data_3H0V # _model_server_result.job_id Ru7vr_NG8ZW4XoiGRXyzEg _model_server_result.datetime_utc '2024-11-25 14:57:14' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 3h0v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":368}' # _entry.id 3H0V # _exptl.entry_id 3H0V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 313.376 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-deoxy-5'-(dimethyl-lambda~4~-sulfanyl)adenosine" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.03 _cell.angle_gamma 90 _cell.entry_id 3H0V _cell.length_a 93.852 _cell.length_b 49.535 _cell.length_c 69.998 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3H0V _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id E _struct_conn.ptnr1_label_atom_id C _struct_conn.ptnr1_label_comp_id PYR _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id PYR _struct_conn.ptnr1_auth_seq_id 68 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id SER _struct_conn.ptnr2_label_seq_id 1 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id SER _struct_conn.ptnr2_auth_seq_id 69 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.528 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C12 H19 N5 O3 S' _chem_comp.formula_weight 313.376 _chem_comp.id M2T _chem_comp.mon_nstd_flag . _chem_comp.name "5'-deoxy-5'-(dimethyl-lambda~4~-sulfanyl)adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag SD CG M2T sing 218 n n CG HG M2T sing 219 n n CG HGA M2T sing 220 n n CG HGB M2T sing 221 n n CE SD M2T sing 222 n n SD C5' M2T sing 223 n n CE HE M2T sing 224 n n CE HEA M2T sing 225 n n CE HEB M2T sing 226 n n C4' C5' M2T sing 227 n n C5' H5' M2T sing 228 n n C5' "H5'A" M2T sing 229 n n O4' C4' M2T sing 230 n n C4' C3' M2T sing 231 n n C4' H4' M2T sing 232 n n C1' O4' M2T sing 233 n n N9 C1' M2T sing 234 n n C1' C2' M2T sing 235 n n C1' H1' M2T sing 236 n n C8 N9 M2T sing 237 n y N9 C4 M2T sing 238 n y C5 C4 M2T sing 239 n y C4 N3 M2T doub 240 n y N3 C2 M2T sing 241 n y N1 C2 M2T doub 242 n y C2 H2 M2T sing 243 n n C6 N1 M2T sing 244 n y C5 C6 M2T doub 245 n y N6 C6 M2T sing 246 n n N6 HN6 M2T sing 247 n n N6 HN6A M2T sing 248 n n N7 C5 M2T sing 249 n y N7 C8 M2T doub 250 n y C8 H8 M2T sing 251 n n O2' C2' M2T sing 252 n n C2' C3' M2T sing 253 n n C2' H2' M2T sing 254 n n O2' HO2' M2T sing 255 n n O3' C3' M2T sing 256 n n C3' H3' M2T sing 257 n n O3' HO3' M2T sing 258 n n SD HSD M2T sing 259 n n # _atom_sites.entry_id 3H0V _atom_sites.fract_transf_matrix[1][1] 0.010655 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002862 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020188 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.014792 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 PUT B 1 350 350 PUT PUT . D 4 M2T A 1 368 368 M2T M2T . E 5 PYR A 1 68 68 PYR PYR . F 6 HOH B 1 68 8 HOH HOH . F 6 HOH B 2 69 10 HOH HOH . F 6 HOH B 3 70 17 HOH HOH . F 6 HOH B 4 71 71 HOH HOH . F 6 HOH B 5 72 27 HOH HOH . F 6 HOH B 6 73 30 HOH HOH . F 6 HOH B 7 74 32 HOH HOH . F 6 HOH B 8 75 35 HOH HOH . F 6 HOH B 9 76 37 HOH HOH . F 6 HOH B 10 77 42 HOH HOH . F 6 HOH B 11 78 78 HOH HOH . F 6 HOH B 12 79 79 HOH HOH . F 6 HOH B 13 80 52 HOH HOH . F 6 HOH B 14 81 55 HOH HOH . F 6 HOH B 15 82 82 HOH HOH . F 6 HOH B 16 83 59 HOH HOH . F 6 HOH B 17 84 60 HOH HOH . F 6 HOH B 18 85 61 HOH HOH . F 6 HOH B 19 86 65 HOH HOH . G 6 HOH A 1 1 1 HOH HOH . G 6 HOH A 2 2 2 HOH HOH . G 6 HOH A 3 3 3 HOH HOH . G 6 HOH A 4 4 4 HOH HOH . G 6 HOH A 5 5 5 HOH HOH . G 6 HOH A 6 6 6 HOH HOH . G 6 HOH A 7 7 7 HOH HOH . G 6 HOH A 8 9 9 HOH HOH . G 6 HOH A 9 11 11 HOH HOH . G 6 HOH A 10 12 12 HOH HOH . G 6 HOH A 11 13 13 HOH HOH . G 6 HOH A 12 14 14 HOH HOH . G 6 HOH A 13 15 15 HOH HOH . G 6 HOH A 14 16 16 HOH HOH . G 6 HOH A 15 18 18 HOH HOH . G 6 HOH A 16 19 19 HOH HOH . G 6 HOH A 17 20 20 HOH HOH . G 6 HOH A 18 21 21 HOH HOH . G 6 HOH A 19 22 22 HOH HOH . G 6 HOH A 20 23 23 HOH HOH . G 6 HOH A 21 24 24 HOH HOH . G 6 HOH A 22 25 25 HOH HOH . G 6 HOH A 23 26 26 HOH HOH . G 6 HOH A 24 28 28 HOH HOH . G 6 HOH A 25 29 29 HOH HOH . G 6 HOH A 26 31 31 HOH HOH . G 6 HOH A 27 34 34 HOH HOH . G 6 HOH A 28 36 36 HOH HOH . G 6 HOH A 29 38 38 HOH HOH . G 6 HOH A 30 40 40 HOH HOH . G 6 HOH A 31 43 43 HOH HOH . G 6 HOH A 32 44 44 HOH HOH . G 6 HOH A 33 45 45 HOH HOH . G 6 HOH A 34 46 46 HOH HOH . G 6 HOH A 35 47 47 HOH HOH . G 6 HOH A 36 48 48 HOH HOH . G 6 HOH A 37 49 49 HOH HOH . G 6 HOH A 38 50 50 HOH HOH . G 6 HOH A 39 51 51 HOH HOH . G 6 HOH A 40 54 54 HOH HOH . G 6 HOH A 41 56 56 HOH HOH . G 6 HOH A 42 57 57 HOH HOH . G 6 HOH A 43 58 58 HOH HOH . G 6 HOH A 44 63 63 HOH HOH . G 6 HOH A 45 64 64 HOH HOH . G 6 HOH A 46 66 66 HOH HOH . G 6 HOH A 47 67 67 HOH HOH . G 6 HOH A 48 335 68 HOH HOH . G 6 HOH A 49 336 69 HOH HOH . G 6 HOH A 50 337 70 HOH HOH . G 6 HOH A 51 338 74 HOH HOH . G 6 HOH A 52 339 76 HOH HOH . G 6 HOH A 53 340 77 HOH HOH . G 6 HOH A 54 341 80 HOH HOH . G 6 HOH A 55 342 81 HOH HOH . G 6 HOH A 56 343 83 HOH HOH . G 6 HOH A 57 344 84 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C CG M2T . . . D 4 -17.736 -8.619 8.397 1 46.27 ? CG M2T 368 A 1 HETATM 2 S SD M2T . . . D 4 -16.829 -8.413 7.007 1 47.16 ? SD M2T 368 A 1 HETATM 3 C CE M2T . . . D 4 -16.491 -9.757 6.454 1 44.89 ? CE M2T 368 A 1 HETATM 4 C C5' M2T . . . D 4 -15.424 -7.558 7.382 1 43.31 ? C5' M2T 368 A 1 HETATM 5 C C4' M2T . . . D 4 -14.544 -7.309 6.172 1 42.82 ? C4' M2T 368 A 1 HETATM 6 O O4' M2T . . . D 4 -15.369 -6.771 5.093 1 41.8 ? O4' M2T 368 A 1 HETATM 7 C C1' M2T . . . D 4 -14.881 -5.493 4.712 1 42.62 ? C1' M2T 368 A 1 HETATM 8 N N9 M2T . . . D 4 -16.038 -4.671 4.347 1 42.8 ? N9 M2T 368 A 1 HETATM 9 C C4 M2T . . . D 4 -17.107 -4.363 5.162 1 44.08 ? C4 M2T 368 A 1 HETATM 10 N N3 M2T . . . D 4 -17.301 -4.744 6.446 1 44.31 ? N3 M2T 368 A 1 HETATM 11 C C2 M2T . . . D 4 -18.453 -4.261 6.924 1 43.73 ? C2 M2T 368 A 1 HETATM 12 N N1 M2T . . . D 4 -19.37 -3.495 6.305 1 44.42 ? N1 M2T 368 A 1 HETATM 13 C C6 M2T . . . D 4 -19.145 -3.128 5.013 1 45.45 ? C6 M2T 368 A 1 HETATM 14 N N6 M2T . . . D 4 -20.062 -2.365 4.394 1 46.5 ? N6 M2T 368 A 1 HETATM 15 C C5 M2T . . . D 4 -17.951 -3.578 4.394 1 43.84 ? C5 M2T 368 A 1 HETATM 16 N N7 M2T . . . D 4 -17.423 -3.393 3.122 1 43.39 ? N7 M2T 368 A 1 HETATM 17 C C8 M2T . . . D 4 -16.295 -4.057 3.146 1 42.46 ? C8 M2T 368 A 1 HETATM 18 C C2' M2T . . . D 4 -14.11 -4.985 5.925 1 41.66 ? C2' M2T 368 A 1 HETATM 19 O O2' M2T . . . D 4 -13.22 -3.938 5.589 1 41.91 ? O2' M2T 368 A 1 HETATM 20 C C3' M2T . . . D 4 -13.457 -6.264 6.423 1 42.4 ? C3' M2T 368 A 1 HETATM 21 O O3' M2T . . . D 4 -12.315 -6.573 5.635 1 41.07 ? O3' M2T 368 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #