data_1TKC # _model_server_result.job_id bYLID4MLvVA81yHT11PGaA _model_server_result.datetime_utc '2024-10-25 20:31:36' _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 1tkc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":681}' # _entry.id 1TKC # _exptl.entry_id 1TKC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 438.333 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6'-METHYL-THIAMIN DIPHOSPHATE" _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 1TKC _cell.length_a 76.3 _cell.length_b 113.3 _cell.length_c 160.9 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TKC _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F 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 metalc ? metalc1 A OD2 ASP 155 A ASP 157 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc2 A OD1 ASN 185 A ASN 187 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.776 ? metalc ? metalc3 A O ILE 187 A ILE 189 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc4 D O1B M6T . A M6T 681 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc5 D O2A M6T . A M6T 681 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc6 B OD2 ASP 155 B ASP 157 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc7 B OD1 ASN 185 B ASN 187 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.739 ? metalc ? metalc8 B ND2 ASN 185 B ASN 187 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.087 ? metalc ? metalc9 B O ILE 187 B ILE 189 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? metalc ? metalc10 F O2B M6T . B M6T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.673 ? metalc ? metalc11 F O3B M6T . B M6T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.075 ? metalc ? metalc12 F O2A M6T . B M6T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? # _chem_comp.formula 'C13 H20 N4 O7 P2 S' _chem_comp.formula_weight 438.333 _chem_comp.id M6T _chem_comp.mon_nstd_flag . _chem_comp.name "6'-METHYL-THIAMIN DIPHOSPHATE" _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 N1' C2' M6T doub 216 n y N1' C6' M6T sing 217 n y C2' CM2 M6T sing 218 n n C2' N3' M6T sing 219 n y CM2 HM21 M6T sing 220 n n CM2 HM22 M6T sing 221 n n CM2 HM23 M6T sing 222 n n N3' C4' M6T doub 223 n y C4' N4' M6T sing 224 n n C4' C5' M6T sing 225 n y N4' HN41 M6T sing 226 n n N4' HN42 M6T sing 227 n n C5' C6' M6T doub 228 n y C5' C7' M6T sing 229 n n C6' CM6 M6T sing 230 n n C7' N3 M6T sing 231 n n C7' "H7'1" M6T sing 232 n n C7' "H7'2" M6T sing 233 n n N3 C2 M6T doub 234 n y N3 C4 M6T sing 235 n y C2 S1 M6T sing 236 n y C2 H2 M6T sing 237 n n S1 C5 M6T sing 238 n y C5 C4 M6T doub 239 n y C5 C6 M6T sing 240 n n C4 CM4 M6T sing 241 n n CM4 HM41 M6T sing 242 n n CM4 HM42 M6T sing 243 n n CM4 HM43 M6T sing 244 n n CM6 HM61 M6T sing 245 n n CM6 HM62 M6T sing 246 n n CM6 HM63 M6T sing 247 n n C6 C7 M6T sing 248 n n C6 H61 M6T sing 249 n n C6 H62 M6T sing 250 n n C7 O7 M6T sing 251 n n C7 H71 M6T sing 252 n n C7 H72 M6T sing 253 n n O7 PA M6T sing 254 n n PA O1A M6T doub 255 n n PA O2A M6T sing 256 n n PA O3A M6T sing 257 n n O2A HOA2 M6T sing 258 n n O3A PB M6T sing 259 n n PB O1B M6T doub 260 n n PB O2B M6T sing 261 n n PB O3B M6T sing 262 n n O2B HOB2 M6T sing 263 n n # _atom_sites.entry_id 1TKC _atom_sites.fract_transf_matrix[1][1] 0.013106 _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] 0.008826 _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] 0.006215 _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 CA A 1 682 682 CA CA . D 3 M6T A 1 681 681 M6T M6T . E 2 CA B 1 682 682 CA CA . F 3 M6T B 1 681 681 M6T M6T . # 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 N N1' M6T . . . D 3 -3.111 60.821 20.064 1 15.84 ? N1' M6T 681 A 1 HETATM 2 C C2' M6T . . . D 3 -2.241 59.851 20.377 1 14 ? C2' M6T 681 A 1 HETATM 3 C CM2 M6T . . . D 3 -0.904 60.264 20.821 1 9.32 ? CM2 M6T 681 A 1 HETATM 4 N N3' M6T . . . D 3 -2.61 58.601 20.455 1 14.72 ? N3' M6T 681 A 1 HETATM 5 C C4' M6T . . . D 3 -3.82 58.246 19.937 1 17.33 ? C4' M6T 681 A 1 HETATM 6 N N4' M6T . . . D 3 -4.114 56.979 19.983 1 17.38 ? N4' M6T 681 A 1 HETATM 7 C C5' M6T . . . D 3 -4.752 59.221 19.507 1 18.39 ? C5' M6T 681 A 1 HETATM 8 C C6' M6T . . . D 3 -4.36 60.514 19.649 1 17.66 ? C6' M6T 681 A 1 HETATM 9 C C7' M6T . . . D 3 -6.164 58.86 19.091 1 23.61 ? C7' M6T 681 A 1 HETATM 10 N N3 M6T . . . D 3 -6.131 58.143 17.771 1 30.15 ? N3 M6T 681 A 1 HETATM 11 C C2 M6T . . . D 3 -6.314 56.819 17.651 1 32.23 ? C2 M6T 681 A 1 HETATM 12 S S1 M6T . . . D 3 -6.236 56.302 16.038 1 32.96 ? S1 M6T 681 A 1 HETATM 13 C C5 M6T . . . D 3 -5.78 57.903 15.589 1 31.14 ? C5 M6T 681 A 1 HETATM 14 C C4 M6T . . . D 3 -6.054 58.771 16.598 1 29.98 ? C4 M6T 681 A 1 HETATM 15 C CM4 M6T . . . D 3 -6.081 60.252 16.493 1 27.44 ? CM4 M6T 681 A 1 HETATM 16 C CM6 M6T . . . D 3 -5.313 61.635 19.5 1 18.28 ? CM6 M6T 681 A 1 HETATM 17 C C6 M6T . . . D 3 -5.428 58.238 14.172 1 31.26 ? C6 M6T 681 A 1 HETATM 18 C C7 M6T . . . D 3 -5.406 57.028 13.261 1 27.62 ? C7 M6T 681 A 1 HETATM 19 O O7 M6T . . . D 3 -4.817 57.396 12.008 1 22.38 ? O7 M6T 681 A 1 HETATM 20 P PA M6T . . . D 3 -3.879 56.364 11.329 1 22.79 ? PA M6T 681 A 1 HETATM 21 O O1A M6T . . . D 3 -2.562 56.207 11.978 1 18.33 ? O1A M6T 681 A 1 HETATM 22 O O2A M6T . . . D 3 -3.786 56.806 9.899 1 20.49 ? O2A M6T 681 A 1 HETATM 23 O O3A M6T . . . D 3 -4.584 54.927 11.282 1 20.77 ? O3A M6T 681 A 1 HETATM 24 P PB M6T . . . D 3 -5.484 54.175 10.222 1 19.84 ? PB M6T 681 A 1 HETATM 25 O O1B M6T . . . D 3 -4.744 54.46 8.95 1 28.32 ? O1B M6T 681 A 1 HETATM 26 O O2B M6T . . . D 3 -6.72 54.939 10.34 1 21.44 ? O2B M6T 681 A 1 HETATM 27 O O3B M6T . . . D 3 -5.596 52.773 10.596 1 23.41 ? O3B M6T 681 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #