data_3BGG # _model_server_result.job_id VAl1yOjbn0PmQ4cyDjq5tA _model_server_result.datetime_utc '2024-10-17 13:21:41' _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 3bgg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1000}' # _entry.id 3BGG # _exptl.entry_id 3BGG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6-HYDROXYURIDINE-5'-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 90 _cell.entry_id 3BGG _cell.length_a 77.596 _cell.length_b 116.886 _cell.length_c 61.985 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BGG _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H13 N2 O10 P' _chem_comp.formula_weight 340.181 _chem_comp.id BMP _chem_comp.mon_nstd_flag . _chem_comp.name "6-HYDROXYURIDINE-5'-PHOSPHATE" _chem_comp.type 'rna 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 P OP1 BMP doub 70 n n P OP2 BMP sing 71 n n P OP3 BMP sing 72 n n P O5' BMP sing 73 n n OP2 HOP2 BMP sing 74 n n OP3 HOP3 BMP sing 75 n n O5' C5' BMP sing 76 n n C5' C4' BMP sing 77 n n C5' H5' BMP sing 78 n n C5' "H5''" BMP sing 79 n n C4' O4' BMP sing 80 n n C4' C3' BMP sing 81 n n C4' H4' BMP sing 82 n n O4' C1' BMP sing 83 n n C3' O3' BMP sing 84 n n C3' C2' BMP sing 85 n n C3' H3' BMP sing 86 n n O3' HO3' BMP sing 87 n n C2' O2' BMP sing 88 n n C2' C1' BMP sing 89 n n C2' H2' BMP sing 90 n n O2' HO2' BMP sing 91 n n C1' N1 BMP sing 92 n n C1' H1' BMP sing 93 n n N1 C2 BMP sing 94 n n N1 C6 BMP sing 95 n n C2 O2 BMP doub 96 n n C2 N3 BMP sing 97 n n N3 C4 BMP sing 98 n n N3 HN3 BMP sing 99 n n C4 O4 BMP doub 100 n n C4 C5 BMP sing 101 n n C5 C6 BMP doub 102 n n C5 H51 BMP sing 103 n n C6 O1 BMP sing 104 n n O1 HO1 BMP sing 105 n n # _atom_sites.entry_id 3BGG _atom_sites.fract_transf_matrix[1][1] 0.012887 _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] 0.008555 _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] 0.016133 _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 BMP A 1 1000 1000 BMP BMP . C 3 HOH A 1 1001 1 HOH HOH . C 3 HOH A 2 1002 2 HOH HOH . C 3 HOH A 3 1003 3 HOH HOH . C 3 HOH A 4 1004 4 HOH HOH . C 3 HOH A 5 1005 5 HOH HOH . C 3 HOH A 6 1006 6 HOH HOH . C 3 HOH A 7 1007 7 HOH HOH . C 3 HOH A 8 1008 8 HOH HOH . C 3 HOH A 9 1009 9 HOH HOH . C 3 HOH A 10 1010 10 HOH HOH . C 3 HOH A 11 1011 11 HOH HOH . C 3 HOH A 12 1012 12 HOH HOH . C 3 HOH A 13 1013 13 HOH HOH . C 3 HOH A 14 1014 14 HOH HOH . C 3 HOH A 15 1015 15 HOH HOH . C 3 HOH A 16 1016 16 HOH HOH . C 3 HOH A 17 1017 17 HOH HOH . C 3 HOH A 18 1018 18 HOH HOH . C 3 HOH A 19 1019 19 HOH HOH . C 3 HOH A 20 1020 20 HOH HOH . C 3 HOH A 21 1021 21 HOH HOH . C 3 HOH A 22 1022 22 HOH HOH . C 3 HOH A 23 1023 23 HOH HOH . C 3 HOH A 24 1024 24 HOH HOH . C 3 HOH A 25 1025 25 HOH HOH . C 3 HOH A 26 1026 26 HOH HOH . C 3 HOH A 27 1027 27 HOH HOH . C 3 HOH A 28 1028 28 HOH HOH . C 3 HOH A 29 1029 29 HOH HOH . C 3 HOH A 30 1030 30 HOH HOH . C 3 HOH A 31 1031 31 HOH HOH . C 3 HOH A 32 1032 32 HOH HOH . C 3 HOH A 33 1033 33 HOH HOH . C 3 HOH A 34 1034 34 HOH HOH . C 3 HOH A 35 1035 35 HOH HOH . C 3 HOH A 36 1036 36 HOH HOH . C 3 HOH A 37 1037 37 HOH HOH . C 3 HOH A 38 1038 38 HOH HOH . C 3 HOH A 39 1039 39 HOH HOH . C 3 HOH A 40 1040 40 HOH HOH . C 3 HOH A 41 1041 41 HOH HOH . C 3 HOH A 42 1042 42 HOH HOH . C 3 HOH A 43 1043 43 HOH HOH . C 3 HOH A 44 1044 44 HOH HOH . C 3 HOH A 45 1045 45 HOH HOH . C 3 HOH A 46 1046 46 HOH HOH . C 3 HOH A 47 1047 47 HOH HOH . C 3 HOH A 48 1048 48 HOH HOH . C 3 HOH A 49 1049 49 HOH HOH . C 3 HOH A 50 1050 50 HOH HOH . C 3 HOH A 51 1051 51 HOH HOH . C 3 HOH A 52 1052 52 HOH HOH . C 3 HOH A 53 1053 53 HOH HOH . C 3 HOH A 54 1054 54 HOH HOH . C 3 HOH A 55 1055 55 HOH HOH . C 3 HOH A 56 1056 56 HOH HOH . C 3 HOH A 57 1057 57 HOH HOH . C 3 HOH A 58 1058 58 HOH HOH . C 3 HOH A 59 1059 59 HOH HOH . C 3 HOH A 60 1060 60 HOH HOH . C 3 HOH A 61 1061 61 HOH HOH . C 3 HOH A 62 1062 62 HOH HOH . C 3 HOH A 63 1063 63 HOH HOH . C 3 HOH A 64 1064 64 HOH HOH . C 3 HOH A 65 1065 65 HOH HOH . C 3 HOH A 66 1066 66 HOH HOH . C 3 HOH A 67 1067 67 HOH HOH . C 3 HOH A 68 1068 68 HOH HOH . C 3 HOH A 69 1069 69 HOH HOH . C 3 HOH A 70 1070 70 HOH HOH . C 3 HOH A 71 1071 71 HOH HOH . C 3 HOH A 72 1072 72 HOH HOH . C 3 HOH A 73 1073 73 HOH HOH . C 3 HOH A 74 1074 75 HOH HOH . C 3 HOH A 75 1075 76 HOH HOH . C 3 HOH A 76 1076 77 HOH HOH . C 3 HOH A 77 1077 78 HOH HOH . C 3 HOH A 78 1078 79 HOH HOH . C 3 HOH A 79 1079 80 HOH HOH . C 3 HOH A 80 1080 81 HOH HOH . C 3 HOH A 81 1081 82 HOH HOH . C 3 HOH A 82 1082 83 HOH HOH . C 3 HOH A 83 1083 84 HOH HOH . C 3 HOH A 84 1084 85 HOH HOH . C 3 HOH A 85 1085 86 HOH HOH . C 3 HOH A 86 1086 87 HOH HOH . C 3 HOH A 87 1087 88 HOH HOH . C 3 HOH A 88 1088 89 HOH HOH . C 3 HOH A 89 1089 90 HOH HOH . C 3 HOH A 90 1090 91 HOH HOH . C 3 HOH A 91 1091 93 HOH HOH . C 3 HOH A 92 1092 94 HOH HOH . C 3 HOH A 93 1093 95 HOH HOH . C 3 HOH A 94 1094 96 HOH HOH . C 3 HOH A 95 1095 97 HOH HOH . C 3 HOH A 96 1096 98 HOH HOH . C 3 HOH A 97 1097 99 HOH HOH . C 3 HOH A 98 1098 100 HOH HOH . C 3 HOH A 99 1099 101 HOH HOH . C 3 HOH A 100 1100 102 HOH HOH . C 3 HOH A 101 1101 103 HOH HOH . C 3 HOH A 102 1102 105 HOH HOH . C 3 HOH A 103 1103 106 HOH HOH . C 3 HOH A 104 1104 108 HOH HOH . C 3 HOH A 105 1105 109 HOH HOH . C 3 HOH A 106 1106 110 HOH HOH . C 3 HOH A 107 1107 111 HOH HOH . C 3 HOH A 108 1108 112 HOH HOH . C 3 HOH A 109 1109 113 HOH HOH . C 3 HOH A 110 1110 114 HOH HOH . C 3 HOH A 111 1111 115 HOH HOH . C 3 HOH A 112 1112 116 HOH HOH . C 3 HOH A 113 1113 117 HOH HOH . C 3 HOH A 114 1114 118 HOH HOH . C 3 HOH A 115 1115 119 HOH HOH . C 3 HOH A 116 1116 120 HOH HOH . C 3 HOH A 117 1117 121 HOH HOH . C 3 HOH A 118 1118 122 HOH HOH . C 3 HOH A 119 1119 123 HOH HOH . C 3 HOH A 120 1120 124 HOH HOH . C 3 HOH A 121 1121 125 HOH HOH . C 3 HOH A 122 1122 126 HOH HOH . C 3 HOH A 123 1123 127 HOH HOH . C 3 HOH A 124 1124 128 HOH HOH . C 3 HOH A 125 1125 129 HOH HOH . C 3 HOH A 126 1126 130 HOH HOH . C 3 HOH A 127 1127 131 HOH HOH . C 3 HOH A 128 1128 132 HOH HOH . C 3 HOH A 129 1129 133 HOH HOH . C 3 HOH A 130 1130 134 HOH HOH . C 3 HOH A 131 1131 135 HOH HOH . C 3 HOH A 132 1132 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 P BMP . . . B 2 12.252 -13.562 -11.096 1 19.74 ? P BMP 1000 A 1 HETATM 2 O OP1 BMP . . . B 2 13.363 -12.779 -11.763 1 19.54 ? OP1 BMP 1000 A 1 HETATM 3 O OP2 BMP . . . B 2 10.95 -13.271 -11.819 1 19.92 ? OP2 BMP 1000 A 1 HETATM 4 O OP3 BMP . . . B 2 12.538 -15.001 -10.761 1 19.11 ? OP3 BMP 1000 A 1 HETATM 5 O O5' BMP . . . B 2 11.974 -12.832 -9.693 1 22.23 ? O5' BMP 1000 A 1 HETATM 6 C C5' BMP . . . B 2 12.979 -12.54 -8.724 1 22.97 ? C5' BMP 1000 A 1 HETATM 7 C C4' BMP . . . B 2 12.215 -12.059 -7.489 1 22.19 ? C4' BMP 1000 A 1 HETATM 8 O O4' BMP . . . B 2 13.128 -11.863 -6.415 1 20.15 ? O4' BMP 1000 A 1 HETATM 9 C C3' BMP . . . B 2 11.603 -10.687 -7.696 1 22.16 ? C3' BMP 1000 A 1 HETATM 10 O O3' BMP . . . B 2 10.398 -10.646 -6.923 1 19.22 ? O3' BMP 1000 A 1 HETATM 11 C C2' BMP . . . B 2 12.626 -9.719 -7.126 1 21.51 ? C2' BMP 1000 A 1 HETATM 12 O O2' BMP . . . B 2 11.981 -8.544 -6.596 1 20.53 ? O2' BMP 1000 A 1 HETATM 13 C C1' BMP . . . B 2 13.315 -10.513 -6.028 1 19.09 ? C1' BMP 1000 A 1 HETATM 14 N N1 BMP . . . B 2 14.773 -10.269 -5.854 1 18.9 ? N1 BMP 1000 A 1 HETATM 15 C C2 BMP . . . B 2 15.661 -10.407 -6.845 1 20.76 ? C2 BMP 1000 A 1 HETATM 16 O O2 BMP . . . B 2 15.302 -10.723 -7.989 1 17.84 ? O2 BMP 1000 A 1 HETATM 17 N N3 BMP . . . B 2 16.987 -10.172 -6.658 1 17.64 ? N3 BMP 1000 A 1 HETATM 18 C C4 BMP . . . B 2 17.512 -9.819 -5.47 1 18.82 ? C4 BMP 1000 A 1 HETATM 19 O O4 BMP . . . B 2 18.771 -9.661 -5.394 1 20.53 ? O4 BMP 1000 A 1 HETATM 20 C C5 BMP . . . B 2 16.667 -9.667 -4.378 1 16.6 ? C5 BMP 1000 A 1 HETATM 21 C C6 BMP . . . B 2 15.289 -9.896 -4.595 1 20.05 ? C6 BMP 1000 A 1 HETATM 22 O O1 BMP . . . B 2 14.472 -9.798 -3.65 1 21.64 ? O1 BMP 1000 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #