data_6YMA # _model_server_result.job_id 1V-PqkoujXe1l1QbD2E_jw _model_server_result.datetime_utc '2024-12-12 19:41:52' _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 6yma # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 6YMA # _exptl.entry_id 6YMA _exptl.method 'ELECTRON CRYSTALLOGRAPHY' # _entity.details ? _entity.formula_weight 78.133 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIMETHYL SULFOXIDE' _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 104.62 _cell.angle_gamma 90 _cell.entry_id 6YMA _cell.length_a 42.55 _cell.length_b 41.53 _cell.length_c 72.11 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YMA _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 # 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 metalc ? metalc1 A NE2 HIS 94 A HIS 94 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc2 A NE2 HIS 96 A HIS 96 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc3 A ND1 HIS 119 A HIS 119 1_555 B ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc4 B ZN ZN . A ZN 301 1_555 C N1 AZM . A AZM 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? # _chem_comp.formula 'C2 H6 O S' _chem_comp.formula_weight 78.133 _chem_comp.id DMS _chem_comp.mon_nstd_flag . _chem_comp.name 'DIMETHYL SULFOXIDE' _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 S O DMS doub 102 n n S C1 DMS sing 103 n n S C2 DMS sing 104 n n C1 H11 DMS sing 105 n n C1 H12 DMS sing 106 n n C1 H13 DMS sing 107 n n C2 H21 DMS sing 108 n n C2 H22 DMS sing 109 n n C2 H23 DMS sing 110 n n # _atom_sites.entry_id 6YMA _atom_sites.fract_transf_matrix[1][1] 0.023502 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006131 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024079 _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] 0.014332 _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 ZN A 1 301 301 ZN ZN . C 3 AZM A 1 302 401 AZM AZM . D 4 DMS A 1 303 501 DMS DMS . E 5 HOH A 1 401 1008 HOH HOH . E 5 HOH A 2 402 1017 HOH HOH . E 5 HOH A 3 403 1018 HOH HOH . E 5 HOH A 4 404 1029 HOH HOH . E 5 HOH A 5 405 1012 HOH HOH . E 5 HOH A 6 406 1006 HOH HOH . E 5 HOH A 7 407 1022 HOH HOH . E 5 HOH A 8 408 1009 HOH HOH . E 5 HOH A 9 409 1023 HOH HOH . E 5 HOH A 10 410 1004 HOH HOH . E 5 HOH A 11 411 1003 HOH HOH . E 5 HOH A 12 412 1005 HOH HOH . E 5 HOH A 13 413 1020 HOH HOH . E 5 HOH A 14 414 1001 HOH HOH . E 5 HOH A 15 415 1026 HOH HOH . E 5 HOH A 16 416 1010 HOH HOH . E 5 HOH A 17 417 1002 HOH HOH . E 5 HOH A 18 418 1014 HOH HOH . E 5 HOH A 19 419 1015 HOH HOH . E 5 HOH A 20 420 1007 HOH HOH . E 5 HOH A 21 421 1028 HOH HOH . E 5 HOH A 22 422 1025 HOH HOH . E 5 HOH A 23 423 1013 HOH HOH . E 5 HOH A 24 424 1027 HOH HOH . E 5 HOH A 25 425 1016 HOH HOH . E 5 HOH A 26 426 1019 HOH HOH . E 5 HOH A 27 427 1024 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 S S DMS . . . D 4 -4.759 0.937 11.313 1 20.63 ? S DMS 303 A 1 HETATM 2 O O DMS . . . D 4 -4.531 2.414 11.38 1 20.63 ? O DMS 303 A 1 HETATM 3 C C1 DMS . . . D 4 -4.413 0.204 12.935 1 20.63 ? C1 DMS 303 A 1 HETATM 4 C C2 DMS . . . D 4 -3.441 0.157 10.34 1 20.63 ? C2 DMS 303 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 4 #