data_3FBC # _model_server_result.job_id OinQsxdNdhkOXu7hE5Ms4A _model_server_result.datetime_utc '2025-07-25 14:15:39' _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 3fbc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":138}' # _entry.id 3FBC # _exptl.entry_id 3FBC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 3FBC _cell.length_a 80.387 _cell.length_b 153.337 _cell.length_c 185.384 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3FBC _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,G,H,I,M,N,O,S,T,U,Y,AA,CA 1 1,2 B,D,F,J,K,L,P,Q,R,V,W,X,Z,BA,DA 2 1,3 # 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 3_755 -x+2,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 160.774 0 92.692 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 H N N ? 3 K N N ? 3 N N N ? 3 Q N N ? 3 T N N ? 3 W N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id N _struct_conn.ptnr1_label_atom_id O2B _struct_conn.ptnr1_label_comp_id TYD _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id C _struct_conn.ptnr1_auth_comp_id TYD _struct_conn.ptnr1_auth_seq_id 138 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id M _struct_conn.ptnr2_label_atom_id MG _struct_conn.ptnr2_label_comp_id MG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id C _struct_conn.ptnr2_auth_comp_id MG _struct_conn.ptnr2_auth_seq_id 162 _struct_conn.ptnr2_symmetry 1_555 _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 2.275 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-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 PA O1A TYD doub 338 n n PA O2A TYD sing 339 n n PA O3A TYD sing 340 n n PA O5' TYD sing 341 n n O2A HOA2 TYD sing 342 n n O3A PB TYD sing 343 n n PB O1B TYD doub 344 n n PB O2B TYD sing 345 n n PB O3B TYD sing 346 n n O2B HOB2 TYD sing 347 n n O3B HOB3 TYD sing 348 n n O5' C5' TYD sing 349 n n C5' C4' TYD sing 350 n n C5' "H5'1" TYD sing 351 n n C5' "H5'2" TYD sing 352 n n C4' O4' TYD sing 353 n n C4' C3' TYD sing 354 n n C4' H4' TYD sing 355 n n O4' C1' TYD sing 356 n n C3' O3' TYD sing 357 n n C3' C2' TYD sing 358 n n C3' H3' TYD sing 359 n n O3' HO3' TYD sing 360 n n C2' C1' TYD sing 361 n n C2' "H2'1" TYD sing 362 n n C2' "H2'2" TYD sing 363 n n C1' N1 TYD sing 364 n n C1' H1' TYD sing 365 n n N1 C2 TYD sing 366 n y N1 C6 TYD sing 367 n y C2 O2 TYD doub 368 n n C2 N3 TYD sing 369 n y N3 C4 TYD sing 370 n y N3 HN3 TYD sing 371 n n C4 O4 TYD doub 372 n n C4 C5 TYD sing 373 n y C5 C5M TYD sing 374 n n C5 C6 TYD doub 375 n y C5M H51 TYD sing 376 n n C5M H52 TYD sing 377 n n C5M H53 TYD sing 378 n n C6 H6 TYD sing 379 n n # _atom_sites.entry_id 3FBC _atom_sites.fract_transf_matrix[1][1] 0.01244 _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] 0.006522 _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] 0.005394 _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 G 2 MG A 1 160 160 MG MG . H 3 TYD A 1 138 160 TYD TYD . I 4 PO4 A 1 139 2 PO4 PO4 . J 2 MG B 1 161 161 MG MG . K 3 TYD B 1 138 161 TYD TYD . L 4 PO4 B 1 139 3 PO4 PO4 . M 2 MG C 1 162 162 MG MG . N 3 TYD C 1 138 162 TYD TYD . O 4 PO4 C 1 139 4 PO4 PO4 . P 2 MG D 1 163 163 MG MG . Q 3 TYD D 1 138 163 TYD TYD . R 4 PO4 D 1 139 5 PO4 PO4 . S 2 MG E 1 164 164 MG MG . T 3 TYD E 1 138 164 TYD TYD . U 4 PO4 E 1 139 1 PO4 PO4 . V 2 MG F 1 165 165 MG MG . W 3 TYD F 1 138 165 TYD TYD . X 4 PO4 F 1 139 6 PO4 PO4 . Y 5 HOH A 1 140 3 HOH HOH . Y 5 HOH A 2 141 5 HOH HOH . Y 5 HOH A 3 142 7 HOH HOH . Y 5 HOH A 4 143 9 HOH HOH . Y 5 HOH A 5 144 10 HOH HOH . Y 5 HOH A 6 145 15 HOH HOH . Y 5 HOH A 7 146 23 HOH HOH . Y 5 HOH A 8 147 24 HOH HOH . Y 5 HOH A 9 148 25 HOH HOH . Y 5 HOH A 10 149 26 HOH HOH . Y 5 HOH A 11 150 39 HOH HOH . Y 5 HOH A 12 151 40 HOH HOH . Y 5 HOH A 13 152 57 HOH HOH . Y 5 HOH A 14 153 73 HOH HOH . Y 5 HOH A 15 154 85 HOH HOH . Y 5 HOH A 16 155 99 HOH HOH . Y 5 HOH A 17 156 102 HOH HOH . Y 5 HOH A 18 157 104 HOH HOH . Y 5 HOH A 19 158 105 HOH HOH . Z 5 HOH B 1 140 30 HOH HOH . Z 5 HOH B 2 141 31 HOH HOH . Z 5 HOH B 3 142 32 HOH HOH . Z 5 HOH B 4 143 42 HOH HOH . Z 5 HOH B 5 144 49 HOH HOH . Z 5 HOH B 6 145 56 HOH HOH . Z 5 HOH B 7 146 59 HOH HOH . Z 5 HOH B 8 147 62 HOH HOH . Z 5 HOH B 9 148 64 HOH HOH . Z 5 HOH B 10 149 92 HOH HOH . Z 5 HOH B 11 150 93 HOH HOH . Z 5 HOH B 12 151 98 HOH HOH . Z 5 HOH B 13 152 101 HOH HOH . AA 5 HOH C 1 140 4 HOH HOH . AA 5 HOH C 2 141 6 HOH HOH . AA 5 HOH C 3 142 8 HOH HOH . AA 5 HOH C 4 143 11 HOH HOH . AA 5 HOH C 5 144 12 HOH HOH . AA 5 HOH C 6 145 14 HOH HOH . AA 5 HOH C 7 146 17 HOH HOH . AA 5 HOH C 8 147 18 HOH HOH . AA 5 HOH C 9 148 21 HOH HOH . AA 5 HOH C 10 149 22 HOH HOH . AA 5 HOH C 11 150 33 HOH HOH . AA 5 HOH C 12 151 34 HOH HOH . AA 5 HOH C 13 152 67 HOH HOH . AA 5 HOH C 14 153 68 HOH HOH . AA 5 HOH C 15 154 69 HOH HOH . AA 5 HOH C 16 155 70 HOH HOH . AA 5 HOH C 17 156 71 HOH HOH . AA 5 HOH C 18 157 72 HOH HOH . AA 5 HOH C 19 158 74 HOH HOH . AA 5 HOH C 20 159 81 HOH HOH . AA 5 HOH C 21 160 84 HOH HOH . AA 5 HOH C 22 161 87 HOH HOH . AA 5 HOH C 23 163 89 HOH HOH . AA 5 HOH C 24 164 95 HOH HOH . BA 5 HOH D 1 140 37 HOH HOH . BA 5 HOH D 2 141 38 HOH HOH . BA 5 HOH D 3 142 41 HOH HOH . BA 5 HOH D 4 143 43 HOH HOH . BA 5 HOH D 5 144 45 HOH HOH . BA 5 HOH D 6 145 52 HOH HOH . BA 5 HOH D 7 146 53 HOH HOH . BA 5 HOH D 8 147 58 HOH HOH . BA 5 HOH D 9 148 75 HOH HOH . BA 5 HOH D 10 149 76 HOH HOH . BA 5 HOH D 11 150 77 HOH HOH . BA 5 HOH D 12 151 78 HOH HOH . BA 5 HOH D 13 152 79 HOH HOH . BA 5 HOH D 14 153 80 HOH HOH . BA 5 HOH D 15 154 88 HOH HOH . BA 5 HOH D 16 155 90 HOH HOH . BA 5 HOH D 17 156 100 HOH HOH . BA 5 HOH D 18 157 103 HOH HOH . CA 5 HOH E 1 140 1 HOH HOH . CA 5 HOH E 2 141 16 HOH HOH . CA 5 HOH E 3 142 19 HOH HOH . CA 5 HOH E 4 143 28 HOH HOH . CA 5 HOH E 5 144 29 HOH HOH . CA 5 HOH E 6 145 35 HOH HOH . CA 5 HOH E 7 146 36 HOH HOH . CA 5 HOH E 8 147 47 HOH HOH . CA 5 HOH E 9 148 48 HOH HOH . CA 5 HOH E 10 149 50 HOH HOH . CA 5 HOH E 11 150 51 HOH HOH . CA 5 HOH E 12 151 55 HOH HOH . CA 5 HOH E 13 152 60 HOH HOH . CA 5 HOH E 14 153 65 HOH HOH . CA 5 HOH E 15 154 66 HOH HOH . CA 5 HOH E 16 155 91 HOH HOH . CA 5 HOH E 17 156 96 HOH HOH . CA 5 HOH E 18 157 106 HOH HOH . DA 5 HOH F 1 140 2 HOH HOH . DA 5 HOH F 2 141 13 HOH HOH . DA 5 HOH F 3 142 20 HOH HOH . DA 5 HOH F 4 143 27 HOH HOH . DA 5 HOH F 5 144 44 HOH HOH . DA 5 HOH F 6 145 46 HOH HOH . DA 5 HOH F 7 146 54 HOH HOH . DA 5 HOH F 8 147 61 HOH HOH . DA 5 HOH F 9 148 63 HOH HOH . DA 5 HOH F 10 149 82 HOH HOH . DA 5 HOH F 11 150 83 HOH HOH . DA 5 HOH F 12 151 86 HOH HOH . DA 5 HOH F 13 152 94 HOH HOH . DA 5 HOH F 14 153 97 HOH HOH . DA 5 HOH F 15 154 107 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 P PA TYD . . . T 3 22.818 15.109 18.066 1 122.13 ? PA TYD 138 E 1 HETATM 2 O O1A TYD . . . T 3 24.148 15.559 17.499 1 107.94 ? O1A TYD 138 E 1 HETATM 3 O O2A TYD . . . T 3 22.15 15.942 19.146 1 104.24 ? O2A TYD 138 E 1 HETATM 4 O O3A TYD . . . T 3 21.745 14.882 16.862 1 116.48 ? O3A TYD 138 E 1 HETATM 5 P PB TYD . . . T 3 22.051 14.448 15.32 1 109.82 ? PB TYD 138 E 1 HETATM 6 O O1B TYD . . . T 3 22.031 12.933 15.326 1 87.01 ? O1B TYD 138 E 1 HETATM 7 O O2B TYD . . . T 3 23.404 15.007 14.947 1 106.01 ? O2B TYD 138 E 1 HETATM 8 O O3B TYD . . . T 3 20.896 15.084 14.58 1 90.48 ? O3B TYD 138 E 1 HETATM 9 O O5' TYD . . . T 3 22.976 13.608 18.642 1 110.05 ? O5' TYD 138 E 1 HETATM 10 C C5' TYD . . . T 3 23.89 12.701 18.015 1 97.7 ? C5' TYD 138 E 1 HETATM 11 C C4' TYD . . . T 3 23.939 11.366 18.754 1 95.77 ? C4' TYD 138 E 1 HETATM 12 O O4' TYD . . . T 3 24.246 11.629 20.126 1 95.06 ? O4' TYD 138 E 1 HETATM 13 C C3' TYD . . . T 3 22.614 10.611 18.703 1 89.82 ? C3' TYD 138 E 1 HETATM 14 O O3' TYD . . . T 3 22.696 9.494 17.808 1 76.73 ? O3' TYD 138 E 1 HETATM 15 C C2' TYD . . . T 3 22.385 10.122 20.122 1 95.05 ? C2' TYD 138 E 1 HETATM 16 C C1' TYD . . . T 3 23.358 10.917 20.99 1 96.86 ? C1' TYD 138 E 1 HETATM 17 N N1 TYD . . . T 3 22.662 11.87 21.864 1 99.98 ? N1 TYD 138 E 1 HETATM 18 C C2 TYD . . . T 3 22.063 11.395 23.054 1 98.71 ? C2 TYD 138 E 1 HETATM 19 O O2 TYD . . . T 3 22.132 10.176 23.326 1 100.26 ? O2 TYD 138 E 1 HETATM 20 N N3 TYD . . . T 3 21.422 12.226 23.889 1 101.84 ? N3 TYD 138 E 1 HETATM 21 C C4 TYD . . . T 3 21.337 13.538 23.621 1 109.91 ? C4 TYD 138 E 1 HETATM 22 O O4 TYD . . . T 3 20.738 14.311 24.406 1 116.72 ? O4 TYD 138 E 1 HETATM 23 C C5 TYD . . . T 3 21.962 14.069 22.38 1 105.62 ? C5 TYD 138 E 1 HETATM 24 C C5M TYD . . . T 3 21.883 15.541 22.052 1 106.5 ? C5M TYD 138 E 1 HETATM 25 C C6 TYD . . . T 3 22.621 13.175 21.541 1 101.28 ? C6 TYD 138 E 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 230 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #