data_1CY1 # _model_server_result.job_id zHcxEQvTE0EwoHlqGPHw3A _model_server_result.datetime_utc '2024-12-26 19:35:22' _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 1cy1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 1CY1 # _exptl.entry_id 1CY1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-3',5'-DIPHOSPHATE" _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 1CY1 _cell.length_a 62.86 _cell.length_b 77.8 _cell.length_c 138.66 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CY1 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id THP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-3',5'-DIPHOSPHATE" _chem_comp.type 'dna linking' _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 P2 O4P THP doub 294 n n P2 O5P THP sing 295 n n P2 O6P THP sing 296 n n P2 O5' THP sing 297 n n O5P HOP5 THP sing 298 n n O6P HOP6 THP sing 299 n n P1 O1P THP doub 300 n n P1 O2P THP sing 301 n n P1 O3P THP sing 302 n n P1 O3' THP sing 303 n n O2P HOP2 THP sing 304 n n O3P HOP3 THP sing 305 n n O5' C5' THP sing 306 n n C5' C4' THP sing 307 n n C5' "H5'1" THP sing 308 n n C5' "H5'2" THP sing 309 n n C4' O4' THP sing 310 n n C4' C3' THP sing 311 n n C4' H4' THP sing 312 n n O4' C1' THP sing 313 n n C3' O3' THP sing 314 n n C3' C2' THP sing 315 n n C3' H3' THP sing 316 n n C2' C1' THP sing 317 n n C2' "H2'1" THP sing 318 n n C2' "H2'2" THP sing 319 n n C1' N1 THP sing 320 n n C1' H1' THP sing 321 n n N1 C2 THP sing 322 n n N1 C6 THP sing 323 n n C2 O2 THP doub 324 n n C2 N3 THP sing 325 n n N3 C4 THP sing 326 n n N3 H3 THP sing 327 n n C4 O4 THP doub 328 n n C4 C5 THP sing 329 n n C5 C5M THP sing 330 n n C5 C6 THP doub 331 n n C5M H51 THP sing 332 n n C5M H52 THP sing 333 n n C5M H53 THP sing 334 n n C6 H6 THP sing 335 n n # _atom_sites.entry_id 1CY1 _atom_sites.fract_transf_matrix[1][1] 0.015908 _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] 0.012853 _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] 0.007212 _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 PO4 A 1 700 700 PO4 PO4 . C 3 TMP A 1 600 600 TMP TMP . D 4 THP A 1 601 601 THP THP . E 3 TMP A 1 602 602 TMP TMP . F 5 HOH A 1 701 1 HOH HOH . F 5 HOH A 2 702 2 HOH HOH . F 5 HOH A 3 703 3 HOH HOH . F 5 HOH A 4 704 4 HOH HOH . F 5 HOH A 5 705 5 HOH HOH . F 5 HOH A 6 706 6 HOH HOH . F 5 HOH A 7 707 7 HOH HOH . F 5 HOH A 8 708 8 HOH HOH . F 5 HOH A 9 709 9 HOH HOH . F 5 HOH A 10 710 10 HOH HOH . F 5 HOH A 11 711 11 HOH HOH . F 5 HOH A 12 712 12 HOH HOH . F 5 HOH A 13 713 13 HOH HOH . F 5 HOH A 14 714 14 HOH HOH . F 5 HOH A 15 715 15 HOH HOH . F 5 HOH A 16 716 16 HOH HOH . F 5 HOH A 17 717 17 HOH HOH . F 5 HOH A 18 718 18 HOH HOH . F 5 HOH A 19 719 19 HOH HOH . F 5 HOH A 20 720 20 HOH HOH . F 5 HOH A 21 721 21 HOH HOH . F 5 HOH A 22 722 22 HOH HOH . F 5 HOH A 23 723 23 HOH HOH . F 5 HOH A 24 724 24 HOH HOH . F 5 HOH A 25 725 25 HOH HOH . F 5 HOH A 26 726 26 HOH HOH . F 5 HOH A 27 727 27 HOH HOH . F 5 HOH A 28 728 28 HOH HOH . F 5 HOH A 29 729 29 HOH HOH . F 5 HOH A 30 730 30 HOH HOH . F 5 HOH A 31 731 31 HOH HOH . F 5 HOH A 32 732 32 HOH HOH . F 5 HOH A 33 733 33 HOH HOH . F 5 HOH A 34 734 34 HOH HOH . F 5 HOH A 35 735 35 HOH HOH . F 5 HOH A 36 736 36 HOH HOH . F 5 HOH A 37 737 37 HOH HOH . F 5 HOH A 38 738 38 HOH HOH . F 5 HOH A 39 739 39 HOH HOH . F 5 HOH A 40 740 40 HOH HOH . F 5 HOH A 41 741 41 HOH HOH . F 5 HOH A 42 742 42 HOH HOH . F 5 HOH A 43 743 43 HOH HOH . F 5 HOH A 44 744 44 HOH HOH . F 5 HOH A 45 745 45 HOH HOH . F 5 HOH A 46 746 46 HOH HOH . F 5 HOH A 47 747 47 HOH HOH . F 5 HOH A 48 748 48 HOH HOH . F 5 HOH A 49 749 49 HOH HOH . F 5 HOH A 50 750 50 HOH HOH . F 5 HOH A 51 751 51 HOH HOH . F 5 HOH A 52 752 52 HOH HOH . F 5 HOH A 53 753 53 HOH HOH . F 5 HOH A 54 754 54 HOH HOH . F 5 HOH A 55 755 55 HOH HOH . F 5 HOH A 56 756 56 HOH HOH . F 5 HOH A 57 757 57 HOH HOH . F 5 HOH A 58 758 58 HOH HOH . F 5 HOH A 59 759 59 HOH HOH . F 5 HOH A 60 760 60 HOH HOH . F 5 HOH A 61 761 61 HOH HOH . F 5 HOH A 62 762 62 HOH HOH . F 5 HOH A 63 763 63 HOH HOH . F 5 HOH A 64 764 64 HOH HOH . F 5 HOH A 65 765 65 HOH HOH . F 5 HOH A 66 766 66 HOH HOH . F 5 HOH A 67 767 67 HOH HOH . F 5 HOH A 68 768 68 HOH HOH . F 5 HOH A 69 769 69 HOH HOH . F 5 HOH A 70 770 70 HOH HOH . F 5 HOH A 71 771 71 HOH HOH . F 5 HOH A 72 772 72 HOH HOH . F 5 HOH A 73 773 73 HOH HOH . F 5 HOH A 74 774 74 HOH HOH . F 5 HOH A 75 775 75 HOH HOH . F 5 HOH A 76 776 76 HOH HOH . F 5 HOH A 77 777 77 HOH HOH . F 5 HOH A 78 778 78 HOH HOH . F 5 HOH A 79 779 79 HOH HOH . F 5 HOH A 80 780 80 HOH HOH . F 5 HOH A 81 781 81 HOH HOH . F 5 HOH A 82 782 82 HOH HOH . F 5 HOH A 83 783 83 HOH HOH . F 5 HOH A 84 784 84 HOH HOH . F 5 HOH A 85 785 85 HOH HOH . F 5 HOH A 86 786 86 HOH HOH . F 5 HOH A 87 787 87 HOH HOH . F 5 HOH A 88 788 88 HOH HOH . F 5 HOH A 89 789 89 HOH HOH . F 5 HOH A 90 790 90 HOH HOH . F 5 HOH A 91 791 91 HOH HOH . F 5 HOH A 92 792 92 HOH HOH . F 5 HOH A 93 793 93 HOH HOH . F 5 HOH A 94 794 94 HOH HOH . F 5 HOH A 95 795 95 HOH HOH . F 5 HOH A 96 796 96 HOH HOH . F 5 HOH A 97 797 97 HOH HOH . F 5 HOH A 98 798 98 HOH HOH . F 5 HOH A 99 799 99 HOH HOH . F 5 HOH A 100 800 100 HOH HOH . F 5 HOH A 101 801 101 HOH HOH . F 5 HOH A 102 802 102 HOH HOH . F 5 HOH A 103 803 103 HOH HOH . F 5 HOH A 104 804 104 HOH HOH . F 5 HOH A 105 805 105 HOH HOH . F 5 HOH A 106 806 106 HOH HOH . F 5 HOH A 107 807 107 HOH HOH . F 5 HOH A 108 808 108 HOH HOH . F 5 HOH A 109 809 109 HOH HOH . F 5 HOH A 110 810 110 HOH HOH . F 5 HOH A 111 811 111 HOH HOH . F 5 HOH A 112 812 112 HOH HOH . F 5 HOH A 113 813 113 HOH HOH . F 5 HOH A 114 814 114 HOH HOH . F 5 HOH A 115 815 115 HOH HOH . F 5 HOH A 116 816 116 HOH HOH . F 5 HOH A 117 817 117 HOH HOH . F 5 HOH A 118 818 118 HOH HOH . F 5 HOH A 119 819 119 HOH HOH . F 5 HOH A 120 820 120 HOH HOH . F 5 HOH A 121 821 121 HOH HOH . F 5 HOH A 122 822 122 HOH HOH . F 5 HOH A 123 823 123 HOH HOH . F 5 HOH A 124 824 124 HOH HOH . F 5 HOH A 125 825 125 HOH HOH . F 5 HOH A 126 826 126 HOH HOH . F 5 HOH A 127 827 127 HOH HOH . F 5 HOH A 128 828 128 HOH HOH . F 5 HOH A 129 829 129 HOH HOH . F 5 HOH A 130 830 130 HOH HOH . F 5 HOH A 131 831 131 HOH HOH . F 5 HOH A 132 832 132 HOH HOH . F 5 HOH A 133 833 133 HOH HOH . F 5 HOH A 134 834 134 HOH HOH . F 5 HOH A 135 835 135 HOH HOH . F 5 HOH A 136 836 136 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 P2 THP . . . D 4 34.444 32.084 21.306 0.7 47.25 ? P2 THP 601 A 1 HETATM 2 O O4P THP . . . D 4 35.175 33.333 21.743 0.7 45.58 ? O4P THP 601 A 1 HETATM 3 O O5P THP . . . D 4 33.717 31.293 22.297 0.7 48.44 ? O5P THP 601 A 1 HETATM 4 O O6P THP . . . D 4 35.379 31.206 20.562 0.7 48.69 ? O6P THP 601 A 1 HETATM 5 P P1 THP . . . D 4 33.131 34.062 14.429 0.7 44.92 ? P1 THP 601 A 1 HETATM 6 O O1P THP . . . D 4 33.94 35.283 14.319 0.7 43.11 ? O1P THP 601 A 1 HETATM 7 O O2P THP . . . D 4 32.036 33.616 13.543 0.7 45.06 ? O2P THP 601 A 1 HETATM 8 O O3P THP . . . D 4 34.16 32.836 14.52 0.7 45.06 ? O3P THP 601 A 1 HETATM 9 O O5' THP . . . D 4 33.41 32.491 20.169 0.7 46.87 ? O5' THP 601 A 1 HETATM 10 C C5' THP . . . D 4 33.876 33.076 18.988 0.7 45.85 ? C5' THP 601 A 1 HETATM 11 C C4' THP . . . D 4 32.718 33.578 18.16 0.7 44.73 ? C4' THP 601 A 1 HETATM 12 O O4' THP . . . D 4 31.85 34.416 18.932 0.7 43.56 ? O4' THP 601 A 1 HETATM 13 C C3' THP . . . D 4 33.248 34.414 17.05 0.7 44.15 ? C3' THP 601 A 1 HETATM 14 O O3' THP . . . D 4 32.462 34.235 15.88 0.7 44.17 ? O3' THP 601 A 1 HETATM 15 C C2' THP . . . D 4 33.202 35.833 17.538 0.7 43.69 ? C2' THP 601 A 1 HETATM 16 C C1' THP . . . D 4 32.014 35.785 18.503 0.7 43.4 ? C1' THP 601 A 1 HETATM 17 N N1 THP . . . D 4 32.29 36.699 19.664 0.7 43.67 ? N1 THP 601 A 1 HETATM 18 C C2 THP . . . D 4 32.513 38.085 19.418 0.7 43.2 ? C2 THP 601 A 1 HETATM 19 O O2 THP . . . D 4 32.353 38.639 18.337 0.7 43.22 ? O2 THP 601 A 1 HETATM 20 N N3 THP . . . D 4 32.936 38.836 20.497 0.7 43.44 ? N3 THP 601 A 1 HETATM 21 C C4 THP . . . D 4 33.148 38.364 21.794 0.7 42.91 ? C4 THP 601 A 1 HETATM 22 O O4 THP . . . D 4 33.558 39.162 22.629 0.7 42.55 ? O4 THP 601 A 1 HETATM 23 C C5 THP . . . D 4 32.906 36.926 22.001 0.7 43.46 ? C5 THP 601 A 1 HETATM 24 C C5M THP . . . D 4 33.051 36.289 23.402 0.7 42.71 ? C5M THP 601 A 1 HETATM 25 C C6 THP . . . D 4 32.487 36.168 20.955 0.7 43.06 ? C6 THP 601 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #