data_1CY7 # _model_server_result.job_id TJMkgy2o3zvY1ZqCHH2VPQ _model_server_result.datetime_utc '2024-12-06 00:42:02' _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 1cy7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 1CY7 # _exptl.entry_id 1CY7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 1CY7 _cell.length_a 63.83 _cell.length_b 79.37 _cell.length_c 141.7 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1CY7 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-PHOSPHATE" _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 P O1P TMP doub 310 n n P O2P TMP sing 311 n n P O3P TMP sing 312 n n P O5' TMP sing 313 n n O2P HOP2 TMP sing 314 n n O3P HOP3 TMP sing 315 n n O5' C5' TMP sing 316 n n C5' C4' TMP sing 317 n n C5' "H5'1" TMP sing 318 n n C5' "H5'2" TMP sing 319 n n C4' O4' TMP sing 320 n n C4' C3' TMP sing 321 n n C4' H4' TMP sing 322 n n O4' C1' TMP sing 323 n n C3' O3' TMP sing 324 n n C3' C2' TMP sing 325 n n C3' H3' TMP sing 326 n n O3' HO3' TMP sing 327 n n C2' C1' TMP sing 328 n n C2' "H2'1" TMP sing 329 n n C2' "H2'2" TMP sing 330 n n C1' N1 TMP sing 331 n n C1' H1' TMP sing 332 n n N1 C2 TMP sing 333 n n N1 C6 TMP sing 334 n n C2 O2 TMP doub 335 n n C2 N3 TMP sing 336 n n N3 C4 TMP sing 337 n n N3 HN3 TMP sing 338 n n C4 O4 TMP doub 339 n n C4 C5 TMP sing 340 n n C5 C5M TMP sing 341 n n C5 C6 TMP doub 342 n n C5M H51 TMP sing 343 n n C5M H52 TMP sing 344 n n C5M H53 TMP sing 345 n n C6 H6 TMP sing 346 n n # _atom_sites.entry_id 1CY7 _atom_sites.fract_transf_matrix[1][1] 0.015667 _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] 0.012599 _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] 0.007057 _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 3 TMP A 1 601 601 TMP TMP . E 3 TMP A 1 602 602 TMP TMP . F 4 HOH A 1 701 1 HOH HOH . F 4 HOH A 2 702 2 HOH HOH . F 4 HOH A 3 703 3 HOH HOH . F 4 HOH A 4 704 4 HOH HOH . F 4 HOH A 5 705 5 HOH HOH . F 4 HOH A 6 706 6 HOH HOH . F 4 HOH A 7 707 7 HOH HOH . F 4 HOH A 8 708 8 HOH HOH . F 4 HOH A 9 709 9 HOH HOH . F 4 HOH A 10 710 10 HOH HOH . F 4 HOH A 11 711 11 HOH HOH . F 4 HOH A 12 712 12 HOH HOH . F 4 HOH A 13 713 13 HOH HOH . F 4 HOH A 14 714 14 HOH HOH . F 4 HOH A 15 715 15 HOH HOH . F 4 HOH A 16 716 16 HOH HOH . F 4 HOH A 17 717 17 HOH HOH . F 4 HOH A 18 718 18 HOH HOH . F 4 HOH A 19 719 19 HOH HOH . F 4 HOH A 20 720 20 HOH HOH . F 4 HOH A 21 721 21 HOH HOH . F 4 HOH A 22 722 22 HOH HOH . F 4 HOH A 23 723 23 HOH HOH . F 4 HOH A 24 724 24 HOH HOH . F 4 HOH A 25 725 25 HOH HOH . F 4 HOH A 26 726 26 HOH HOH . F 4 HOH A 27 727 27 HOH HOH . F 4 HOH A 28 728 28 HOH HOH . F 4 HOH A 29 729 29 HOH HOH . F 4 HOH A 30 730 30 HOH HOH . F 4 HOH A 31 731 31 HOH HOH . F 4 HOH A 32 732 32 HOH HOH . F 4 HOH A 33 733 33 HOH HOH . F 4 HOH A 34 734 34 HOH HOH . F 4 HOH A 35 735 35 HOH HOH . F 4 HOH A 36 736 36 HOH HOH . F 4 HOH A 37 737 37 HOH HOH . F 4 HOH A 38 738 38 HOH HOH . F 4 HOH A 39 739 39 HOH HOH . F 4 HOH A 40 740 40 HOH HOH . F 4 HOH A 41 741 41 HOH HOH . F 4 HOH A 42 742 42 HOH HOH . F 4 HOH A 43 743 43 HOH HOH . F 4 HOH A 44 744 44 HOH HOH . F 4 HOH A 45 745 45 HOH HOH . F 4 HOH A 46 746 46 HOH HOH . F 4 HOH A 47 747 47 HOH HOH . F 4 HOH A 48 748 48 HOH HOH . F 4 HOH A 49 749 49 HOH HOH . F 4 HOH A 50 750 50 HOH HOH . F 4 HOH A 51 751 51 HOH HOH . F 4 HOH A 52 752 52 HOH HOH . F 4 HOH A 53 753 53 HOH HOH . F 4 HOH A 54 754 54 HOH HOH . F 4 HOH A 55 755 55 HOH HOH . F 4 HOH A 56 756 56 HOH HOH . F 4 HOH A 57 757 57 HOH HOH . F 4 HOH A 58 758 58 HOH HOH . F 4 HOH A 59 759 59 HOH HOH . F 4 HOH A 60 760 60 HOH HOH . F 4 HOH A 61 761 61 HOH HOH . F 4 HOH A 62 762 62 HOH HOH . F 4 HOH A 63 763 63 HOH HOH . F 4 HOH A 64 764 64 HOH HOH . F 4 HOH A 65 765 65 HOH HOH . F 4 HOH A 66 766 66 HOH HOH . F 4 HOH A 67 767 67 HOH HOH . F 4 HOH A 68 768 68 HOH HOH . F 4 HOH A 69 769 69 HOH HOH . F 4 HOH A 70 770 70 HOH HOH . F 4 HOH A 71 771 71 HOH HOH . F 4 HOH A 72 772 72 HOH HOH . F 4 HOH A 73 773 73 HOH HOH . F 4 HOH A 74 774 74 HOH HOH . F 4 HOH A 75 775 75 HOH HOH . F 4 HOH A 76 776 76 HOH HOH . F 4 HOH A 77 777 77 HOH HOH . F 4 HOH A 78 778 78 HOH HOH . F 4 HOH A 79 779 79 HOH HOH . F 4 HOH A 80 780 80 HOH HOH . F 4 HOH A 81 781 81 HOH HOH . F 4 HOH A 82 782 82 HOH HOH . F 4 HOH A 83 783 83 HOH HOH . F 4 HOH A 84 784 84 HOH HOH . F 4 HOH A 85 785 85 HOH HOH . F 4 HOH A 86 786 86 HOH HOH . F 4 HOH A 87 787 87 HOH HOH . F 4 HOH A 88 788 88 HOH HOH . F 4 HOH A 89 789 89 HOH HOH . F 4 HOH A 90 790 90 HOH HOH . F 4 HOH A 91 791 91 HOH HOH . F 4 HOH A 92 792 92 HOH HOH . F 4 HOH A 93 793 93 HOH HOH . F 4 HOH A 94 794 94 HOH HOH . F 4 HOH A 95 795 95 HOH HOH . F 4 HOH A 96 796 96 HOH HOH . F 4 HOH A 97 797 97 HOH HOH . F 4 HOH A 98 798 98 HOH HOH . F 4 HOH A 99 799 99 HOH HOH . F 4 HOH A 100 800 100 HOH HOH . F 4 HOH A 101 801 101 HOH HOH . F 4 HOH A 102 802 102 HOH HOH . F 4 HOH A 103 803 103 HOH HOH . F 4 HOH A 104 804 104 HOH HOH . F 4 HOH A 105 805 105 HOH HOH . F 4 HOH A 106 806 106 HOH HOH . F 4 HOH A 107 807 107 HOH HOH . F 4 HOH A 108 808 108 HOH HOH . F 4 HOH A 109 809 109 HOH HOH . F 4 HOH A 110 810 110 HOH HOH . F 4 HOH A 111 811 111 HOH HOH . F 4 HOH A 112 812 112 HOH HOH . F 4 HOH A 113 813 113 HOH HOH . F 4 HOH A 114 814 114 HOH HOH . F 4 HOH A 115 815 115 HOH HOH . F 4 HOH A 116 816 116 HOH HOH . F 4 HOH A 117 817 117 HOH HOH . F 4 HOH A 118 818 118 HOH HOH . F 4 HOH A 119 819 119 HOH HOH . F 4 HOH A 120 820 120 HOH HOH . F 4 HOH A 121 821 121 HOH HOH . F 4 HOH A 122 822 122 HOH HOH . F 4 HOH A 123 823 123 HOH HOH . F 4 HOH A 124 824 124 HOH HOH . F 4 HOH A 125 825 125 HOH HOH . F 4 HOH A 126 826 126 HOH HOH . F 4 HOH A 127 827 127 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 P TMP . . . D 3 34.704 45.798 21.68 0.5 51.43 ? P TMP 601 A 1 HETATM 2 O O1P TMP . . . D 3 35.163 46.673 22.828 0.5 51.71 ? O1P TMP 601 A 1 HETATM 3 O O2P TMP . . . D 3 34.798 46.512 20.406 0.5 51.43 ? O2P TMP 601 A 1 HETATM 4 O O3P TMP . . . D 3 33.343 45.307 21.921 0.5 51.98 ? O3P TMP 601 A 1 HETATM 5 O O5' TMP . . . D 3 35.697 44.597 21.675 0.5 51.89 ? O5' TMP 601 A 1 HETATM 6 C C5' TMP . . . D 3 35.69 43.45 20.729 0.5 52.15 ? C5' TMP 601 A 1 HETATM 7 C C4' TMP . . . D 3 34.921 42.314 21.414 0.5 52.18 ? C4' TMP 601 A 1 HETATM 8 O O4' TMP . . . D 3 34.573 41.341 20.385 0.5 51.48 ? O4' TMP 601 A 1 HETATM 9 C C3' TMP . . . D 3 35.715 41.516 22.477 0.5 52.34 ? C3' TMP 601 A 1 HETATM 10 O O3' TMP . . . D 3 35.406 42.065 23.751 0.5 52.44 ? O3' TMP 601 A 1 HETATM 11 C C2' TMP . . . D 3 35.15 40.087 22.381 0.5 51.75 ? C2' TMP 601 A 1 HETATM 12 C C1' TMP . . . D 3 34.363 40.085 21.059 0.5 50.68 ? C1' TMP 601 A 1 HETATM 13 N N1 TMP . . . D 3 33.699 38.97 20.332 0.5 49.18 ? N1 TMP 601 A 1 HETATM 14 C C2 TMP . . . D 3 33.256 39.079 18.988 0.5 49.18 ? C2 TMP 601 A 1 HETATM 15 O O2 TMP . . . D 3 33.37 40.096 18.293 0.5 49.84 ? O2 TMP 601 A 1 HETATM 16 N N3 TMP . . . D 3 32.661 37.906 18.491 0.5 48.78 ? N3 TMP 601 A 1 HETATM 17 C C4 TMP . . . D 3 32.486 36.7 19.196 0.5 48.25 ? C4 TMP 601 A 1 HETATM 18 O O4 TMP . . . D 3 31.952 35.734 18.659 0.5 47.7 ? O4 TMP 601 A 1 HETATM 19 C C5 TMP . . . D 3 32.972 36.675 20.576 0.5 48.21 ? C5 TMP 601 A 1 HETATM 20 C C5M TMP . . . D 3 32.841 35.465 21.405 0.5 48.1 ? C5M TMP 601 A 1 HETATM 21 C C6 TMP . . . D 3 33.567 37.842 21.081 0.5 48.64 ? C6 TMP 601 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 21 #