data_6O9V # _model_server_result.job_id znO9G04ESnkqxPg_hHYBpA _model_server_result.datetime_utc '2025-02-28 21:26:19' _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 6o9v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":401}' # _entry.id 6O9V # _exptl.entry_id 6O9V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 236.353 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1,1-Methanediyl Bismethanethiosulfonate' _entity.pdbx_number_of_molecules 2 _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 90 _cell.entry_id 6O9V _cell.length_a 83.298 _cell.length_b 114.683 _cell.length_c 89.457 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6O9V _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -83.298 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 H N N ? 5 I N 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 covale ? covale1 A SG CYS 129 A CYS 129 1_555 H S01 M1M . B M1M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? covale ? covale2 A SG CYS 135 A CYS 135 1_555 I S03 M1M . B M1M 402 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? covale ? covale3 B SG CYS 129 B CYS 129 1_555 I S01 M1M . B M1M 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? covale ? covale4 B SG CYS 135 B CYS 135 1_555 H S03 M1M . B M1M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc1 A O THR 96 A THR 96 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.19 ? metalc ? metalc2 A O THR 96 A THR 96 1_555 E K K . A K 403 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 3.19 ? metalc ? metalc3 A O THR 96 A THR 96 1_555 F K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc4 A OG1 THR 96 A THR 96 1_555 F K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? metalc ? metalc5 A O THR 96 A THR 96 1_555 F K K . A K 404 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc6 A OG1 THR 96 A THR 96 1_555 F K K . A K 404 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? metalc ? metalc7 A O ILE 97 A ILE 97 1_555 E K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc8 A O ILE 97 A ILE 97 1_555 E K K . A K 403 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc9 A O GLY 98 A GLY 98 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc10 A O GLY 98 A GLY 98 1_555 D K K . A K 402 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc11 A O TYR 99 A TYR 99 1_555 D K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc12 A O TYR 99 A TYR 99 1_555 D K K . A K 402 2_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc13 D K K . A K 402 1_555 B O GLY 98 B GLY 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.834 ? metalc ? metalc14 D K K . A K 402 2_455 B O GLY 98 B GLY 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.834 ? metalc ? metalc15 D K K . A K 402 1_555 B O TYR 99 B TYR 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc16 D K K . A K 402 2_455 B O TYR 99 B TYR 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc17 E K K . A K 403 1_555 B O THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc18 E K K . A K 403 2_455 B O THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc19 E K K . A K 403 1_555 B O ILE 97 B ILE 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc20 E K K . A K 403 2_455 B O ILE 97 B ILE 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc21 F K K . A K 404 1_555 B O THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc22 F K K . A K 404 1_555 B OG1 THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc23 F K K . A K 404 2_455 B O THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc24 F K K . A K 404 2_455 B OG1 THR 96 B THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? # _chem_comp.formula 'C3 H8 O4 S4' _chem_comp.formula_weight 236.353 _chem_comp.id M1M _chem_comp.mon_nstd_flag . _chem_comp.name '1,1-Methanediyl Bismethanethiosulfonate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "S,S'-methylene dimethanesulfonothioate" # 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 S03 C02 M1M sing 258 n n C02 S01 M1M sing 259 n n C02 H2 M1M sing 260 n n C02 H3 M1M sing 261 n n S01 S11 M1M sing 262 n n S11 O12 M1M doub 263 n n S11 O11 M1M doub 264 n n S11 C13 M1M sing 265 n n S03 S31 M1M sing 266 n n S31 O31 M1M doub 267 n n S31 O32 M1M doub 268 n n S31 C33 M1M sing 269 n n C13 H1 M1M sing 270 n n C13 H4 M1M sing 271 n n C13 H5 M1M sing 272 n n C33 H6 M1M sing 273 n n C33 H7 M1M sing 274 n n C33 H8 M1M sing 275 n n # _atom_sites.entry_id 6O9V _atom_sites.fract_transf_matrix[1][1] 0.012005 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00872 _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] 0.011179 _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 2 TMO A 1 401 1 TMO TMO . D 3 K A 1 402 1 K K . E 3 K A 1 403 3 K K . F 3 K A 1 404 4 K K . G 4 DDQ A 1 405 1 DDQ LD3 . H 5 M1M B 1 401 500 M1M MTS . I 5 M1M B 1 402 500 M1M MTS . J 2 TMO B 1 403 2 TMO TMO . K 4 DDQ B 1 404 2 DDQ LD3 . L 6 HOH A 1 501 20 HOH HOH . L 6 HOH A 2 502 17 HOH HOH . L 6 HOH A 3 503 12 HOH HOH . L 6 HOH A 4 504 10 HOH HOH . L 6 HOH A 5 505 6 HOH HOH . L 6 HOH A 6 506 25 HOH HOH . L 6 HOH A 7 507 22 HOH HOH . L 6 HOH A 8 508 13 HOH HOH . L 6 HOH A 9 509 21 HOH HOH . M 6 HOH B 1 501 9 HOH HOH . M 6 HOH B 2 502 7 HOH HOH . M 6 HOH B 3 503 24 HOH HOH . M 6 HOH B 4 504 15 HOH HOH . M 6 HOH B 5 505 28 HOH HOH . M 6 HOH B 6 506 16 HOH HOH . M 6 HOH B 7 507 23 HOH HOH . M 6 HOH B 8 508 4 HOH HOH . M 6 HOH B 9 509 18 HOH HOH . M 6 HOH B 10 510 3 HOH HOH . M 6 HOH B 11 511 26 HOH HOH . M 6 HOH B 12 512 5 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 S01 M1M . . . H 5 -38.157 8.704 -42.265 1 96.84 ? S01 M1M 401 B 1 HETATM 2 C C02 M1M . . . H 5 -36.867 9.53 -43.288 1 91.51 ? C02 M1M 401 B 1 HETATM 3 S S03 M1M . . . H 5 -35.452 8.525 -43.898 1 153.65 ? S03 M1M 401 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 3 #