data_34213 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of EphA2-Sam stapled peptides (S13ST) ; _BMRB_accession_number 34213 _BMRB_flat_file_name bmr34213.str _Entry_type original _Submission_date 2017-12-11 _Accession_date 2017-12-11 _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 Mercurio F. A. . 2 Leone M. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 174 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-08-14 update BMRB 'update entry citation' 2018-07-26 original author 'original release' stop_ _Original_release_date 2018-07-23 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Sam domain-based stapled peptides: Structural analysis and interaction studies with the Sam domains from the EphA2 receptor and the lipid phosphatase Ship2 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30036816 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mercurio F. A. . 2 Pirone L. . . 3 'Di Natale' C. . . 4 Marasco D. . . 5 Pedone E. M. . 6 Leone M. . . stop_ _Journal_abbreviation 'Bioorg. Chem.' _Journal_volume 80 _Journal_issue . _Journal_ASTM BOCMBM _Journal_ISSN 0045-2068 _Journal_CSD 0368 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 602 _Page_last 610 _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Ephrin type-A receptor 2 (E.C.2.7.10.1)' _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 2905.534 _Mol_thiol_state 'not present' _Details ; Fragment 945-969 of Human EphA2 receptor (Uniprot entry P29317) with I958 and L962 mutated in MK8 (=(S)-2-(4'-pentenyl) alanine). ; ############################## # Polymer residue sequence # ############################## _Residue_count 27 _Mol_residue_sequence ; XKRIGVRLPGHQKRXAYSXL GLKDQVX ; loop_ _Residue_seq_code _Residue_label 1 ACE 2 LYS 3 ARG 4 ILE 5 GLY 6 VAL 7 ARG 8 LEU 9 PRO 10 GLY 11 HIS 12 GLN 13 LYS 14 ARG 15 MK8 16 ALA 17 TYR 18 SER 19 MK8 20 LEU 21 GLY 22 LEU 23 LYS 24 ASP 25 GLN 26 VAL 27 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_MK8 _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common 2-methyl-L-norleucine _BMRB_code MK8 _PDB_code MK8 _Standard_residue_derivative . _Molecular_mass 145.199 _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 . ? N N N . 0 . ? O O O . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CD CD C . 0 . ? CE CE C . 0 . ? CG CG C . 0 . ? CB1 CB1 C . 0 . ? OXT OXT O . 0 . ? HN HN H . 0 . ? HNA HNA H . 0 . ? HB HB H . 0 . ? HBA HBA H . 0 . ? HD HD H . 0 . ? HDA HDA H . 0 . ? HE HE H . 0 . ? HEA HEA H . 0 . ? HEB HEB H . 0 . ? HG HG H . 0 . ? HGA HGA H . 0 . ? HB1 HB1 H . 0 . ? HB1A HB1A H . 0 . ? HB1B HB1B 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 C CA ? ? SING C OXT ? ? SING N HN ? ? SING N HNA ? ? DOUB O C ? ? SING CA N ? ? SING CA CB ? ? SING CB HB ? ? SING CB HBA ? ? SING CD CG ? ? SING CD HD ? ? SING CD HDA ? ? SING CE CD ? ? SING CE HE ? ? SING CE HEA ? ? SING CE HEB ? ? SING CG CB ? ? SING CG HG ? ? SING CG HGA ? ? SING CB1 CA ? ? SING CB1 HB1 ? ? SING CB1 HB1A ? ? SING CB1 HB1B ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _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 . ? HN1 HN1 H . 0 . ? HN2 HN2 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 HN1 ? ? SING N HN2 ? ? stop_ save_ 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_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_1 Human 9606 Eukaryota Metazoa Homo sapiens 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 '650 uM S13ST, trifluoroethanol/water' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 650 uM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name VNMRJ _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Bartels et al.' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_4 _Saveframe_category software _Name Chimera _Version 1.10.1 loop_ _Vendor _Address _Electronic_address 'Pettersen et al.' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details 'Cold probe' 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_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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 pH 7.1 . pH pressure 1 . atm temperature 298 . 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 TSP 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 TOCSY' '2D 1H-1H NOESY' '2D DQF-COSY' 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 ACE H1 H 2.06 0.01 1 2 2 2 LYS H H 8.14 0.01 1 3 2 2 LYS HA H 4.27 0.01 1 4 2 2 LYS HB2 H 1.81 0.01 2 5 2 2 LYS HB3 H 1.76 0.01 2 6 2 2 LYS HG2 H 1.49 0.01 2 7 2 2 LYS HG3 H 1.45 0.01 2 8 2 2 LYS HD2 H 1.72 0.01 1 9 2 2 LYS HD3 H 1.72 0.01 1 10 2 2 LYS HE2 H 3.01 0.01 1 11 2 2 LYS HE3 H 3.01 0.01 1 12 3 3 ARG H H 8.20 0.01 1 13 3 3 ARG HA H 4.43 0.01 1 14 3 3 ARG HB2 H 1.82 0.01 2 15 3 3 ARG HB3 H 1.75 0.01 2 16 3 3 ARG HG2 H 1.61 0.01 2 17 3 3 ARG HG3 H 1.56 0.01 2 18 3 3 ARG HD2 H 3.18 0.01 1 19 3 3 ARG HD3 H 3.18 0.01 1 20 4 4 ILE H H 8.00 0.01 1 21 4 4 ILE HA H 4.20 0.01 1 22 4 4 ILE HB H 1.90 0.01 1 23 4 4 ILE HG12 H 1.52 0.01 2 24 4 4 ILE HG13 H 1.22 0.01 2 25 4 4 ILE HG2 H 0.94 0.01 1 26 4 4 ILE HD1 H 0.89 0.01 1 27 5 5 GLY H H 7.85 0.01 1 28 5 5 GLY HA2 H 3.99 0.01 2 29 5 5 GLY HA3 H 3.93 0.01 2 30 6 6 VAL H H 7.69 0.01 1 31 6 6 VAL HA H 4.12 0.01 1 32 6 6 VAL HB H 2.07 0.01 1 33 6 6 VAL HG1 H 0.93 0.01 2 34 6 6 VAL HG2 H 0.93 0.01 2 35 7 7 ARG H H 8.20 0.01 1 36 7 7 ARG HA H 4.41 0.01 1 37 7 7 ARG HB2 H 1.85 0.01 1 38 7 7 ARG HB3 H 1.85 0.01 1 39 7 7 ARG HG2 H 1.64 0.01 2 40 7 7 ARG HG3 H 1.59 0.01 2 41 7 7 ARG HD2 H 3.22 0.01 1 42 7 7 ARG HD3 H 3.22 0.01 1 43 8 8 LEU H H 8.08 0.01 1 44 8 8 LEU HA H 4.66 0.01 1 45 8 8 LEU HB2 H 1.56 0.01 2 46 8 8 LEU HB3 H 1.52 0.01 2 47 8 8 LEU HG H 1.65 0.01 1 48 8 8 LEU HD1 H 0.90 0.01 1 49 8 8 LEU HD2 H 0.90 0.01 1 50 9 9 PRO HA H 4.47 0.01 1 51 9 9 PRO HB2 H 2.35 0.01 2 52 9 9 PRO HB3 H 1.92 0.01 2 53 9 9 PRO HG2 H 2.06 0.01 1 54 9 9 PRO HG3 H 2.06 0.01 1 55 9 9 PRO HD2 H 3.85 0.01 2 56 9 9 PRO HD3 H 3.65 0.01 2 57 10 10 GLY H H 8.31 0.01 1 58 10 10 GLY HA2 H 3.96 0.01 1 59 10 10 GLY HA3 H 3.96 0.01 1 60 11 11 HIS H H 8.07 0.01 1 61 11 11 HIS HA H 4.47 0.01 1 62 11 11 HIS HB2 H 3.20 0.01 1 63 11 11 HIS HB3 H 3.20 0.01 1 64 11 11 HIS HD1 H 7.00 0.01 1 65 11 11 HIS HE1 H 7.73 0.01 1 66 12 12 GLN H H 8.20 0.01 1 67 12 12 GLN HA H 4.16 0.01 1 68 12 12 GLN HB2 H 2.12 0.01 2 69 12 12 GLN HB3 H 2.02 0.01 2 70 12 12 GLN HG2 H 2.33 0.01 1 71 12 12 GLN HG3 H 2.33 0.01 1 72 12 12 GLN HE21 H 7.29 0.01 2 73 12 12 GLN HE22 H 6.71 0.01 2 74 13 13 LYS H H 7.98 0.01 1 75 13 13 LYS HA H 4.09 0.01 1 76 13 13 LYS HB2 H 1.87 0.01 1 77 13 13 LYS HB3 H 1.87 0.01 1 78 13 13 LYS HG2 H 1.50 0.01 2 79 13 13 LYS HG3 H 1.40 0.01 2 80 13 13 LYS HD2 H 1.72 0.01 1 81 13 13 LYS HD3 H 1.72 0.01 1 82 13 13 LYS HE2 H 3.00 0.01 1 83 13 13 LYS HE3 H 3.00 0.01 1 84 14 14 ARG H H 7.82 0.01 1 85 14 14 ARG HA H 4.09 0.01 1 86 14 14 ARG HB2 H 1.93 0.01 2 87 14 14 ARG HB3 H 1.86 0.01 2 88 14 14 ARG HG2 H 1.62 0.01 1 89 14 14 ARG HG3 H 1.62 0.01 1 90 14 14 ARG HD2 H 3.20 0.01 1 91 14 14 ARG HD3 H 3.20 0.01 1 92 15 15 MK8 HB H 2.03 0.01 2 93 15 15 MK8 HB1 H 1.52 0.01 1 94 15 15 MK8 HB1A H 1.52 0.01 1 95 15 15 MK8 HB1B H 1.52 0.01 1 96 15 15 MK8 HBA H 2.01 0.01 2 97 15 15 MK8 HD H 2.01 0.01 2 98 15 15 MK8 HDA H 1.67 0.01 2 99 15 15 MK8 HE H 5.44 0.01 1 100 15 15 MK8 HG H 1.18 0.01 1 101 15 15 MK8 HGA H 1.18 0.01 1 102 15 15 MK8 HN H 8.03 0.01 1 103 16 16 ALA H H 8.21 0.01 1 104 16 16 ALA HA H 4.02 0.01 1 105 16 16 ALA HB H 1.46 0.01 1 106 17 17 TYR H H 7.86 0.01 1 107 17 17 TYR HA H 4.19 0.01 1 108 17 17 TYR HB2 H 3.19 0.01 1 109 17 17 TYR HB3 H 3.19 0.01 1 110 17 17 TYR HD1 H 7.16 0.01 3 111 17 17 TYR HD2 H 7.14 0.01 3 112 17 17 TYR HE1 H 6.80 0.01 3 113 17 17 TYR HE2 H 6.79 0.01 3 114 18 18 SER H H 7.60 0.01 1 115 18 18 SER HA H 4.36 0.01 1 116 18 18 SER HB2 H 4.13 0.01 2 117 18 18 SER HB3 H 4.01 0.01 2 118 19 19 MK8 HB H 2.09 0.01 2 119 19 19 MK8 HB1 H 1.45 0.01 1 120 19 19 MK8 HB1A H 1.45 0.01 1 121 19 19 MK8 HB1B H 1.45 0.01 1 122 19 19 MK8 HBA H 2.05 0.01 2 123 19 19 MK8 HD H 2.03 0.01 2 124 19 19 MK8 HDA H 1.69 0.01 2 125 19 19 MK8 HE H 5.40 0.01 1 126 19 19 MK8 HG H 1.56 0.01 2 127 19 19 MK8 HGA H 1.37 0.01 2 128 19 19 MK8 HN H 8.37 0.01 1 129 20 20 LEU H H 8.21 0.01 1 130 20 20 LEU HA H 4.20 0.01 1 131 20 20 LEU HB2 H 1.86 0.01 2 132 20 20 LEU HB3 H 1.59 0.01 2 133 20 20 LEU HG H 1.83 0.01 1 134 20 20 LEU HD1 H 0.87 0.01 1 135 20 20 LEU HD2 H 0.87 0.01 1 136 21 21 GLY H H 7.85 0.01 1 137 21 21 GLY HA2 H 3.98 0.01 1 138 21 21 GLY HA3 H 3.98 0.01 1 139 22 22 LEU H H 7.78 0.01 1 140 22 22 LEU HA H 4.30 0.01 1 141 22 22 LEU HB2 H 1.61 0.01 1 142 22 22 LEU HB3 H 1.61 0.01 1 143 22 22 LEU HG H 1.62 0.01 1 144 22 22 LEU HD1 H 0.82 0.01 1 145 22 22 LEU HD2 H 0.82 0.01 1 146 23 23 LYS H H 7.96 0.01 1 147 23 23 LYS HA H 4.21 0.01 1 148 23 23 LYS HB2 H 1.86 0.01 1 149 23 23 LYS HB3 H 1.86 0.01 1 150 23 23 LYS HG2 H 1.49 0.01 2 151 23 23 LYS HG3 H 1.45 0.01 2 152 23 23 LYS HD2 H 1.71 0.01 1 153 23 23 LYS HD3 H 1.71 0.01 1 154 23 23 LYS HE2 H 3.02 0.01 1 155 23 23 LYS HE3 H 3.02 0.01 1 156 24 24 ASP H H 8.15 0.01 1 157 24 24 ASP HA H 4.63 0.01 1 158 24 24 ASP HB2 H 2.75 0.01 2 159 24 24 ASP HB3 H 2.68 0.01 2 160 25 25 GLN H H 8.07 0.01 1 161 25 25 GLN HA H 4.35 0.01 1 162 25 25 GLN HB2 H 2.20 0.01 2 163 25 25 GLN HB3 H 2.06 0.01 2 164 25 25 GLN HG2 H 2.39 0.01 1 165 25 25 GLN HG3 H 2.39 0.01 1 166 25 25 GLN HE21 H 7.48 0.01 2 167 25 25 GLN HE22 H 6.70 0.01 2 168 26 26 VAL H H 7.91 0.01 1 169 26 26 VAL HA H 4.10 0.01 1 170 26 26 VAL HB H 2.13 0.01 1 171 26 26 VAL HG1 H 0.98 0.01 1 172 26 26 VAL HG2 H 0.98 0.01 1 173 27 27 NH2 HN1 H 7.47 0.01 2 174 27 27 NH2 HN2 H 6.98 0.01 2 stop_ save_