data_36166 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of H-RasT35S mutant protein in complex with KBFM123 ; _BMRB_accession_number 36166 _BMRB_flat_file_name bmr36166.str _Entry_type original _Submission_date 2018-02-15 _Accession_date 2018-10-01 _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 Matsumoto S. . . 2 Hayashi Y. . . 3 Hiraga T. . . 4 Matsuo K. . . 5 Kataoka T. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 15 "13C chemical shifts" 5 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-12-07 original BMRB . stop_ _Original_release_date 2018-10-01 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Molecular Basis for Allosteric Inhibition of GTP-Bound H-Ras Protein by a Small-Molecule Compound Carrying a Naphthalene Ring ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 30141910 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Matsumoto S. . . 2 Hiraga T. . . 3 Hayashi Y. . . 4 Yoshikawa Y. . . 5 Tsuda C. . . 6 Araki M. . . 7 Neya M. . . 8 Shima F. . . 9 Kataoka T. . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full Biochemistry _Journal_volume 57 _Journal_issue 36 _Journal_ASTM BICHAW _Journal_ISSN 1520-4995 _Journal_CSD 0033 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2018 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'GTPase HRas' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 entity_GNP $entity_GNP entity_KBF $entity_KBF entity_MG $entity_MG 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 'GTPase HRas' _Molecular_mass 18861.166 _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 166 _Mol_residue_sequence ; MTEYKLVVVGAGGVGKSALT IQLIQNHFVDEYDPSIEDSY RKQVVIDGETCLLDILDTAG QEEYSAMRDQYMRTGEGFLC VFAINNTKSFEDIHQYREQI KRVKDSDDVPMVLVGNKCDL AARTVESRQAQDLARSYGIP YIETSAKTRQGVEDAFYTLV REIRQH ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 MET 2 2 THR 3 3 GLU 4 4 TYR 5 5 LYS 6 6 LEU 7 7 VAL 8 8 VAL 9 9 VAL 10 10 GLY 11 11 ALA 12 12 GLY 13 13 GLY 14 14 VAL 15 15 GLY 16 16 LYS 17 17 SER 18 18 ALA 19 19 LEU 20 20 THR 21 21 ILE 22 22 GLN 23 23 LEU 24 24 ILE 25 25 GLN 26 26 ASN 27 27 HIS 28 28 PHE 29 29 VAL 30 30 ASP 31 31 GLU 32 32 TYR 33 33 ASP 34 34 PRO 35 35 SER 36 36 ILE 37 37 GLU 38 38 ASP 39 39 SER 40 40 TYR 41 41 ARG 42 42 LYS 43 43 GLN 44 44 VAL 45 45 VAL 46 46 ILE 47 47 ASP 48 48 GLY 49 49 GLU 50 50 THR 51 51 CYS 52 52 LEU 53 53 LEU 54 54 ASP 55 55 ILE 56 56 LEU 57 57 ASP 58 58 THR 59 59 ALA 60 60 GLY 61 61 GLN 62 62 GLU 63 63 GLU 64 64 TYR 65 65 SER 66 66 ALA 67 67 MET 68 68 ARG 69 69 ASP 70 70 GLN 71 71 TYR 72 72 MET 73 73 ARG 74 74 THR 75 75 GLY 76 76 GLU 77 77 GLY 78 78 PHE 79 79 LEU 80 80 CYS 81 81 VAL 82 82 PHE 83 83 ALA 84 84 ILE 85 85 ASN 86 86 ASN 87 87 THR 88 88 LYS 89 89 SER 90 90 PHE 91 91 GLU 92 92 ASP 93 93 ILE 94 94 HIS 95 95 GLN 96 96 TYR 97 97 ARG 98 98 GLU 99 99 GLN 100 100 ILE 101 101 LYS 102 102 ARG 103 103 VAL 104 104 LYS 105 105 ASP 106 106 SER 107 107 ASP 108 108 ASP 109 109 VAL 110 110 PRO 111 111 MET 112 112 VAL 113 113 LEU 114 114 VAL 115 115 GLY 116 116 ASN 117 117 LYS 118 118 CYS 119 119 ASP 120 120 LEU 121 121 ALA 122 122 ALA 123 123 ARG 124 124 THR 125 125 VAL 126 126 GLU 127 127 SER 128 128 ARG 129 129 GLN 130 130 ALA 131 131 GLN 132 132 ASP 133 133 LEU 134 134 ALA 135 135 ARG 136 136 SER 137 137 TYR 138 138 GLY 139 139 ILE 140 140 PRO 141 141 TYR 142 142 ILE 143 143 GLU 144 144 THR 145 145 SER 146 146 ALA 147 147 LYS 148 148 THR 149 149 ARG 150 150 GLN 151 151 GLY 152 152 VAL 153 153 GLU 154 154 ASP 155 155 ALA 156 156 PHE 157 157 TYR 158 158 THR 159 159 LEU 160 160 VAL 161 161 ARG 162 162 GLU 163 163 ILE 164 164 ARG 165 165 GLN 166 166 HIS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_GNP _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _BMRB_code GNP _PDB_code GNP _Molecular_mass 522.196 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons PG PG P . 0 . ? O1G O1G O . 0 . ? O2G O2G O . 0 . ? O3G O3G O . 0 . ? N3B N3B N . 0 . ? PB PB P . 0 . ? O1B O1B O . 0 . ? O2B O2B O . 0 . ? O3A O3A O . 0 . ? PA PA P . 0 . ? O1A O1A O . 0 . ? O2A O2A O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? HOG2 HOG2 H . 0 . ? HOG3 HOG3 H . 0 . ? HNB3 HNB3 H . 0 . ? HOB2 HOB2 H . 0 . ? HOA2 HOA2 H . 0 . ? H5'2 H5'2 H . 0 . ? H5'1 H5'1 H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? HO2' HO2' H . 0 . ? H1' H1' H . 0 . ? H8 H8 H . 0 . ? HN1 HN1 H . 0 . ? HN21 HN21 H . 0 . ? HN22 HN22 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 PG O1G ? ? SING PG O2G ? ? SING PG O3G ? ? SING PG N3B ? ? SING O2G HOG2 ? ? SING O3G HOG3 ? ? SING N3B PB ? ? SING N3B HNB3 ? ? DOUB PB O1B ? ? SING PB O2B ? ? SING PB O3A ? ? SING O2B HOB2 ? ? SING O3A PA ? ? DOUB PA O1A ? ? SING PA O2A ? ? SING PA O5' ? ? SING O2A HOA2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5'2 ? ? SING C5' H5'1 ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' O2' ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING O2' HO2' ? ? SING C1' N9 ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C5 C4 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING N1 C2 ? ? SING N1 HN1 ? ? SING C2 N2 ? ? DOUB C2 N3 ? ? SING N2 HN21 ? ? SING N2 HN22 ? ? SING N3 C4 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ save_KBF _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "3-oxidanyl-~{N}-[[(2~{S})-oxolan-2-yl]methyl]naphthalene-2-carboxamide (3-oxidanyl-~{N}-[[(2~{R})-oxolan-2-yl]methyl]naphthalene-2-carboxamide)" _BMRB_code KBF _PDB_code KBF _Molecular_mass 271.311 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? C9 C9 C . 0 . ? C10 C10 C . 0 . ? C1 C1 C . 0 . ? O1 O1 O . 0 . ? C2 C2 C . 0 . ? C11 C11 C . 0 . ? N N N . 0 . ? C12 C12 C . 0 . ? O2 O2 O . 0 . ? C15 C15 C . 0 . ? C14 C14 C . 0 . ? C13 C13 C . 0 . ? O3 O3 O . 0 . ? C16 C16 C . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H22 H22 H . 0 . ? H1 H1 H . 0 . ? H21 H21 H . 0 . ? H8 H8 H . 0 . ? H7 H7 H . 0 . ? H12 H12 H . 0 . ? H13 H13 H . 0 . ? H10 H10 H . 0 . ? H11 H11 H . 0 . ? H9 H9 H . 0 . ? H15 H15 H . 0 . ? H14 H14 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 C4 C5 ? ? SING C4 C3 ? ? SING C15 C16 ? ? SING C15 C14 ? ? SING C5 C6 ? ? DOUB C2 C3 ? ? SING C2 C1 ? ? SING C3 C8 ? ? SING O1 C1 ? ? SING C16 O3 ? ? DOUB C1 C10 ? ? SING C14 C13 ? ? DOUB C6 C7 ? ? SING C8 C7 ? ? DOUB C8 C9 ? ? SING C10 C9 ? ? SING C10 C11 ? ? SING O3 C13 ? ? SING C13 C12 ? ? SING N C11 ? ? SING N C12 ? ? DOUB C11 O2 ? ? SING C4 H2 ? ? SING C5 H3 ? ? SING C6 H4 ? ? SING C7 H5 ? ? SING C9 H6 ? ? SING O1 H22 ? ? SING C2 H1 ? ? SING N H21 ? ? SING C12 H8 ? ? SING C12 H7 ? ? SING C15 H12 ? ? SING C15 H13 ? ? SING C14 H10 ? ? SING C14 H11 ? ? SING C13 H9 ? ? SING C16 H15 ? ? SING C16 H14 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ save_MG _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 'MAGNESIUM ION' _BMRB_code MG _PDB_code MG _Molecular_mass 24.305 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons MG MG MG . 2 . ? 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 _Gene_mnemonic $entity_1 Human 9606 Eukaryota Metazoa Homo sapiens 'HRAS, HRAS1' 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 'recombinant technology' . Escherichia coli . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 0.8 mM [U-99% 13C; U-99% 15N] H-RasT35S, 3.0 mM KBFM123, 20 mM sodium phosphate, 40 mM sodium chloride, 8 mM MAGNESIUM ION, 0.8 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, 80% D2O/20% d6-DMSO ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.8 mM '[U-99% 13C; U-99% 15N]' $entity_KBF 3.0 mM 'natural abundance' $entity_MG 8 mM 'natural abundance' $entity_GNP 0.8 mM 'natural abundance' 'sodium chloride' 40 mM 'natural abundance' 'sodium phosphate' 20 mM 'natural abundance' D2O 80 % [U-2H] d6-DMSO 20 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'BRUNGER A. T. ET.AL.' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 600 _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_3D_1H-13C_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _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' 50 . mM pH 6.8 . 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 TSP C 13 'methyl protons' ppm 0 external indirect . . . 0.251449530 TSP H 1 'methyl protons' ppm 0 external direct . . . 1 TSP N 15 'methyl protons' ppm 0 external indirect . . . 0.101329118 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '3D 1H-13C NOESY' '2D 1H-13C HSQC aliphatic' 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 5 5 LYS HE2 H 2.728 0.030 2 2 5 5 LYS HE3 H 2.728 0.030 2 3 5 5 LYS CE C 41.651 0.000 1 4 7 7 VAL HG2 H 0.998 0.010 2 5 7 7 VAL CG2 C 22.315 0.000 1 6 56 56 LEU HD2 H 0.543 0.010 2 7 56 56 LEU CD2 C 24.120 0.000 1 8 67 67 MET HE H 2.026 0.002 1 9 67 67 MET CE C 17.159 0.000 1 10 74 74 THR HG2 H 1.209 0.006 1 11 74 74 THR CG2 C 55.057 0.000 1 stop_ save_ save_assigned_chemical_shifts_1_3 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '3D 1H-13C NOESY' '2D 1H-13C HSQC aliphatic' 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_KBF _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 1 202 1 KBF H1 H 7.330 0.000 1 2 202 1 KBF H2 H 7.757 0.000 1 3 202 1 KBF H3 H 7.553 0.000 1 4 202 1 KBF H4 H 7.397 0.000 1 5 202 1 KBF H5 H 7.923 0.000 1 6 202 1 KBF H6 H 8.403 0.000 1 7 202 1 KBF H11 H 1.670 0.000 1 8 202 1 KBF H12 H 1.974 0.000 2 9 202 1 KBF H13 H 1.974 0.000 2 stop_ save_