data_9BEZ # _model_server_result.job_id Y7QtaRCrgC5Wf-ecMhysag _model_server_result.datetime_utc '2024-12-01 12:20:57' _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 9bez # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 9BEZ # _exptl.entry_id 9BEZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 468.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(3~{S},4~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 86.005 _cell.angle_beta 74.022 _cell.angle_gamma 84.76 _cell.entry_id 9BEZ _cell.length_a 37.549 _cell.length_b 46.899 _cell.length_c 66.209 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9BEZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,G,H,I _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 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C9 H15 N2 O14 P3' _chem_comp.formula_weight 468.142 _chem_comp.id A1ANT _chem_comp.mon_nstd_flag . _chem_comp.name '[(3~{S},4~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen 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 O1 C1 A1ANT sing 1 n n C1 C2 A1ANT sing 2 n n C2 O2 A1ANT sing 3 n n O2 P1 A1ANT sing 4 n n P1 O3 A1ANT sing 5 n n P1 O4 A1ANT sing 6 n n O4 P2 A1ANT sing 7 n n P2 O5 A1ANT sing 8 n n P2 O6 A1ANT sing 9 n n O6 P3 A1ANT sing 10 n n P3 O7 A1ANT sing 11 n n P3 O8 A1ANT sing 12 n n P3 O9 A1ANT doub 13 n n P2 O10 A1ANT doub 14 n n P1 O11 A1ANT doub 15 n n C2 C3 A1ANT sing 16 n n C3 O12 A1ANT sing 17 n n O12 C4 A1ANT sing 18 n n C4 N1 A1ANT sing 19 n n N1 C5 A1ANT sing 20 n n C5 N2 A1ANT sing 21 n n C5 O13 A1ANT doub 22 n n N1 C6 A1ANT sing 23 n n C6 C7 A1ANT doub 24 n n C7 C8 A1ANT sing 25 n n C7 C9 A1ANT sing 26 n n C9 O14 A1ANT doub 27 n n C1 C4 A1ANT sing 28 n n N2 C9 A1ANT sing 29 n n C1 H2 A1ANT sing 30 n n C2 H3 A1ANT sing 31 n n C3 H5 A1ANT sing 32 n n C3 H4 A1ANT sing 33 n n C4 H6 A1ANT sing 34 n n C6 H8 A1ANT sing 35 n n N2 H7 A1ANT sing 36 n n O1 H1 A1ANT sing 37 n n C8 H11 A1ANT sing 38 n n C8 H9 A1ANT sing 39 n n C8 H10 A1ANT sing 40 n n O3 H12 A1ANT sing 41 n n O5 H13 A1ANT sing 42 n n O7 H14 A1ANT sing 43 n n O8 H15 A1ANT sing 44 n n # _atom_sites.entry_id 9BEZ _atom_sites.fract_transf_matrix[1][1] 0.026632 _atom_sites.fract_transf_matrix[1][2] -0.002442 _atom_sites.fract_transf_matrix[1][3] -0.00752 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021412 _atom_sites.fract_transf_matrix[2][3] -0.000997 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015728 _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 D 2 A1ANT A 1 601 2 A1ANT TNT . E 2 A1ANT B 1 601 1 A1ANT TNT . F 2 A1ANT C 1 601 3 A1ANT TNT . G 3 HOH A 1 701 25 HOH HOH . G 3 HOH A 2 702 18 HOH HOH . G 3 HOH A 3 703 103 HOH HOH . G 3 HOH A 4 704 7 HOH HOH . G 3 HOH A 5 705 13 HOH HOH . G 3 HOH A 6 706 17 HOH HOH . G 3 HOH A 7 707 8 HOH HOH . G 3 HOH A 8 708 14 HOH HOH . G 3 HOH A 9 709 15 HOH HOH . G 3 HOH A 10 710 29 HOH HOH . G 3 HOH A 11 711 23 HOH HOH . G 3 HOH A 12 712 24 HOH HOH . G 3 HOH A 13 713 40 HOH HOH . G 3 HOH A 14 714 27 HOH HOH . G 3 HOH A 15 715 19 HOH HOH . G 3 HOH A 16 716 65 HOH HOH . G 3 HOH A 17 717 64 HOH HOH . G 3 HOH A 18 718 10 HOH HOH . G 3 HOH A 19 719 3 HOH HOH . G 3 HOH A 20 720 78 HOH HOH . G 3 HOH A 21 721 36 HOH HOH . G 3 HOH A 22 722 81 HOH HOH . G 3 HOH A 23 723 74 HOH HOH . G 3 HOH A 24 724 100 HOH HOH . G 3 HOH A 25 725 94 HOH HOH . G 3 HOH A 26 726 91 HOH HOH . G 3 HOH A 27 727 61 HOH HOH . G 3 HOH A 28 728 41 HOH HOH . H 3 HOH B 1 701 92 HOH HOH . H 3 HOH B 2 702 44 HOH HOH . H 3 HOH B 3 703 11 HOH HOH . H 3 HOH B 4 704 102 HOH HOH . H 3 HOH B 5 705 1 HOH HOH . H 3 HOH B 6 706 62 HOH HOH . H 3 HOH B 7 707 6 HOH HOH . H 3 HOH B 8 708 99 HOH HOH . H 3 HOH B 9 709 30 HOH HOH . H 3 HOH B 10 710 51 HOH HOH . I 3 HOH C 1 701 80 HOH HOH . I 3 HOH C 2 702 26 HOH HOH . I 3 HOH C 3 703 83 HOH HOH . I 3 HOH C 4 704 79 HOH HOH . I 3 HOH C 5 705 84 HOH HOH . I 3 HOH C 6 706 28 HOH HOH . I 3 HOH C 7 707 20 HOH HOH . I 3 HOH C 8 708 73 HOH HOH . I 3 HOH C 9 709 16 HOH HOH . I 3 HOH C 10 710 34 HOH HOH . I 3 HOH C 11 711 2 HOH HOH . I 3 HOH C 12 712 71 HOH HOH . I 3 HOH C 13 713 12 HOH HOH . I 3 HOH C 14 714 47 HOH HOH . I 3 HOH C 15 715 60 HOH HOH . I 3 HOH C 16 716 9 HOH HOH . I 3 HOH C 17 717 4 HOH HOH . I 3 HOH C 18 718 33 HOH HOH . I 3 HOH C 19 719 85 HOH HOH . I 3 HOH C 20 720 72 HOH HOH . I 3 HOH C 21 721 43 HOH HOH . I 3 HOH C 22 722 5 HOH HOH . I 3 HOH C 23 723 31 HOH HOH . I 3 HOH C 24 724 86 HOH HOH . I 3 HOH C 25 725 35 HOH HOH . I 3 HOH C 26 726 98 HOH HOH . I 3 HOH C 27 727 88 HOH HOH . I 3 HOH C 28 728 101 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 C C1 A1ANT . . . E 2 -4.592 13.479 -20.599 1 128.11 ? C1 A1ANT 601 B 1 HETATM 2 C C2 A1ANT . . . E 2 -5.271 14.484 -21.539 1 114.58 ? C2 A1ANT 601 B 1 HETATM 3 C C3 A1ANT . . . E 2 -4.617 15.827 -21.228 1 119.91 ? C3 A1ANT 601 B 1 HETATM 4 C C4 A1ANT . . . E 2 -3.939 14.385 -19.539 1 136.35 ? C4 A1ANT 601 B 1 HETATM 5 C C5 A1ANT . . . E 2 -5.699 14.793 -17.865 1 89.44 ? C5 A1ANT 601 B 1 HETATM 6 C C6 A1ANT . . . E 2 -3.759 13.505 -17.218 1 95.04 ? C6 A1ANT 601 B 1 HETATM 7 C C7 A1ANT . . . E 2 -4.181 13.328 -15.956 1 93.38 ? C7 A1ANT 601 B 1 HETATM 8 N N1 A1ANT . . . E 2 -4.485 14.204 -18.171 1 102.91 ? N1 A1ANT 601 B 1 HETATM 9 N N2 A1ANT . . . E 2 -6.123 14.598 -16.581 1 72.51 ? N2 A1ANT 601 B 1 HETATM 10 O O1 A1ANT . . . E 2 -3.665 12.676 -21.307 1 92.54 ? O1 A1ANT 601 B 1 HETATM 11 C C8 A1ANT . . . E 2 -3.398 12.553 -14.929 1 91.38 ? C8 A1ANT 601 B 1 HETATM 12 C C9 A1ANT . . . E 2 -5.451 13.919 -15.585 1 81.51 ? C9 A1ANT 601 B 1 HETATM 13 O O10 A1ANT . . . E 2 -9.06 15.321 -22.75 1 91.38 ? O10 A1ANT 601 B 1 HETATM 14 O O11 A1ANT . . . E 2 -7.166 12.348 -22.223 1 105.76 ? O11 A1ANT 601 B 1 HETATM 15 O O12 A1ANT . . . E 2 -4.151 15.743 -19.892 1 133.62 ? O12 A1ANT 601 B 1 HETATM 16 O O13 A1ANT . . . E 2 -6.371 15.433 -18.661 1 116.58 ? O13 A1ANT 601 B 1 HETATM 17 O O14 A1ANT . . . E 2 -5.96 13.855 -14.48 1 88.48 ? O14 A1ANT 601 B 1 HETATM 18 O O2 A1ANT . . . E 2 -6.671 14.611 -21.293 1 103.28 ? O2 A1ANT 601 B 1 HETATM 19 O O3 A1ANT . . . E 2 -7.071 12.728 -19.664 1 124.33 ? O3 A1ANT 601 B 1 HETATM 20 O O4 A1ANT . . . E 2 -8.968 13.642 -20.905 1 104.22 ? O4 A1ANT 601 B 1 HETATM 21 O O5 A1ANT . . . E 2 -11.133 15.101 -21.138 1 48.04 ? O5 A1ANT 601 B 1 HETATM 22 O O6 A1ANT . . . E 2 -10.308 13.257 -22.866 1 137.83 ? O6 A1ANT 601 B 1 HETATM 23 O O7 A1ANT . . . E 2 -12.677 13.041 -23.669 1 122.07 ? O7 A1ANT 601 B 1 HETATM 24 O O8 A1ANT . . . E 2 -11.705 11.417 -21.987 1 150.84 ? O8 A1ANT 601 B 1 HETATM 25 O O9 A1ANT . . . E 2 -10.903 11.378 -24.389 1 114.08 ? O9 A1ANT 601 B 1 HETATM 26 P P1 A1ANT . . . E 2 -7.422 13.216 -21.03 1 112.14 ? P1 A1ANT 601 B 1 HETATM 27 P P2 A1ANT . . . E 2 -9.937 14.469 -21.88 1 132.56 ? P2 A1ANT 601 B 1 HETATM 28 P P3 A1ANT . . . E 2 -11.475 12.214 -23.251 1 141.15 ? P3 A1ANT 601 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 28 #