SING NZ HZ2 ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DPR _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-PROLINE _BMRB_code DPR _PDB_code DPR _Standard_residue_derivative . _Molecular_mass 115.130 _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 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 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 CD ? ? SING N H ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD HD2 ? ? SING CD HD3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DTR _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-TRYPTOPHAN _BMRB_code DTR _PDB_code DTR _Standard_residue_derivative . _Molecular_mass 204.225 _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 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? NE1 NE1 N . 0 . ? CE2 CE2 C . 0 . ? CZ2 CZ2 C . 0 . ? CH2 CH2 C . 0 . ? CZ3 CZ3 C . 0 . ? CE3 CE3 C . 0 . ? CD2 CD2 C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? HN2 HN2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HD1 HD1 H . 0 . ? HE1 HE1 H . 0 . ? HZ2 HZ2 H . 0 . ? HH2 HH2 H . 0 . ? HZ3 HZ3 H . 0 . ? HE3 HE3 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 HN2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB CG CD1 ? ? SING CG CD2 ? ? SING CD1 NE1 ? ? SING CD1 HD1 ? ? SING NE1 CE2 ? ? SING NE1 HE1 ? ? DOUB CE2 CZ2 ? ? SING CE2 CD2 ? ? SING CZ2 CH2 ? ? SING CZ2 HZ2 ? ? DOUB CH2 CZ3 ? ? SING CH2 HH2 ? ? SING CZ3 CE3 ? ? SING CZ3 HZ3 ? ? DOUB CE3 CD2 ? ? SING CE3 HE3 ? ? DOUB C O ? ? SING C OXT ? ? 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 $entity_1 . 32630 . . . . 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '25 mM NA potassium phosphate, 100 mM NA sodium chloride, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'potassium phosphate' 25 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TopSpin _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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 'ionic strength' 125 . mM pH 6.4 . pH pressure 1 . atm temperature 278 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 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_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_1 _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 TRP H H 7.71 0.00 1 2 1 1 TRP HA H 4.58 0.00 1 3 1 1 TRP HB2 H 3.06 0.00 . 4 1 1 TRP HD1 H 7.15 0.00 1 5 1 1 TRP HE1 H 10.06 0.00 1 6 1 1 TRP HE3 H 7.62 0.00 1 7 1 1 TRP HZ2 H 7.18 0.00 1 8 1 1 TRP HZ3 H 7.48 0.00 1 9 1 1 TRP HH2 H 7.24 0.00 1 10 1 1 TRP CA C 59.22 0.00 1 11 1 1 TRP CB C 28.97 0.00 1 12 1 1 TRP CD1 C 122.21 0.00 1 13 1 1 TRP CE3 C 121.06 0.00 1 14 1 1 TRP CZ2 C 121.94 0.00 1 15 1 1 TRP CZ3 C 114.73 0.00 1 16 1 1 TRP CH2 C 124.66 0.00 1 17 2 2 DTR H H 7.85 0.00 1 18 2 2 DTR CA C 56.89 0.00 1 19 2 2 DTR CB C 28.97 0.00 1 20 2 2 DTR CD1 C 127.38 0.00 1 21 2 2 DTR CE3 C 120.90 0.00 1 22 2 2 DTR CH2 C 124.66 0.00 1 23 2 2 DTR CZ2 C 121.91 0.00 1 24 2 2 DTR CZ3 C 114.69 0.00 1 25 2 2 DTR HA H 4.60 0.00 1 26 2 2 DTR HB2 H 3.09 0.00 . 27 2 2 DTR HB3 H 3.32 0.00 . 28 2 2 DTR HD1 H 7.09 0.00 1 29 2 2 DTR HE1 H 10.13 0.00 1 30 2 2 DTR HE3 H 7.58 0.00 1 31 2 2 DTR HH2 H 7.24 0.00 1 32 2 2 DTR HZ2 H 7.15 0.00 1 33 2 2 DTR HZ3 H 7.48 0.00 1 34 3 3 VAL H H 7.97 0.00 1 35 3 3 VAL HA H 4.48 0.00 1 36 3 3 VAL HB H 1.93 0.00 1 37 3 3 VAL HG1 H 0.68 0.00 . 38 3 3 VAL HG2 H 0.49 0.00 . 39 3 3 VAL CA C 59.22 0.00 1 40 3 3 VAL CB C 32.18 0.00 1 41 3 3 VAL CG1 C 21.08 0.00 . 42 3 3 VAL CG2 C 19.12 0.00 . 43 4 4 DPR CA C 63.66 0.00 1 44 4 4 DPR CB C 31.68 0.00 1 45 4 4 DPR CD C 50.81 0.00 1 46 4 4 DPR CG C 37.43 0.00 1 47 4 4 DPR HA H 4.34 0.00 1 48 4 4 DPR HB2 H 1.98 0.00 . 49 4 4 DPR HB3 H 2.25 0.00 . 50 4 4 DPR HD2 H 3.65 0.00 . 51 4 4 DPR HD3 H 3.71 0.00 . 52 4 4 DPR HG2 H 1.99 0.00 . 53 4 4 DPR HG3 H 2.04 0.00 . 54 5 5 GLU H H 8.85 0.00 1 55 5 5 GLU HA H 4.22 0.00 1 56 5 5 GLU HB2 H 2.86 0.00 . 57 5 5 GLU HB3 H 2.16 0.00 . 58 5 5 GLU HG2 H 2.23 0.00 . 59 5 5 GLU CA C 56.76 0.00 1 60 5 5 GLU CB C 29.59 0.00 1 61 5 5 GLU CG C 35.98 0.00 1 62 6 6 ALA H H 8.02 0.00 1 63 6 6 ALA HA H 4.27 0.00 1 64 6 6 ALA HB H 1.35 0.00 1 65 6 6 ALA CA C 52.83 0.00 1 66 6 6 ALA CB C 18.88 0.00 1 67 7 7 DLY H H 7.87 0.00 1 68 7 7 DLY CA C 56.90 0.00 1 69 7 7 DLY CB C 32.28 0.00 1 70 7 7 DLY CD C 29.04 0.00 1 71 7 7 DLY CE C 42.05 0.00 1 72 7 7 DLY CG C 24.58 0.00 1 73 7 7 DLY HA H 4.15 0.00 1 74 7 7 DLY HB2 H 1.76 0.00 . 75 7 7 DLY HB3 H 1.80 0.00 . 76 7 7 DLY HD3 H 1.65 0.00 . 77 7 7 DLY HE3 H 2.97 0.00 . 78 7 7 DLY HG3 H 1.37 0.00 . 79 8 8 ASP H H 7.87 0.00 1 80 8 8 ASP HA H 4.43 0.00 1 81 8 8 ASP HB2 H 2.50 0.00 . 82 8 8 ASP HB3 H 2.15 0.00 . 83 8 8 ASP CA C 55.22 0.00 1 84 8 8 ASP CB C 40.16 0.00 1 stop_ save_