data_34215 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of an Odin-Sam1 stapled peptide ; _BMRB_accession_number 34215 _BMRB_flat_file_name bmr34215.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 Leone M. . . 2 Mercurio F. A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 91 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 2017-12-22 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 1610.916 _Mol_thiol_state 'not present' _Details "Fragment 745-757 of ANKS1A protein (Uniprot entry Q92625) with R749 and L753 mutated in MK8 (=(S)-2-(4'-pentenyl) alanine )." ############################## # Polymer residue sequence # ############################## _Residue_count 15 _Mol_residue_sequence ; XDPQHXRKLXQAARX ; loop_ _Residue_seq_code _Residue_label 1 ACE 2 ASP 3 PRO 4 GLN 5 HIS 6 MK8 7 ARG 8 LYS 9 LEU 10 MK8 11 GLN 12 ALA 13 ALA 14 ARG 15 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 '930 uM A5ST, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 930 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 7.5 . 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 2.02 0.01 1 2 2 2 ASP H H 8.31 0.01 1 3 2 2 ASP HA H 4.89 0.01 1 4 2 2 ASP HB2 H 2.75 0.01 2 5 2 2 ASP HB3 H 2.67 0.01 2 6 3 3 PRO HA H 4.47 0.01 1 7 3 3 PRO HB2 H 2.40 0.01 2 8 3 3 PRO HB3 H 1.99 0.01 2 9 3 3 PRO HG2 H 2.09 0.01 1 10 3 3 PRO HG3 H 2.09 0.01 1 11 3 3 PRO HD2 H 4.00 0.01 2 12 3 3 PRO HD3 H 3.90 0.01 2 13 4 4 GLN H H 8.44 0.01 1 14 4 4 GLN HA H 4.18 0.01 1 15 4 4 GLN HB2 H 2.12 0.01 1 16 4 4 GLN HB3 H 2.12 0.01 1 17 4 4 GLN HG2 H 2.40 0.01 2 18 4 4 GLN HG3 H 2.34 0.01 2 19 5 5 HIS H H 7.95 0.01 1 20 5 5 HIS HA H 4.36 0.01 1 21 5 5 HIS HB2 H 3.19 0.01 1 22 5 5 HIS HB3 H 3.19 0.01 1 23 5 5 HIS HD1 H 7.05 0.01 1 24 5 5 HIS HE1 H 7.82 0.01 1 25 6 6 MK8 HB H 2.03 0.01 2 26 6 6 MK8 HB1 H 1.43 0.01 1 27 6 6 MK8 HB1A H 1.43 0.01 1 28 6 6 MK8 HB1B H 1.43 0.01 1 29 6 6 MK8 HBA H 1.97 0.01 2 30 6 6 MK8 HD H 1.98 0.01 2 31 6 6 MK8 HDA H 1.74 0.01 2 32 6 6 MK8 HE H 5.46 0.01 1 33 6 6 MK8 HG H 1.15 0.01 1 34 6 6 MK8 HGA H 1.15 0.01 1 35 6 6 MK8 HN H 7.98 0.01 1 36 7 7 ARG H H 8.14 0.01 1 37 7 7 ARG HA H 3.96 0.01 1 38 7 7 ARG HB2 H 1.96 0.01 2 39 7 7 ARG HB3 H 1.92 0.01 2 40 7 7 ARG HG2 H 1.71 0.01 1 41 7 7 ARG HG3 H 1.71 0.01 1 42 7 7 ARG HD2 H 3.23 0.01 1 43 7 7 ARG HD3 H 3.23 0.01 1 44 8 8 LYS H H 7.69 0.01 1 45 8 8 LYS HA H 4.03 0.01 1 46 8 8 LYS HB2 H 1.95 0.01 1 47 8 8 LYS HB3 H 1.95 0.01 1 48 8 8 LYS HG2 H 1.62 0.01 2 49 8 8 LYS HG3 H 1.43 0.01 2 50 8 8 LYS HD2 H 1.72 0.01 1 51 8 8 LYS HD3 H 1.72 0.01 1 52 8 8 LYS HE2 H 3.00 0.01 1 53 8 8 LYS HE3 H 3.00 0.01 1 54 9 9 LEU H H 7.48 0.01 1 55 9 9 LEU HA H 4.08 0.01 1 56 9 9 LEU HB2 H 1.80 0.01 2 57 9 9 LEU HB3 H 1.61 0.01 2 58 9 9 LEU HG H 1.51 0.01 1 59 9 9 LEU HD1 H 0.84 0.01 2 60 9 9 LEU HD2 H 0.82 0.01 2 61 10 10 MK8 HB H 1.99 0.01 2 62 10 10 MK8 HB1 H 1.46 0.01 1 63 10 10 MK8 HB1A H 1.46 0.01 1 64 10 10 MK8 HB1B H 1.46 0.01 1 65 10 10 MK8 HBA H 1.62 0.01 2 66 10 10 MK8 HD H 2.10 0.01 2 67 10 10 MK8 HDA H 1.73 0.01 2 68 10 10 MK8 HE H 5.55 0.01 1 69 10 10 MK8 HG H 1.50 0.01 2 70 10 10 MK8 HGA H 1.38 0.01 2 71 10 10 MK8 HN H 8.40 0.01 1 72 11 11 GLN H H 7.91 0.01 1 73 11 11 GLN HA H 4.04 0.01 1 74 11 11 GLN HB2 H 2.19 0.01 2 75 11 11 GLN HB3 H 2.16 0.01 2 76 11 11 GLN HG2 H 2.56 0.01 2 77 11 11 GLN HG3 H 2.46 0.01 2 78 12 12 ALA H H 7.69 0.01 1 79 12 12 ALA HA H 4.27 0.01 1 80 12 12 ALA HB H 1.54 0.01 1 81 13 13 ALA H H 7.66 0.01 1 82 13 13 ALA HA H 4.32 0.01 1 83 13 13 ALA HB H 1.50 0.01 1 84 14 14 ARG H H 7.84 0.01 1 85 14 14 ARG HA H 4.29 0.01 1 86 14 14 ARG HB2 H 1.97 0.01 2 87 14 14 ARG HB3 H 1.84 0.01 2 88 14 14 ARG HG2 H 1.78 0.01 2 89 14 14 ARG HG3 H 1.72 0.01 2 90 14 14 ARG HD2 H 3.23 0.01 1 91 14 14 ARG HD3 H 3.23 0.01 1 stop_ save_