data_1NE6 # _model_server_result.job_id 3pcR5rkyurEeezkyeGi9HQ _model_server_result.datetime_utc '2025-01-11 00:38:08' _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 1ne6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 1NE6 # _exptl.entry_id 1NE6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 345.272 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL _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 120 _cell.entry_id 1NE6 _cell.length_a 87.4 _cell.length_b 87.4 _cell.length_c 178.7 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NE6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _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 _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 ? 2 B N N ? 2 C N N # _chem_comp.formula 'C10 H12 N5 O5 P S' _chem_comp.formula_weight 345.272 _chem_comp.id SP1 _chem_comp.mon_nstd_flag . _chem_comp.name 6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "SP-ADENOSINE-3',5'-CYCLIC-MONOPHOSPHOROTHIOATE" # 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 S1P SP1 doub 290 n n P O2P SP1 sing 291 n n P O5' SP1 sing 292 n n P O3' SP1 sing 293 n n O2P HOP2 SP1 sing 294 n n O5' C5' SP1 sing 295 n n C5' C4' SP1 sing 296 n n C5' "H5'1" SP1 sing 297 n n C5' "H5'2" SP1 sing 298 n n C4' O4' SP1 sing 299 n n C4' C3' SP1 sing 300 n n C4' H4' SP1 sing 301 n n O4' C1' SP1 sing 302 n n C3' O3' SP1 sing 303 n n C3' C2' SP1 sing 304 n n C3' H3' SP1 sing 305 n n C2' O2' SP1 sing 306 n n C2' C1' SP1 sing 307 n n C2' H2' SP1 sing 308 n n O2' HO2' SP1 sing 309 n n C1' N9 SP1 sing 310 n n C1' H1' SP1 sing 311 n n N9 C8 SP1 sing 312 n y N9 C4 SP1 sing 313 n y C8 N7 SP1 doub 314 n y C8 H8 SP1 sing 315 n n N7 C5 SP1 sing 316 n y C5 C6 SP1 doub 317 n y C5 C4 SP1 sing 318 n y C6 N6 SP1 sing 319 n n C6 N1 SP1 sing 320 n y N6 HN61 SP1 sing 321 n n N6 HN62 SP1 sing 322 n n N1 C2 SP1 doub 323 n y C2 N3 SP1 sing 324 n y C2 H2 SP1 sing 325 n n N3 C4 SP1 doub 326 n y # _atom_sites.entry_id 1NE6 _atom_sites.fract_transf_matrix[1][1] 0.011442 _atom_sites.fract_transf_matrix[1][2] 0.006606 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013212 _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] 0.005596 _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 SP1 A 1 401 401 SP1 SP . C 2 SP1 A 1 601 601 SP1 SP . D 3 HOH A 1 701 701 HOH WAT . D 3 HOH A 2 702 702 HOH WAT . D 3 HOH A 3 703 703 HOH WAT . D 3 HOH A 4 704 704 HOH WAT . D 3 HOH A 5 705 705 HOH WAT . D 3 HOH A 6 706 706 HOH WAT . D 3 HOH A 7 707 707 HOH WAT . D 3 HOH A 8 708 708 HOH WAT . D 3 HOH A 9 709 709 HOH WAT . D 3 HOH A 10 710 710 HOH WAT . D 3 HOH A 11 711 711 HOH WAT . D 3 HOH A 12 712 712 HOH WAT . D 3 HOH A 13 713 713 HOH WAT . D 3 HOH A 14 714 714 HOH WAT . D 3 HOH A 15 715 715 HOH WAT . D 3 HOH A 16 716 716 HOH WAT . D 3 HOH A 17 717 717 HOH WAT . D 3 HOH A 18 718 718 HOH WAT . D 3 HOH A 19 719 719 HOH WAT . D 3 HOH A 20 720 720 HOH WAT . D 3 HOH A 21 721 721 HOH WAT . D 3 HOH A 22 722 722 HOH WAT . D 3 HOH A 23 723 723 HOH WAT . D 3 HOH A 24 724 724 HOH WAT . D 3 HOH A 25 725 725 HOH WAT . D 3 HOH A 26 726 726 HOH WAT . D 3 HOH A 27 727 727 HOH WAT . D 3 HOH A 28 728 728 HOH WAT . D 3 HOH A 29 729 729 HOH WAT . D 3 HOH A 30 730 730 HOH WAT . D 3 HOH A 31 731 731 HOH WAT . D 3 HOH A 32 732 732 HOH WAT . D 3 HOH A 33 733 733 HOH WAT . D 3 HOH A 34 734 734 HOH WAT . D 3 HOH A 35 735 735 HOH WAT . D 3 HOH A 36 736 736 HOH WAT . D 3 HOH A 37 737 737 HOH WAT . D 3 HOH A 38 738 738 HOH WAT . D 3 HOH A 39 739 739 HOH WAT . D 3 HOH A 40 740 740 HOH WAT . D 3 HOH A 41 741 741 HOH WAT . D 3 HOH A 42 742 742 HOH WAT . D 3 HOH A 43 743 743 HOH WAT . D 3 HOH A 44 744 744 HOH WAT . D 3 HOH A 45 745 745 HOH WAT . D 3 HOH A 46 746 746 HOH WAT . D 3 HOH A 47 747 747 HOH WAT . D 3 HOH A 48 748 748 HOH WAT . D 3 HOH A 49 749 749 HOH WAT . D 3 HOH A 50 750 750 HOH WAT . D 3 HOH A 51 751 751 HOH WAT . D 3 HOH A 52 752 752 HOH WAT . D 3 HOH A 53 753 753 HOH WAT . D 3 HOH A 54 754 754 HOH WAT . D 3 HOH A 55 755 755 HOH WAT . D 3 HOH A 56 756 756 HOH WAT . D 3 HOH A 57 757 757 HOH WAT . D 3 HOH A 58 758 758 HOH WAT . D 3 HOH A 59 759 759 HOH WAT . D 3 HOH A 60 760 760 HOH WAT . D 3 HOH A 61 761 761 HOH WAT . D 3 HOH A 62 762 762 HOH WAT . D 3 HOH A 63 763 763 HOH WAT . D 3 HOH A 64 764 764 HOH WAT . D 3 HOH A 65 765 765 HOH WAT . D 3 HOH A 66 766 766 HOH WAT . D 3 HOH A 67 767 767 HOH WAT . D 3 HOH A 68 768 768 HOH WAT . D 3 HOH A 69 769 769 HOH WAT . D 3 HOH A 70 770 770 HOH WAT . D 3 HOH A 71 771 771 HOH WAT . D 3 HOH A 72 772 772 HOH WAT . D 3 HOH A 73 773 773 HOH WAT . D 3 HOH A 74 774 774 HOH WAT . D 3 HOH A 75 775 775 HOH WAT . D 3 HOH A 76 776 776 HOH WAT . D 3 HOH A 77 777 777 HOH WAT . D 3 HOH A 78 778 778 HOH WAT . D 3 HOH A 79 779 779 HOH WAT . D 3 HOH A 80 780 780 HOH WAT . D 3 HOH A 81 781 781 HOH WAT . D 3 HOH A 82 782 782 HOH WAT . D 3 HOH A 83 783 783 HOH WAT . D 3 HOH A 84 784 784 HOH WAT . D 3 HOH A 85 785 785 HOH WAT . D 3 HOH A 86 786 786 HOH WAT . D 3 HOH A 87 787 787 HOH WAT . D 3 HOH A 88 788 788 HOH WAT . D 3 HOH A 89 789 789 HOH WAT . D 3 HOH A 90 790 790 HOH WAT . D 3 HOH A 91 791 791 HOH WAT . D 3 HOH A 92 792 792 HOH WAT . D 3 HOH A 93 793 793 HOH WAT . D 3 HOH A 94 794 794 HOH WAT . D 3 HOH A 95 795 795 HOH WAT . D 3 HOH A 96 796 796 HOH WAT . D 3 HOH A 97 797 797 HOH WAT . D 3 HOH A 98 799 799 HOH WAT . D 3 HOH A 99 800 800 HOH WAT . D 3 HOH A 100 801 801 HOH WAT . D 3 HOH A 101 802 802 HOH WAT . D 3 HOH A 102 803 803 HOH WAT . # 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 SP1 . . . C 2 73.418 50.131 94.802 1 48.77 ? P SP1 601 A 1 HETATM 2 S S1P SP1 . . . C 2 74.293 49.495 96.246 1 46.02 ? S1P SP1 601 A 1 HETATM 3 O O2P SP1 . . . C 2 72.165 50.896 95 1 48.45 ? O2P SP1 601 A 1 HETATM 4 O O5' SP1 . . . C 2 74.439 50.983 93.909 1 46.8 ? O5' SP1 601 A 1 HETATM 5 C C5' SP1 . . . C 2 75.395 50.335 93.047 1 48.47 ? C5' SP1 601 A 1 HETATM 6 C C4' SP1 . . . C 2 74.703 49.231 92.299 1 48.39 ? C4' SP1 601 A 1 HETATM 7 O O4' SP1 . . . C 2 75.568 48.448 91.443 1 49.47 ? O4' SP1 601 A 1 HETATM 8 C C3' SP1 . . . C 2 74.166 48.194 93.246 1 46.76 ? C3' SP1 601 A 1 HETATM 9 O O3' SP1 . . . C 2 73.095 48.837 93.894 1 47.48 ? O3' SP1 601 A 1 HETATM 10 C C2' SP1 . . . C 2 73.841 47.04 92.306 1 48.81 ? C2' SP1 601 A 1 HETATM 11 O O2' SP1 . . . C 2 72.606 47.189 91.636 1 46.9 ? O2' SP1 601 A 1 HETATM 12 C C1' SP1 . . . C 2 74.991 47.153 91.295 1 41.08 ? C1' SP1 601 A 1 HETATM 13 N N9 SP1 . . . C 2 76.039 46.141 91.44 1 45.11 ? N9 SP1 601 A 1 HETATM 14 C C8 SP1 . . . C 2 76.571 45.362 90.439 1 44.91 ? C8 SP1 601 A 1 HETATM 15 N N7 SP1 . . . C 2 77.493 44.528 90.851 1 46.96 ? N7 SP1 601 A 1 HETATM 16 C C5 SP1 . . . C 2 77.577 44.772 92.216 1 47.41 ? C5 SP1 601 A 1 HETATM 17 C C6 SP1 . . . C 2 78.374 44.21 93.23 1 46.6 ? C6 SP1 601 A 1 HETATM 18 N N6 SP1 . . . C 2 79.27 43.248 93.017 1 46.97 ? N6 SP1 601 A 1 HETATM 19 N N1 SP1 . . . C 2 78.214 44.676 94.486 1 46.91 ? N1 SP1 601 A 1 HETATM 20 C C2 SP1 . . . C 2 77.313 45.643 94.701 1 46.77 ? C2 SP1 601 A 1 HETATM 21 N N3 SP1 . . . C 2 76.505 46.251 93.833 1 47.01 ? N3 SP1 601 A 1 HETATM 22 C C4 SP1 . . . C 2 76.687 45.763 92.593 1 45.53 ? C4 SP1 601 A 1 # _model_server_stats.io_time_ms 81 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 22 #