data_9FM3 # _model_server_result.job_id tTIRF6pdmX1nc2XUIZSloA _model_server_result.datetime_utc '2024-11-15 03:21:10' _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 9fm3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":901}' # _entry.id 9FM3 # _exptl.entry_id 9FM3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 597.16 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' _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 120 _cell.entry_id 9FM3 _cell.length_a 114.164 _cell.length_b 114.164 _cell.length_c 91.399 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9FM3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 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 _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order covale ? covale1 B O3' DA 11 B DA 111 1_555 F P DOC . B DOC 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.598 ? metalc ? metalc1 A OD1 ASP 318 A ASP 610 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc2 A O TYR 319 A TYR 611 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc3 A OD2 ASP 493 A ASP 785 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc4 D O15 A1IDZ . A A1IDZ 901 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc5 D O20 A1IDZ . A A1IDZ 901 1_555 E MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 B DG 101 1_555 C N3 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 B DG 101 1_555 C O2 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 B DG 101 1_555 C N4 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DA 2 B DA 102 1_555 C N3 DT 15 C DT 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 DA 2 B DA 102 1_555 C O4 DT 15 C DT 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 3 B DC 103 1_555 C N1 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 3 B DC 103 1_555 C O6 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 3 B DC 103 1_555 C N2 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DC 4 B DC 104 1_555 C N1 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 DC 4 B DC 104 1_555 C O6 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 DC 4 B DC 104 1_555 C N2 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DA 5 B DA 105 1_555 C N3 DT 12 C DT 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N6 DA 5 B DA 105 1_555 C O4 DT 12 C DT 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DC 6 B DC 106 1_555 C N1 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 DC 6 B DC 106 1_555 C O6 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 DC 6 B DC 106 1_555 C N2 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 DG 7 B DG 107 1_555 C N3 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N2 DG 7 B DG 107 1_555 C O2 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O6 DG 7 B DG 107 1_555 C N4 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 DG 8 B DG 108 1_555 C N3 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N2 DG 8 B DG 108 1_555 C O2 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B O6 DG 8 B DG 108 1_555 C N4 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N3 DC 9 B DC 109 1_555 C N1 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N4 DC 9 B DC 109 1_555 C O6 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O2 DC 9 B DC 109 1_555 C N2 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N3 DC 10 B DC 110 1_555 C N1 DG 7 C DG 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N4 DC 10 B DC 110 1_555 C O6 DG 7 C DG 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O2 DC 10 B DC 110 1_555 C N2 DG 7 C DG 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N1 DA 11 B DA 111 1_555 C N3 DT 6 C DT 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N6 DA 11 B DA 111 1_555 C O4 DT 6 C DT 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C13 H17 N2 O14 P3 Se' _chem_comp.formula_weight 597.16 _chem_comp.id A1IDZ _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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 C2 A1IDZ doub 1 n n C2 N3 A1IDZ sing 2 n n N3 C4 A1IDZ sing 3 n n C4 O5 A1IDZ doub 4 n n C4 N6 A1IDZ sing 5 n n N6 C7 A1IDZ sing 6 n n C7 C8 A1IDZ sing 7 n n C8 C9 A1IDZ sing 8 n n C9 O10 A1IDZ sing 9 n n C9 C11 A1IDZ sing 10 n n C11 C12 A1IDZ sing 11 n n C12 O13 A1IDZ sing 12 n n O13 P14 A1IDZ sing 13 n n P14 O15 A1IDZ doub 14 n n P14 O16 A1IDZ sing 15 n n P14 O17 A1IDZ sing 16 n n O17 P18 A1IDZ sing 17 n n P18 O19 A1IDZ doub 18 n n P18 O20 A1IDZ sing 19 n n P18 O21 A1IDZ sing 20 n n O21 P22 A1IDZ sing 21 n n P22 O23 A1IDZ doub 22 n n P22 O24 A1IDZ sing 23 n n P22 O25 A1IDZ sing 24 n n C11 O26 A1IDZ sing 25 n n N6 C27 A1IDZ sing 26 n n C27 C28 A1IDZ doub 27 n n C28 C29 A1IDZ sing 28 n n C29 C30 A1IDZ doub 29 n y C30 C31 A1IDZ sing 30 n y C31 C32 A1IDZ doub 31 n y C32 SE33 A1IDZ sing 32 n y O26 C7 A1IDZ sing 33 n n C28 C2 A1IDZ sing 34 n n SE33 C29 A1IDZ sing 35 n y C8 H8A A1IDZ sing 36 n n C8 H8B A1IDZ sing 37 n n C9 H9 A1IDZ sing 38 n n C12 H12A A1IDZ sing 39 n n C12 H12B A1IDZ sing 40 n n C11 H11 A1IDZ sing 41 n n C7 H7 A1IDZ sing 42 n n C27 H27 A1IDZ sing 43 n n C30 H30 A1IDZ sing 44 n n C31 H31 A1IDZ sing 45 n n C32 H32 A1IDZ sing 46 n n N3 H3 A1IDZ sing 47 n n O10 H10 A1IDZ sing 48 n n O16 H1 A1IDZ sing 49 n n O20 H2 A1IDZ sing 50 n n O24 H4 A1IDZ sing 51 n n O25 H5 A1IDZ sing 52 n n # _atom_sites.entry_id 9FM3 _atom_sites.fract_transf_matrix[1][1] 0.008759 _atom_sites.fract_transf_matrix[1][2] 0.005057 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010114 _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] 0.010941 _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 4 A1IDZ A 1 901 1 A1IDZ WYZ . E 5 MG A 1 902 1 MG MG . F 6 DOC B 1 201 112 DOC DOC . G 7 HOH A 1 1001 12 HOH HOH . G 7 HOH A 2 1002 11 HOH HOH . G 7 HOH A 3 1003 14 HOH HOH . G 7 HOH A 4 1004 8 HOH HOH . G 7 HOH A 5 1005 6 HOH HOH . G 7 HOH A 6 1006 3 HOH HOH . G 7 HOH A 7 1007 13 HOH HOH . G 7 HOH A 8 1008 1 HOH HOH . G 7 HOH A 9 1009 10 HOH HOH . G 7 HOH A 10 1010 7 HOH HOH . G 7 HOH A 11 1011 9 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 C2 A1IDZ . . . D 4 29.152 7.504 10.116 1 67.55 ? C2 A1IDZ 901 A 1 HETATM 2 C C4 A1IDZ . . . D 4 30.759 5.9 9.14 1 78.09 ? C4 A1IDZ 901 A 1 HETATM 3 C C8 A1IDZ . . . D 4 30.377 4.595 6.193 1 75.61 ? C8 A1IDZ 901 A 1 HETATM 4 C C9 A1IDZ . . . D 4 29.644 5.141 4.977 1 78.48 ? C9 A1IDZ 901 A 1 HETATM 5 O O5 A1IDZ . . . D 4 31.552 4.983 9.309 1 76.61 ? O5 A1IDZ 901 A 1 HETATM 6 C C12 A1IDZ . . . D 4 29.992 7.287 3.63 1 67.21 ? C12 A1IDZ 901 A 1 HETATM 7 C C11 A1IDZ . . . D 4 30.612 6.204 4.477 1 75.44 ? C11 A1IDZ 901 A 1 HETATM 8 O O1 A1IDZ . . . D 4 28.618 7.898 11.15 1 82.86 ? O1 A1IDZ 901 A 1 HETATM 9 C C7 A1IDZ . . . D 4 31.131 5.808 6.727 1 81.95 ? C7 A1IDZ 901 A 1 HETATM 10 C C27 A1IDZ . . . D 4 29.59 7.459 7.739 1 75.73 ? C27 A1IDZ 901 A 1 HETATM 11 C C28 A1IDZ . . . D 4 28.912 8.019 8.782 1 71.3 ? C28 A1IDZ 901 A 1 HETATM 12 C C29 A1IDZ . . . D 4 27.983 9.118 8.534 1 78.05 ? C29 A1IDZ 901 A 1 HETATM 13 C C30 A1IDZ . . . D 4 27.826 9.877 7.39 1 84.95 ? C30 A1IDZ 901 A 1 HETATM 14 C C31 A1IDZ . . . D 4 26.847 10.879 7.469 1 80.25 ? C31 A1IDZ 901 A 1 HETATM 15 C C32 A1IDZ . . . D 4 26.212 10.949 8.645 1 90.74 ? C32 A1IDZ 901 A 1 HETATM 16 N N3 A1IDZ . . . D 4 30.072 6.472 10.18 1 72.59 ? N3 A1IDZ 901 A 1 HETATM 17 N N6 A1IDZ . . . D 4 30.483 6.426 7.893 1 85.79 ? N6 A1IDZ 901 A 1 HETATM 18 O O10 A1IDZ . . . D 4 29.458 4.114 4.004 1 71.63 ? O10 A1IDZ 901 A 1 HETATM 19 O O13 A1IDZ . . . D 4 28.921 7.914 4.359 1 77.59 ? O13 A1IDZ 901 A 1 HETATM 20 O O15 A1IDZ . . . D 4 28.149 8.899 2.188 1 75.28 ? O15 A1IDZ 901 A 1 HETATM 21 O O16 A1IDZ . . . D 4 27.204 9.726 4.4 1 77.44 -1 O16 A1IDZ 901 A 1 HETATM 22 O O17 A1IDZ . . . D 4 26.635 7.427 3.535 1 72.17 ? O17 A1IDZ 901 A 1 HETATM 23 O O19 A1IDZ . . . D 4 26.78 4.924 3.631 1 71.51 ? O19 A1IDZ 901 A 1 HETATM 24 O O20 A1IDZ . . . D 4 27.323 6.152 1.474 1 81.43 -1 O20 A1IDZ 901 A 1 HETATM 25 O O21 A1IDZ . . . D 4 24.96 6.047 2.351 1 90.03 ? O21 A1IDZ 901 A 1 HETATM 26 O O23 A1IDZ . . . D 4 23.613 6.713 0.255 1 80.95 ? O23 A1IDZ 901 A 1 HETATM 27 O O24 A1IDZ . . . D 4 23.751 8.305 2.207 1 77.46 -1 O24 A1IDZ 901 A 1 HETATM 28 O O25 A1IDZ . . . D 4 25.747 7.972 0.712 1 84.58 -1 O25 A1IDZ 901 A 1 HETATM 29 O O26 A1IDZ . . . D 4 31.173 6.772 5.678 1 84.67 ? O26 A1IDZ 901 A 1 HETATM 30 P P14 A1IDZ . . . D 4 27.716 8.609 3.571 1 75.35 ? P14 A1IDZ 901 A 1 HETATM 31 P P18 A1IDZ . . . D 4 26.521 6.054 2.718 1 76.64 ? P18 A1IDZ 901 A 1 HETATM 32 P P22 A1IDZ . . . D 4 24.501 7.346 1.303 1 74.65 ? P22 A1IDZ 901 A 1 HETATM 33 SE SE33 A1IDZ . . . D 4 26.802 9.697 9.848 1 93.97 ? SE33 A1IDZ 901 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 38 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 245 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #