data_9JHV # _model_server_result.job_id MiNhWK2QxebBT9Y7lFBp2A _model_server_result.datetime_utc '2024-11-22 00:26:58' _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 9jhv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 9JHV # _exptl.entry_id 9JHV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.334 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 90 _cell.angle_gamma 120 _cell.entry_id 9JHV _cell.length_a 78.854 _cell.length_b 78.854 _cell.length_c 233.369 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9JHV _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -39.427 -68.289567 0 3 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 39.427 -68.289567 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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 143 A CYS 143 1_555 A SG CYS 210 A CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 205 A CYS 205 1_555 A SG CYS 266 A CYS 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 264 A CYS 264 1_555 A SG CYS 267 A CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? # _chem_comp.formula 'C11 H15 N5 O3 S' _chem_comp.formula_weight 297.334 _chem_comp.id MTA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 CS S5' MTA sing 237 n n CS HCS1 MTA sing 238 n n CS HCS2 MTA sing 239 n n CS HCS3 MTA sing 240 n n S5' C5' MTA sing 241 n n C5' C4' MTA sing 242 n n C5' "H5'1" MTA sing 243 n n C5' "H5'2" MTA sing 244 n n C4' O4' MTA sing 245 n n C4' C3' MTA sing 246 n n C4' H4' MTA sing 247 n n O4' C1' MTA sing 248 n n C2' O2' MTA sing 249 n n C2' C3' MTA sing 250 n n C2' C1' MTA sing 251 n n C2' H2' MTA sing 252 n n O2' HO2' MTA sing 253 n n C3' O3' MTA sing 254 n n C3' H3' MTA sing 255 n n O3' H3T MTA sing 256 n n C1' N9 MTA sing 257 n n C1' H1' MTA sing 258 n n N9 C8 MTA sing 259 n y N9 C4 MTA sing 260 n y C8 N7 MTA doub 261 n y C8 H8 MTA sing 262 n n N7 C5 MTA sing 263 n y C5 C6 MTA sing 264 n y C5 C4 MTA doub 265 n y C6 N6 MTA sing 266 n n C6 N1 MTA doub 267 n y N6 H61 MTA sing 268 n n N6 H62 MTA sing 269 n n N1 C2 MTA sing 270 n y C2 N3 MTA doub 271 n y C2 H2 MTA sing 272 n n N3 C4 MTA sing 273 n y # _atom_sites.entry_id 9JHV _atom_sites.fract_transf_matrix[1][1] 0.012682 _atom_sites.fract_transf_matrix[1][2] 0.007322 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014644 _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] 0.004285 _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 B 2 PEG A 1 301 301 PEG PEG . C 3 PO4 A 1 302 400 PO4 PO4 . D 4 MTA A 1 303 401 MTA MTA . E 5 HOH A 1 401 44 HOH HOH . E 5 HOH A 2 402 51 HOH HOH . E 5 HOH A 3 403 45 HOH HOH . E 5 HOH A 4 404 28 HOH HOH . E 5 HOH A 5 405 22 HOH HOH . E 5 HOH A 6 406 38 HOH HOH . E 5 HOH A 7 407 25 HOH HOH . E 5 HOH A 8 408 32 HOH HOH . E 5 HOH A 9 409 50 HOH HOH . E 5 HOH A 10 410 8 HOH HOH . E 5 HOH A 11 411 31 HOH HOH . E 5 HOH A 12 412 55 HOH HOH . E 5 HOH A 13 413 27 HOH HOH . E 5 HOH A 14 414 48 HOH HOH . E 5 HOH A 15 415 39 HOH HOH . E 5 HOH A 16 416 21 HOH HOH . E 5 HOH A 17 417 6 HOH HOH . E 5 HOH A 18 418 40 HOH HOH . E 5 HOH A 19 419 16 HOH HOH . E 5 HOH A 20 420 34 HOH HOH . E 5 HOH A 21 421 30 HOH HOH . E 5 HOH A 22 422 15 HOH HOH . E 5 HOH A 23 423 54 HOH HOH . E 5 HOH A 24 424 5 HOH HOH . E 5 HOH A 25 425 33 HOH HOH . E 5 HOH A 26 426 18 HOH HOH . E 5 HOH A 27 427 11 HOH HOH . E 5 HOH A 28 428 2 HOH HOH . E 5 HOH A 29 429 9 HOH HOH . E 5 HOH A 30 430 52 HOH HOH . E 5 HOH A 31 431 53 HOH HOH . E 5 HOH A 32 432 24 HOH HOH . E 5 HOH A 33 433 17 HOH HOH . E 5 HOH A 34 434 10 HOH HOH . E 5 HOH A 35 435 20 HOH HOH . E 5 HOH A 36 436 46 HOH HOH . E 5 HOH A 37 437 19 HOH HOH . E 5 HOH A 38 438 47 HOH HOH . E 5 HOH A 39 439 12 HOH HOH . E 5 HOH A 40 440 35 HOH HOH . E 5 HOH A 41 441 3 HOH HOH . E 5 HOH A 42 442 4 HOH HOH . E 5 HOH A 43 443 43 HOH HOH . E 5 HOH A 44 444 1 HOH HOH . E 5 HOH A 45 445 37 HOH HOH . E 5 HOH A 46 446 41 HOH HOH . E 5 HOH A 47 447 14 HOH HOH . E 5 HOH A 48 448 7 HOH HOH . E 5 HOH A 49 449 13 HOH HOH . E 5 HOH A 50 450 26 HOH HOH . E 5 HOH A 51 451 36 HOH HOH . E 5 HOH A 52 452 29 HOH HOH . E 5 HOH A 53 453 23 HOH HOH . E 5 HOH A 54 454 49 HOH HOH . E 5 HOH A 55 455 42 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 CS MTA . . . D 4 5.475 -23.812 -21.707 1 32.8 ? CS MTA 303 A 1 HETATM 2 S S5' MTA . . . D 4 4.203 -24.609 -20.726 1 28.45 ? S5' MTA 303 A 1 HETATM 3 C C5' MTA . . . D 4 4.512 -26.34 -21.088 1 26.04 ? C5' MTA 303 A 1 HETATM 4 C C4' MTA . . . D 4 5.79 -26.932 -20.559 1 24.17 ? C4' MTA 303 A 1 HETATM 5 O O4' MTA . . . D 4 5.783 -26.832 -19.127 1 25.29 ? O4' MTA 303 A 1 HETATM 6 C C2' MTA . . . D 4 6.357 -29.067 -19.486 1 22.13 ? C2' MTA 303 A 1 HETATM 7 O O2' MTA . . . D 4 7.502 -29.904 -19.582 1 22.87 ? O2' MTA 303 A 1 HETATM 8 C C3' MTA . . . D 4 5.921 -28.437 -20.839 1 22.85 ? C3' MTA 303 A 1 HETATM 9 O O3' MTA . . . D 4 6.752 -28.682 -21.979 1 20.85 ? O3' MTA 303 A 1 HETATM 10 C C1' MTA . . . D 4 6.57 -27.866 -18.556 1 22.25 ? C1' MTA 303 A 1 HETATM 11 N N9 MTA . . . D 4 6.026 -27.909 -17.189 1 20.65 ? N9 MTA 303 A 1 HETATM 12 C C8 MTA . . . D 4 6.094 -26.824 -16.344 1 20.02 ? C8 MTA 303 A 1 HETATM 13 N N7 MTA . . . D 4 5.375 -26.932 -15.262 1 19.35 ? N7 MTA 303 A 1 HETATM 14 C C5 MTA . . . D 4 4.707 -28.141 -15.427 1 17.7 ? C5 MTA 303 A 1 HETATM 15 C C6 MTA . . . D 4 3.734 -28.79 -14.654 1 17.75 ? C6 MTA 303 A 1 HETATM 16 N N6 MTA . . . D 4 3.249 -28.329 -13.481 1 18.86 ? N6 MTA 303 A 1 HETATM 17 N N1 MTA . . . D 4 3.28 -29.978 -15.116 1 18.28 ? N1 MTA 303 A 1 HETATM 18 C C2 MTA . . . D 4 3.743 -30.45 -16.273 1 16.88 ? C2 MTA 303 A 1 HETATM 19 N N3 MTA . . . D 4 4.648 -29.913 -17.085 1 17.45 ? N3 MTA 303 A 1 HETATM 20 C C4 MTA . . . D 4 5.065 -28.73 -16.631 1 18.09 ? C4 MTA 303 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #