data_9FFJ # _model_server_result.job_id Ahh2kRRAdAgsiVXU_WZ6zg _model_server_result.datetime_utc '2025-02-24 18:17:02' _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 9ffj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 9FFJ # _exptl.entry_id 9FFJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 574.275 _entity.id 3 _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 9FFJ _cell.length_a 57.46 _cell.length_b 57.46 _cell.length_c 172.46 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9FFJ _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,E,F,G,H,I,J _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 3 _struct_asym.id C _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 9FFJ _atom_sites.fract_transf_matrix[1][1] 0.017403 _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] 0.017403 _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] 0.005798 _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 EDO A 1 201 206 EDO EDO . C 3 A1ICD A 1 202 210 A1ICD YZT . D 4 PEG A 1 203 211 PEG PEG . E 4 PEG A 1 204 212 PEG PEG . F 2 EDO A 1 205 213 EDO EDO . G 5 SO4 A 1 206 1 SO4 SO4 . H 5 SO4 A 1 207 2 SO4 SO4 . I 6 NH4 A 1 208 1 NH4 NH4 . J 7 HOH A 1 301 17 HOH HOH . J 7 HOH A 2 302 13 HOH HOH . J 7 HOH A 3 303 32 HOH HOH . J 7 HOH A 4 304 4 HOH HOH . J 7 HOH A 5 305 9 HOH HOH . J 7 HOH A 6 306 7 HOH HOH . J 7 HOH A 7 307 1 HOH HOH . J 7 HOH A 8 308 5 HOH HOH . J 7 HOH A 9 309 6 HOH HOH . J 7 HOH A 10 310 25 HOH HOH . J 7 HOH A 11 311 37 HOH HOH . J 7 HOH A 12 312 39 HOH HOH . J 7 HOH A 13 313 50 HOH HOH . J 7 HOH A 14 314 31 HOH HOH . J 7 HOH A 15 315 11 HOH HOH . J 7 HOH A 16 316 21 HOH HOH . J 7 HOH A 17 317 14 HOH HOH . J 7 HOH A 18 318 2 HOH HOH . J 7 HOH A 19 319 41 HOH HOH . J 7 HOH A 20 320 48 HOH HOH . J 7 HOH A 21 321 3 HOH HOH . J 7 HOH A 22 322 10 HOH HOH . J 7 HOH A 23 323 23 HOH HOH . J 7 HOH A 24 324 51 HOH HOH . J 7 HOH A 25 325 8 HOH HOH . J 7 HOH A 26 326 46 HOH HOH . J 7 HOH A 27 327 45 HOH HOH . J 7 HOH A 28 328 27 HOH HOH . J 7 HOH A 29 329 15 HOH HOH . J 7 HOH A 30 330 36 HOH HOH . J 7 HOH A 31 331 12 HOH HOH . J 7 HOH A 32 332 33 HOH HOH . J 7 HOH A 33 333 29 HOH HOH . J 7 HOH A 34 334 16 HOH HOH . J 7 HOH A 35 335 43 HOH HOH . J 7 HOH A 36 336 49 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 . A . C 3 0.657 -13.418 8.172 0.52 18.48 ? C02 A1ICD 202 A 1 HETATM 2 C C02 A1ICD . B . C 3 0.831 -12.961 8.425 0.48 64.34 ? C02 A1ICD 202 A 1 HETATM 3 C C04 A1ICD . A . C 3 0.287 -11.499 9.393 0.52 15.74 ? C04 A1ICD 202 A 1 HETATM 4 C C04 A1ICD . B . C 3 0.687 -10.791 8.986 0.48 61.77 ? C04 A1ICD 202 A 1 HETATM 5 C C05 A1ICD . A . C 3 0.581 -11.222 7.758 0.52 17.9 ? C05 A1ICD 202 A 1 HETATM 6 C C05 A1ICD . B . C 3 0.342 -11.086 7.359 0.48 62.01 ? C05 A1ICD 202 A 1 HETATM 7 C C06 A1ICD . A . C 3 -0.483 -10.742 7.325 0.52 19.14 ? C06 A1ICD 202 A 1 HETATM 8 C C06 A1ICD . B . C 3 -0.804 -10.706 7.181 0.48 61.55 ? C06 A1ICD 202 A 1 HETATM 9 C C09 A1ICD . A . C 3 -1.008 -10.999 9.617 0.52 19.23 ? C09 A1ICD 202 A 1 HETATM 10 C C09 A1ICD . B . C 3 -0.466 -10.264 9.536 0.48 61.49 ? C09 A1ICD 202 A 1 HETATM 11 C C10 A1ICD . A . C 3 -1.593 -11.776 10.767 0.52 20.74 ? C10 A1ICD 202 A 1 HETATM 12 C C10 A1ICD . B . C 3 -1.225 -11.316 10.3 0.48 61.77 ? C10 A1ICD 202 A 1 HETATM 13 C C11 A1ICD . A . C 3 -2.458 -10.791 11.69 0.52 17.92 ? C11 A1ICD 202 A 1 HETATM 14 C C11 A1ICD . B . C 3 -1.791 -10.72 11.693 0.48 63.39 ? C11 A1ICD 202 A 1 HETATM 15 C C12 A1ICD . A . C 3 -2.872 -11.637 13.03 0.52 22.94 ? C12 A1ICD 202 A 1 HETATM 16 C C12 A1ICD . B . C 3 -2.761 -11.752 12.512 0.48 67.26 ? C12 A1ICD 202 A 1 HETATM 17 C C13 A1ICD . A . C 3 -3.912 -10.783 13.929 0.52 26.82 ? C13 A1ICD 202 A 1 HETATM 18 C C13 A1ICD . B . C 3 -3.754 -10.904 13.487 0.48 72.06 ? C13 A1ICD 202 A 1 HETATM 19 C C14 A1ICD . A . C 3 -3.1 -9.474 14.447 0.52 30.24 ? C14 A1ICD 202 A 1 HETATM 20 C C14 A1ICD . B . C 3 -2.959 -9.633 14.149 0.48 77.54 ? C14 A1ICD 202 A 1 HETATM 21 C C16 A1ICD . A . C 3 -2.865 -6.87 14.662 0.52 40.2 ? C16 A1ICD 202 A 1 HETATM 22 C C16 A1ICD . B . C 3 -2.925 -7.083 15.023 0.48 89.58 ? C16 A1ICD 202 A 1 HETATM 23 C C17 A1ICD . A . C 3 -3.77 -6.306 15.883 0.52 44.17 ? C17 A1ICD 202 A 1 HETATM 24 C C17 A1ICD . B . C 3 -3.865 -6.327 16.135 0.48 95.93 ? C17 A1ICD 202 A 1 HETATM 25 C C18 A1ICD . A . C 3 -4.559 -7.231 16.659 0.52 44.84 ? C18 A1ICD 202 A 1 HETATM 26 C C18 A1ICD . B . C 3 -4.779 -7.088 16.953 0.48 98.86 ? C18 A1ICD 202 A 1 HETATM 27 C C19 A1ICD . A . C 3 -5.405 -6.72 17.763 0.52 45.29 ? C19 A1ICD 202 A 1 HETATM 28 C C19 A1ICD . B . C 3 -5.634 -6.396 17.96 0.48 101.38 ? C19 A1ICD 202 A 1 HETATM 29 C C26 A1ICD . A . C 3 -4.697 -4.347 17.343 0.52 45.98 ? C26 A1ICD 202 A 1 HETATM 30 C C26 A1ICD . B . C 3 -4.712 -4.147 17.396 0.48 101.8 ? C26 A1ICD 202 A 1 HETATM 31 C C27 A1ICD . A . C 3 -3.802 -4.863 16.17 0.52 45.51 ? C27 A1ICD 202 A 1 HETATM 32 C C27 A1ICD . B . C 3 -3.798 -4.856 16.323 0.48 99.01 ? C27 A1ICD 202 A 1 HETATM 33 C C28 A1ICD . A . C 3 -2.987 -3.935 15.367 0.52 46.39 ? C28 A1ICD 202 A 1 HETATM 34 C C28 A1ICD . B . C 3 -2.871 -4.059 15.5 0.48 99.3 ? C28 A1ICD 202 A 1 HETATM 35 C C29 A1ICD . A . C 3 -3.012 -2.571 15.635 0.52 47.7 ? C29 A1ICD 202 A 1 HETATM 36 C C29 A1ICD . B . C 3 -2.798 -2.679 15.666 0.48 100.25 ? C29 A1ICD 202 A 1 HETATM 37 C C30 A1ICD . A . C 3 -3.872 -2.034 16.763 0.52 47.37 ? C30 A1ICD 202 A 1 HETATM 38 C C30 A1ICD . B . C 3 -3.666 -1.972 16.691 0.48 101.64 ? C30 A1ICD 202 A 1 HETATM 39 C C31 A1ICD . A . C 3 -4.718 -2.991 17.613 0.52 46.42 ? C31 A1ICD 202 A 1 HETATM 40 C C31 A1ICD . B . C 3 -4.64 -2.773 17.562 0.48 102.71 ? C31 A1ICD 202 A 1 HETATM 41 C C33 A1ICD . A . C 3 -5.53 -1.09 18.927 0.52 48.71 ? C33 A1ICD 202 A 1 HETATM 42 C C33 A1ICD . B . C 3 -5.349 -0.693 18.662 0.48 103.93 ? C33 A1ICD 202 A 1 HETATM 43 C C34 A1ICD . A . C 3 -4.729 -0.119 18.135 0.52 49.22 ? C34 A1ICD 202 A 1 HETATM 44 C C34 A1ICD . B . C 3 -4.42 0.125 17.84 0.48 103.05 ? C34 A1ICD 202 A 1 HETATM 45 C C35 A1ICD . A . C 3 -3.902 -0.592 17.057 0.52 49.25 ? C35 A1ICD 202 A 1 HETATM 46 C C35 A1ICD . B . C 3 -3.582 -0.511 16.858 0.48 102.24 ? C35 A1ICD 202 A 1 HETATM 47 N N03 A1ICD . A . C 3 0.356 -12.69 9.544 0.52 20.22 ? N03 A1ICD 202 A 1 HETATM 48 N N03 A1ICD . B . C 3 0.951 -11.815 9.509 0.48 62.8 ? N03 A1ICD 202 A 1 HETATM 49 N N08 A1ICD . A . C 3 0.813 -12.354 7.177 0.52 15.14 ? N08 A1ICD 202 A 1 HETATM 50 N N08 A1ICD . B . C 3 0.444 -12.328 7.151 0.48 62.98 ? N08 A1ICD 202 A 1 HETATM 51 N N15 A1ICD . A . C 3 -3.679 -8.09 14.158 0.52 35.82 ? N15 A1ICD 202 A 1 HETATM 52 N N15 A1ICD . B . C 3 -3.694 -8.29 14.391 0.48 83.5 ? N15 A1ICD 202 A 1 HETATM 53 N N20 A1ICD . A . C 3 -5.431 -5.269 18.058 0.52 43.49 ? N20 A1ICD 202 A 1 HETATM 54 N N20 A1ICD . B . C 3 -5.566 -4.921 18.148 0.48 103.61 ? N20 A1ICD 202 A 1 HETATM 55 N N32 A1ICD . A . C 3 -5.509 -2.501 18.639 0.52 44.61 ? N32 A1ICD 202 A 1 HETATM 56 N N32 A1ICD . B . C 3 -5.437 -2.121 18.503 0.48 104.55 ? N32 A1ICD 202 A 1 HETATM 57 O O01 A1ICD . A . C 3 0.761 -14.655 7.982 0.52 17.43 ? O01 A1ICD 202 A 1 HETATM 58 O O01 A1ICD . B . C 3 1.027 -14.183 8.617 0.48 66.4 ? O01 A1ICD 202 A 1 HETATM 59 O O22 A1ICD . A . C 3 -4.954 -4.42 20.904 0.52 48.46 ? O22 A1ICD 202 A 1 HETATM 60 O O22 A1ICD . B . C 3 -5.177 -3.883 20.951 0.48 108.16 ? O22 A1ICD 202 A 1 HETATM 61 O O23 A1ICD . A . C 3 -8.155 -4.044 18.26 0.52 41.44 ? O23 A1ICD 202 A 1 HETATM 62 O O23 A1ICD . B . C 3 -8.157 -3.401 18.072 0.48 107.47 ? O23 A1ICD 202 A 1 HETATM 63 O O24 A1ICD . A . C 3 -7.201 -6.116 20.056 0.52 43.7 ? O24 A1ICD 202 A 1 HETATM 64 O O24 A1ICD . B . C 3 -7.477 -5.472 20.036 0.48 107.91 ? O24 A1ICD 202 A 1 HETATM 65 O O25 A1ICD . A . C 3 -7.731 -3.536 21.138 0.52 42.86 ? O25 A1ICD 202 A 1 HETATM 66 O O25 A1ICD . B . C 3 -7.918 -2.806 20.96 0.48 107.47 ? O25 A1ICD 202 A 1 HETATM 67 O O36 A1ICD . A . C 3 -2.022 -9.576 15.072 0.52 29.44 ? O36 A1ICD 202 A 1 HETATM 68 O O36 A1ICD . B . C 3 -1.759 -9.746 14.467 0.48 77.95 ? O36 A1ICD 202 A 1 HETATM 69 S S07 A1ICD . A . C 3 -1.769 -10.91 8.443 0.52 17.96 ? S07 A1ICD 202 A 1 HETATM 70 S S07 A1ICD . B . C 3 -1.21 -9.807 8.539 0.48 61.33 ? S07 A1ICD 202 A 1 HETATM 71 NI NI21 A1ICD . A . C 3 -6.545 -4.213 19.566 0.4 42.22 ? NI21 A1ICD 202 A 1 HETATM 72 NI NI21 A1ICD . B . C 3 -6.668 -3.643 19.512 0.3 108.09 ? NI21 A1ICD 202 A 1 HETATM 73 C C36 A1ICD . A . C 3 -4.595 -7.987 13.634 0.52 35.94 ? C36 A1ICD 202 A 1 HETATM 74 C C36 A1ICD . B . C 3 -4.706 -8.196 14.116 0.48 83.09 ? C36 A1ICD 202 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 74 #