data_1TKB # _model_server_result.job_id 32V-nXNGW4Jo7SlwM0AV4w _model_server_result.datetime_utc '2024-11-22 10:51:16' _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 1tkb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":681}' # _entry.id 1TKB # _exptl.entry_id 1TKB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 423.318 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "1'-DEAZO-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 1TKB _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 1TKB _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc2 A ND2 ASN 185 A ASN 187 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.254 ? metalc ? metalc3 A OD1 ASN 185 A ASN 187 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? metalc ? metalc4 A O ILE 187 A ILE 189 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc5 D O1B N1T . A N1T 681 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.669 ? metalc ? metalc6 D O2A N1T . A N1T 681 1_555 C CA CA . A CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc7 B OD2 ASP 155 B ASP 157 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc8 B OD1 ASN 185 B ASN 187 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? metalc ? metalc9 B ND2 ASN 185 B ASN 187 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.159 ? metalc ? metalc10 B O ILE 187 B ILE 189 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc11 F O2B N1T . B N1T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.71 ? metalc ? metalc12 F O3B N1T . B N1T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.173 ? metalc ? metalc13 F O3A N1T . B N1T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.33 ? metalc ? metalc14 F O2A N1T . B N1T 681 1_555 E CA CA . B CA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? # _chem_comp.formula 'C13 H19 N3 O7 P2 S' _chem_comp.formula_weight 423.318 _chem_comp.id N1T _chem_comp.mon_nstd_flag . _chem_comp.name "1'-DEAZO-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 C1' C2' N1T sing 235 n y C1' C6' N1T doub 236 n y C1' H1' N1T sing 237 n n C2' CM2 N1T sing 238 n n C2' N3' N1T doub 239 n y CM2 HM21 N1T sing 240 n n CM2 HM22 N1T sing 241 n n CM2 HM23 N1T sing 242 n n N3' C4' N1T sing 243 n y C4' N4' N1T sing 244 n n C4' C5' N1T doub 245 n y N4' HN41 N1T sing 246 n n N4' HN42 N1T sing 247 n n C5' C6' N1T sing 248 n y C5' C7' N1T sing 249 n n C6' H6' N1T sing 250 n n C7' N3 N1T sing 251 n n C7' "H7'1" N1T sing 252 n n C7' "H7'2" N1T sing 253 n n N3 C2 N1T doub 254 n y N3 C4 N1T sing 255 n y C2 S1 N1T sing 256 n y C2 H2 N1T sing 257 n n S1 C5 N1T sing 258 n y C5 C4 N1T doub 259 n y C5 C6 N1T sing 260 n n C4 CM4 N1T sing 261 n n CM4 HM41 N1T sing 262 n n CM4 HM42 N1T sing 263 n n CM4 HM43 N1T sing 264 n n C6 C7 N1T sing 265 n n C6 H61 N1T sing 266 n n C6 H62 N1T sing 267 n n C7 O7 N1T sing 268 n n C7 H71 N1T sing 269 n n C7 H72 N1T sing 270 n n O7 PA N1T sing 271 n n PA O1A N1T doub 272 n n PA O2A N1T sing 273 n n PA O3A N1T sing 274 n n O2A HOA2 N1T sing 275 n n O3A PB N1T sing 276 n n PB O1B N1T doub 277 n n PB O2B N1T sing 278 n n PB O3B N1T sing 279 n n O3B HOB3 N1T sing 280 n n # _atom_sites.entry_id 1TKB _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 N1T A 1 681 681 N1T N1T . E 2 CA B 1 682 682 CA CA . F 3 N1T B 1 681 681 N1T N1T . # 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 C1' N1T . . . D 3 -3.342 60.818 20.002 1 4.19 ? C1' N1T 681 A 1 HETATM 2 C C2' N1T . . . D 3 -2.303 59.828 20.192 1 2.47 ? C2' N1T 681 A 1 HETATM 3 C CM2 N1T . . . D 3 -0.979 60.27 20.655 1 2 ? CM2 N1T 681 A 1 HETATM 4 N N3' N1T . . . D 3 -2.632 58.53 20.139 1 6.25 ? N3' N1T 681 A 1 HETATM 5 C C4' N1T . . . D 3 -3.914 58.154 19.809 1 7.56 ? C4' N1T 681 A 1 HETATM 6 N N4' N1T . . . D 3 -4.104 56.839 19.727 1 4.74 ? N4' N1T 681 A 1 HETATM 7 C C5' N1T . . . D 3 -4.891 59.087 19.325 1 4.52 ? C5' N1T 681 A 1 HETATM 8 C C6' N1T . . . D 3 -4.662 60.377 19.556 1 3.17 ? C6' N1T 681 A 1 HETATM 9 C C7' N1T . . . D 3 -6.176 58.682 18.679 1 7.87 ? C7' N1T 681 A 1 HETATM 10 N N3 N1T . . . D 3 -5.898 58.128 17.298 1 16.46 ? N3 N1T 681 A 1 HETATM 11 C C2 N1T . . . D 3 -5.797 56.827 17.049 1 18.35 ? C2 N1T 681 A 1 HETATM 12 S S1 N1T . . . D 3 -5.396 56.474 15.464 1 17.9 ? S1 N1T 681 A 1 HETATM 13 C C5 N1T . . . D 3 -5.39 58.135 15.112 1 19.93 ? C5 N1T 681 A 1 HETATM 14 C C4 N1T . . . D 3 -5.714 58.887 16.221 1 18.14 ? C4 N1T 681 A 1 HETATM 15 C CM4 N1T . . . D 3 -5.833 60.387 16.289 1 15.94 ? CM4 N1T 681 A 1 HETATM 16 C C6 N1T . . . D 3 -5.106 58.594 13.712 1 20.15 ? C6 N1T 681 A 1 HETATM 17 C C7 N1T . . . D 3 -5.603 57.571 12.742 1 19.82 ? C7 N1T 681 A 1 HETATM 18 O O7 N1T . . . D 3 -4.608 57.585 11.728 1 18.47 ? O7 N1T 681 A 1 HETATM 19 P PA N1T . . . D 3 -3.783 56.302 11.342 1 11.28 ? PA N1T 681 A 1 HETATM 20 O O1A N1T . . . D 3 -2.532 56.048 12.102 1 17.13 ? O1A N1T 681 A 1 HETATM 21 O O2A N1T . . . D 3 -3.502 56.665 9.905 1 19.41 ? O2A N1T 681 A 1 HETATM 22 O O3A N1T . . . D 3 -4.812 55.112 11.351 1 12.69 ? O3A N1T 681 A 1 HETATM 23 P PB N1T . . . D 3 -5.527 54.344 10.198 1 13.24 ? PB N1T 681 A 1 HETATM 24 O O1B N1T . . . D 3 -4.692 54.632 8.984 1 23.16 ? O1B N1T 681 A 1 HETATM 25 O O2B N1T . . . D 3 -6.863 54.942 10.082 1 12.86 ? O2B N1T 681 A 1 HETATM 26 O O3B N1T . . . D 3 -5.525 52.978 10.663 1 15.29 ? O3B N1T 681 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #