data_9FNR # _model_server_result.job_id 5gFzqZXiExXcR6lw5poFlA _model_server_result.datetime_utc '2025-02-24 18:41:54' _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 9fnr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 9FNR # _exptl.entry_id 9FNR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 574.275 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-methyl-N-[(4,4,6,6-tetrahydroxy-4,6-dioxido-1,3,3a,5,6a-tetrahydrothien[3,4-d]imidazol-4-ium-2-yl)methyl]-5-(2,4,4-trihydroxy-2-keto-3,3a,5,6-tetrahydro-1H-thien[3,4-d]imidazol-4-ium-6-yl _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 90 _cell.entry_id 9FNR _cell.length_a 57.1 _cell.length_b 57.1 _cell.length_c 172.197 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9FNR _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall 'I 4bw 2bw' _symmetry.space_group_name_H-M 'I 41 2 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 10_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 4 'crystal symmetry operation' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C24 H29 N5 Ni O6 S' _chem_comp.formula_weight 574.275 _chem_comp.id A1ICD _chem_comp.mon_nstd_flag . _chem_comp.name N-methyl-N-[(4,4,6,6-tetrahydroxy-4,6-dioxido-1,3,3a,5,6a-tetrahydrothien[3,4-d]imidazol-4-ium-2-yl)methyl]-5-(2,4,4-trihydroxy-2-keto-3,3a,5,6-tetrahydro-1H-thien[3,4-d]imidazol-4-ium-6-yl _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 C02 O01 A1ICD doub 1 n n N03 C02 A1ICD sing 2 n n C04 N03 A1ICD sing 3 n n S07 C06 A1ICD sing 4 n n C06 C05 A1ICD sing 5 n n N08 C05 A1ICD sing 6 n n C05 C04 A1ICD sing 7 n n C09 C04 A1ICD sing 8 n n C10 C09 A1ICD sing 9 n n C11 C10 A1ICD sing 10 n n C12 C11 A1ICD sing 11 n n C13 C12 A1ICD sing 12 n n C14 C13 A1ICD sing 13 n n C16 N15 A1ICD sing 14 n n C17 C16 A1ICD sing 15 n n C18 C17 A1ICD doub 16 n y C19 C18 A1ICD sing 17 n y N20 C19 A1ICD doub 18 n y O22 NI21 A1ICD sing 19 n n O23 NI21 A1ICD sing 20 n n O24 NI21 A1ICD sing 21 n n O25 NI21 A1ICD sing 22 n n NI21 N20 A1ICD sing 23 n n C26 N20 A1ICD sing 24 n y C27 C26 A1ICD doub 25 n y C28 C27 A1ICD sing 26 n y C29 C28 A1ICD doub 27 n y C30 C29 A1ICD sing 28 n y C31 C30 A1ICD doub 29 n y N32 C31 A1ICD sing 30 n y C33 N32 A1ICD doub 31 n y C34 C33 A1ICD sing 32 n y C35 C34 A1ICD doub 33 n y N15 C14 A1ICD sing 34 n n O36 C14 A1ICD doub 35 n n C02 N08 A1ICD sing 36 n n S07 C09 A1ICD sing 37 n n C17 C27 A1ICD sing 38 n y NI21 N32 A1ICD sing 39 n n C26 C31 A1ICD sing 40 n y C30 C35 A1ICD sing 41 n y C36 N15 A1ICD sing 42 n n C04 H1 A1ICD sing 43 n n C05 H2 A1ICD sing 44 n n C06 H3 A1ICD sing 45 n n C06 H4 A1ICD sing 46 n n C09 H5 A1ICD sing 47 n n C10 H6 A1ICD sing 48 n n C10 H7 A1ICD sing 49 n n C11 H8 A1ICD sing 50 n n C11 H9 A1ICD sing 51 n n C12 H10 A1ICD sing 52 n n C12 H11 A1ICD sing 53 n n C13 H12 A1ICD sing 54 n n C13 H13 A1ICD sing 55 n n C16 H14 A1ICD sing 56 n n C16 H15 A1ICD sing 57 n n C18 H16 A1ICD sing 58 n n C19 H17 A1ICD sing 59 n n C28 H18 A1ICD sing 60 n n C29 H19 A1ICD sing 61 n n C33 H20 A1ICD sing 62 n n C34 H21 A1ICD sing 63 n n C35 H22 A1ICD sing 64 n n N03 H23 A1ICD sing 65 n n N08 H24 A1ICD sing 66 n n C36 H29 A1ICD sing 67 n n C36 H30 A1ICD sing 68 n n C36 H31 A1ICD sing 69 n n O24 H25 A1ICD sing 70 n n O25 H26 A1ICD sing 71 n n # _atom_sites.entry_id 9FNR _atom_sites.fract_transf_matrix[1][1] 0.017513 _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] 0.017513 _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] 0.005807 _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 A1ICD A 1 201 201 A1ICD YZT . C 3 SO4 A 1 202 1 SO4 SO4 . D 4 HOH A 1 301 59 HOH HOH . D 4 HOH A 2 302 4 HOH HOH . D 4 HOH A 3 303 34 HOH HOH . D 4 HOH A 4 304 9 HOH HOH . D 4 HOH A 5 305 72 HOH HOH . D 4 HOH A 6 306 32 HOH HOH . D 4 HOH A 7 307 35 HOH HOH . D 4 HOH A 8 308 11 HOH HOH . D 4 HOH A 9 309 6 HOH HOH . D 4 HOH A 10 310 1 HOH HOH . D 4 HOH A 11 311 37 HOH HOH . D 4 HOH A 12 312 3 HOH HOH . D 4 HOH A 13 313 81 HOH HOH . D 4 HOH A 14 314 26 HOH HOH . D 4 HOH A 15 315 8 HOH HOH . D 4 HOH A 16 316 87 HOH HOH . D 4 HOH A 17 317 14 HOH HOH . D 4 HOH A 18 318 15 HOH HOH . D 4 HOH A 19 319 27 HOH HOH . D 4 HOH A 20 320 7 HOH HOH . D 4 HOH A 21 321 25 HOH HOH . D 4 HOH A 22 322 89 HOH HOH . D 4 HOH A 23 323 10 HOH HOH . D 4 HOH A 24 324 17 HOH HOH . D 4 HOH A 25 325 24 HOH HOH . D 4 HOH A 26 326 86 HOH HOH . D 4 HOH A 27 327 88 HOH HOH . D 4 HOH A 28 328 85 HOH HOH . D 4 HOH A 29 329 53 HOH HOH . D 4 HOH A 30 330 90 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 C02 A1ICD . . . B 2 0.645 -13.301 7.952 1 64.29 ? C02 A1ICD 201 A 1 HETATM 2 C C04 A1ICD . . . B 2 0.373 -11.401 9.143 1 55.37 ? C04 A1ICD 201 A 1 HETATM 3 C C05 A1ICD . . . B 2 0.622 -11.132 7.508 1 56.15 ? C05 A1ICD 201 A 1 HETATM 4 C C06 A1ICD . . . B 2 -0.373 -10.547 7.104 1 55.08 ? C06 A1ICD 201 A 1 HETATM 5 C C09 A1ICD . . . B 2 -0.869 -10.847 9.421 1 57.55 ? C09 A1ICD 201 A 1 HETATM 6 C C10 A1ICD . . . B 2 -1.597 -11.708 10.413 1 54.47 ? C10 A1ICD 201 A 1 HETATM 7 C C11 A1ICD . . . B 2 -1.659 -11.077 11.902 1 51.8 ? C11 A1ICD 201 A 1 HETATM 8 C C12 A1ICD . . . B 2 -2.305 -12.122 12.976 1 52.12 ? C12 A1ICD 201 A 1 HETATM 9 C C13 A1ICD . . . B 2 -3.503 -11.489 13.876 1 56.88 ? C13 A1ICD 201 A 1 HETATM 10 C C14 A1ICD . . . B 2 -3.687 -9.882 13.662 1 63.7 ? C14 A1ICD 201 A 1 HETATM 11 C C16 A1ICD . . . B 2 -2.991 -7.348 13.898 1 67.37 ? C16 A1ICD 201 A 1 HETATM 12 C C17 A1ICD . . . B 2 -3.541 -6.765 15.314 1 70.3 ? C17 A1ICD 201 A 1 HETATM 13 C C18 A1ICD . . . B 2 -4.298 -7.666 16.146 1 70.3 ? C18 A1ICD 201 A 1 HETATM 14 C C19 A1ICD . . . B 2 -4.822 -7.219 17.473 1 72.67 ? C19 A1ICD 201 A 1 HETATM 15 C C26 A1ICD . . . B 2 -3.845 -4.93 17.201 1 78.12 ? C26 A1ICD 201 A 1 HETATM 16 C C27 A1ICD . . . B 2 -3.276 -5.383 15.789 1 74.51 ? C27 A1ICD 201 A 1 HETATM 17 C C28 A1ICD . . . B 2 -2.495 -4.444 14.955 1 72.69 ? C28 A1ICD 201 A 1 HETATM 18 C C29 A1ICD . . . B 2 -2.253 -3.148 15.401 1 73.77 ? C29 A1ICD 201 A 1 HETATM 19 C C30 A1ICD . . . B 2 -2.784 -2.681 16.749 1 77.48 ? C30 A1ICD 201 A 1 HETATM 20 C C31 A1ICD . . . B 2 -3.599 -3.634 17.645 1 78.47 ? C31 A1ICD 201 A 1 HETATM 21 C C33 A1ICD . . . B 2 -3.819 -1.861 19.327 1 79.47 ? C33 A1ICD 201 A 1 HETATM 22 C C34 A1ICD . . . B 2 -3.042 -0.901 18.494 1 80.81 ? C34 A1ICD 201 A 1 HETATM 23 C C35 A1ICD . . . B 2 -2.525 -1.306 17.211 1 79.51 ? C35 A1ICD 201 A 1 HETATM 24 N N03 A1ICD . . . B 2 0.403 -12.572 9.332 1 63.46 ? N03 A1ICD 201 A 1 HETATM 25 N N08 A1ICD . . . B 2 0.76 -12.252 6.939 1 59.07 ? N08 A1ICD 201 A 1 HETATM 26 N N15 A1ICD . . . B 2 -2.675 -8.855 14.17 1 65.39 ? N15 A1ICD 201 A 1 HETATM 27 N N20 A1ICD . . . B 2 -4.572 -5.837 17.959 1 74.66 ? N20 A1ICD 201 A 1 HETATM 28 N N32 A1ICD . . . B 2 -4.082 -3.208 18.886 1 76.37 ? N32 A1ICD 201 A 1 HETATM 29 O O01 A1ICD . . . B 2 0.726 -14.534 7.739 1 63.95 ? O01 A1ICD 201 A 1 HETATM 30 O O22 A1ICD . . . B 2 -3.412 -5.576 20.676 1 77.39 ? O22 A1ICD 201 A 1 HETATM 31 O O23 A1ICD . . . B 2 -6.967 -4.208 18.919 1 75.59 ? O23 A1ICD 201 A 1 HETATM 32 O O24 A1ICD . . . B 2 -6.047 -6.764 20.157 1 72.16 ? O24 A1ICD 201 A 1 HETATM 33 O O25 A1ICD . . . B 2 -5.961 -4.343 21.681 1 75.77 ? O25 A1ICD 201 A 1 HETATM 34 O O36 A1ICD . . . B 2 -4.679 -9.427 13.084 1 76.3 ? O36 A1ICD 201 A 1 HETATM 35 S S07 A1ICD . . . B 2 -1.565 -10.727 8.275 1 55.66 ? S07 A1ICD 201 A 1 HETATM 36 NI NI21 A1ICD . . . B 2 -5.189 -4.89 19.807 0.61 71.17 ? NI21 A1ICD 201 A 1 HETATM 37 C C36 A1ICD . . . B 2 -1.804 -9.161 14.678 1 57.71 ? C36 A1ICD 201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 37 #