data_3TQ4 # _model_server_result.job_id zo0fnHGPT8q1hJRwJqbFjg _model_server_result.datetime_utc '2024-11-13 04:20:05' _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 3tq4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":154}' # _entry.id 3TQ4 # _exptl.entry_id 3TQ4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 3TQ4 _cell.length_a 60.564 _cell.length_b 60.564 _cell.length_c 64.018 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TQ4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_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 1,2,3 # 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' 2_775 -y+2,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 60.564 104.899925 0 3 'crystal symmetry operation' 3_575 -x+y,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -60.564 104.899925 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 metalc ? metalc1 C MG MG . A MG 153 1_555 D O1A DUP . A DUP 154 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.952 ? metalc ? metalc2 C MG MG . A MG 153 1_555 D O1B DUP . A DUP 154 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.242 ? metalc ? metalc3 C MG MG . A MG 153 1_555 D O2G DUP . A DUP 154 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.25 ? metalc ? metalc4 C MG MG . A MG 153 1_555 F O HOH . A HOH 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.978 ? metalc ? metalc5 C MG MG . A MG 153 1_555 B OP1 UMP . A UMP 777 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.385 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DUP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 O4 C4 DUP doub 83 n n C4 C5 DUP sing 84 n y C4 N3 DUP sing 85 n y C5 C6 DUP doub 86 n y C5 H5 DUP sing 87 n n C6 N1 DUP sing 88 n y C6 H6 DUP sing 89 n n N3 C2 DUP sing 90 n y N3 HN3 DUP sing 91 n n C2 O2 DUP doub 92 n n C2 N1 DUP sing 93 n y N1 C1' DUP sing 94 n n C1' C2' DUP sing 95 n n C1' O4' DUP sing 96 n n C1' H1' DUP sing 97 n n C2' C3' DUP sing 98 n n C2' "H2'1" DUP sing 99 n n C2' "H2'2" DUP sing 100 n n C3' O3' DUP sing 101 n n C3' C4' DUP sing 102 n n C3' H1 DUP sing 103 n n O3' H3' DUP sing 104 n n O4' C4' DUP sing 105 n n C4' C5' DUP sing 106 n n C4' H4' DUP sing 107 n n C5' O5' DUP sing 108 n n C5' "H5'1" DUP sing 109 n n C5' "H5'2" DUP sing 110 n n O5' PA DUP sing 111 n n PA O1A DUP doub 112 n n PA O2A DUP sing 113 n n PA N3A DUP sing 114 n n O2A H2A DUP sing 115 n n N3A PB DUP sing 116 n n N3A H3A DUP sing 117 n n PB O1B DUP doub 118 n n PB O2B DUP sing 119 n n PB O3B DUP sing 120 n n O2B H2B DUP sing 121 n n O3B PG DUP sing 122 n n PG O2G DUP doub 123 n n PG O1G DUP sing 124 n n PG O3G DUP sing 125 n n O1G H1G DUP sing 126 n n O3G H3G DUP sing 127 n n # _atom_sites.entry_id 3TQ4 _atom_sites.fract_transf_matrix[1][1] 0.016511 _atom_sites.fract_transf_matrix[1][2] 0.009533 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019066 _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] 0.015621 _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 UMP A 1 777 777 UMP UMP . C 3 MG A 1 153 1 MG MG . D 4 DUP A 1 154 777 DUP DUP . E 5 TRS A 1 155 1 TRS TRS . F 6 HOH A 1 156 1 HOH HOH . F 6 HOH A 2 157 2 HOH HOH . F 6 HOH A 3 158 3 HOH HOH . F 6 HOH A 4 159 4 HOH HOH . F 6 HOH A 5 160 5 HOH HOH . F 6 HOH A 6 161 6 HOH HOH . F 6 HOH A 7 162 7 HOH HOH . F 6 HOH A 8 163 8 HOH HOH . F 6 HOH A 9 164 9 HOH HOH . F 6 HOH A 10 165 10 HOH HOH . F 6 HOH A 11 166 11 HOH HOH . F 6 HOH A 12 167 12 HOH HOH . F 6 HOH A 13 168 13 HOH HOH . F 6 HOH A 14 169 14 HOH HOH . F 6 HOH A 15 170 15 HOH HOH . F 6 HOH A 16 171 16 HOH HOH . F 6 HOH A 17 172 17 HOH HOH . F 6 HOH A 18 173 18 HOH HOH . F 6 HOH A 19 174 19 HOH HOH . F 6 HOH A 20 175 20 HOH HOH . F 6 HOH A 21 176 21 HOH HOH . F 6 HOH A 22 177 22 HOH HOH . F 6 HOH A 23 178 23 HOH HOH . F 6 HOH A 24 179 24 HOH HOH . F 6 HOH A 25 180 25 HOH HOH . F 6 HOH A 26 181 26 HOH HOH . F 6 HOH A 27 182 27 HOH HOH . F 6 HOH A 28 183 28 HOH HOH . F 6 HOH A 29 184 29 HOH HOH . F 6 HOH A 30 185 30 HOH HOH . F 6 HOH A 31 186 31 HOH HOH . F 6 HOH A 32 187 32 HOH HOH . F 6 HOH A 33 188 33 HOH HOH . F 6 HOH A 34 189 34 HOH HOH . F 6 HOH A 35 190 35 HOH HOH . F 6 HOH A 36 191 36 HOH HOH . F 6 HOH A 37 192 37 HOH HOH . F 6 HOH A 38 193 38 HOH HOH . F 6 HOH A 39 194 39 HOH HOH . F 6 HOH A 40 195 40 HOH HOH . F 6 HOH A 41 196 41 HOH HOH . F 6 HOH A 42 197 42 HOH HOH . F 6 HOH A 43 198 43 HOH HOH . F 6 HOH A 44 199 44 HOH HOH . F 6 HOH A 45 200 45 HOH HOH . F 6 HOH A 46 201 46 HOH HOH . F 6 HOH A 47 202 47 HOH HOH . F 6 HOH A 48 203 48 HOH HOH . F 6 HOH A 49 204 49 HOH HOH . F 6 HOH A 50 205 50 HOH HOH . F 6 HOH A 51 206 54 HOH HOH . F 6 HOH A 52 207 55 HOH HOH . F 6 HOH A 53 208 56 HOH HOH . F 6 HOH A 54 209 57 HOH HOH . F 6 HOH A 55 210 58 HOH HOH . F 6 HOH A 56 211 59 HOH HOH . F 6 HOH A 57 212 60 HOH HOH . F 6 HOH A 58 213 61 HOH HOH . F 6 HOH A 59 214 62 HOH HOH . F 6 HOH A 60 215 63 HOH HOH . F 6 HOH A 61 216 64 HOH HOH . F 6 HOH A 62 217 65 HOH HOH . F 6 HOH A 63 218 66 HOH HOH . F 6 HOH A 64 219 67 HOH HOH . F 6 HOH A 65 220 68 HOH HOH . F 6 HOH A 66 221 69 HOH HOH . F 6 HOH A 67 222 70 HOH HOH . F 6 HOH A 68 223 71 HOH HOH . F 6 HOH A 69 224 72 HOH HOH . F 6 HOH A 70 225 73 HOH HOH . F 6 HOH A 71 226 74 HOH HOH . F 6 HOH A 72 227 75 HOH HOH . F 6 HOH A 73 228 76 HOH HOH . F 6 HOH A 74 229 77 HOH HOH . F 6 HOH A 75 230 78 HOH HOH . F 6 HOH A 76 231 79 HOH HOH . F 6 HOH A 77 232 80 HOH HOH . F 6 HOH A 78 233 81 HOH HOH . F 6 HOH A 79 234 82 HOH HOH . F 6 HOH A 80 235 83 HOH HOH . F 6 HOH A 81 236 84 HOH HOH . F 6 HOH A 82 237 87 HOH HOH . F 6 HOH A 83 238 88 HOH HOH . F 6 HOH A 84 239 89 HOH HOH . F 6 HOH A 85 240 90 HOH HOH . F 6 HOH A 86 241 91 HOH HOH . F 6 HOH A 87 242 92 HOH HOH . F 6 HOH A 88 243 93 HOH HOH . F 6 HOH A 89 244 95 HOH HOH . F 6 HOH A 90 245 96 HOH HOH . F 6 HOH A 91 246 98 HOH HOH . F 6 HOH A 92 247 99 HOH HOH . F 6 HOH A 93 248 100 HOH HOH . F 6 HOH A 94 249 101 HOH HOH . F 6 HOH A 95 250 102 HOH HOH . F 6 HOH A 96 251 103 HOH HOH . F 6 HOH A 97 252 104 HOH HOH . F 6 HOH A 98 253 105 HOH HOH . F 6 HOH A 99 254 106 HOH HOH . F 6 HOH A 100 255 107 HOH HOH . F 6 HOH A 101 256 108 HOH HOH . F 6 HOH A 102 257 109 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 O O4 DUP . B . D 4 -2.686 59.843 28.642 0.2 17.59 ? O4 DUP 154 A 1 HETATM 2 C C4 DUP . B . D 4 -3.454 59.139 29.309 0.2 14.33 ? C4 DUP 154 A 1 HETATM 3 C C5 DUP . B . D 4 -4.605 59.686 29.875 0.2 16.53 ? C5 DUP 154 A 1 HETATM 4 C C6 DUP . B . D 4 -5.466 58.884 30.624 0.2 14.79 ? C6 DUP 154 A 1 HETATM 5 N N3 DUP . B . D 4 -3.171 57.804 29.515 0.2 14.42 ? N3 DUP 154 A 1 HETATM 6 C C2 DUP . B . D 4 -4.02 57.018 30.259 0.2 13.6 ? C2 DUP 154 A 1 HETATM 7 O O2 DUP . B . D 4 -3.752 55.822 30.42 0.2 18.15 ? O2 DUP 154 A 1 HETATM 8 N N1 DUP . B . D 4 -5.164 57.558 30.817 0.2 15.85 ? N1 DUP 154 A 1 HETATM 9 C C1' DUP . B . D 4 -6.047 56.675 31.607 0.2 17.28 ? C1' DUP 154 A 1 HETATM 10 C C2' DUP . B . D 4 -5.808 56.864 33.107 0.2 16.36 ? C2' DUP 154 A 1 HETATM 11 C C3' DUP . B . D 4 -7.087 57.499 33.599 0.2 18.13 ? C3' DUP 154 A 1 HETATM 12 O O3' DUP . B . D 4 -7.497 56.989 34.841 0.2 17.22 ? O3' DUP 154 A 1 HETATM 13 O O4' DUP . B . D 4 -7.404 56.969 31.339 0.2 17.25 ? O4' DUP 154 A 1 HETATM 14 C C4' DUP . B . D 4 -8.115 57.137 32.545 0.2 14.43 ? C4' DUP 154 A 1 HETATM 15 C C5' DUP . B . D 4 -9.137 58.241 32.383 0.2 14.7 ? C5' DUP 154 A 1 HETATM 16 O O5' DUP . B . D 4 -8.521 59.288 31.673 0.2 12.65 ? O5' DUP 154 A 1 HETATM 17 P PA DUP . B . D 4 -9.444 60.553 31.298 0.2 6.53 ? PA DUP 154 A 1 HETATM 18 O O1A DUP . B . D 4 -10.347 60.832 32.459 0.2 6.4 ? O1A DUP 154 A 1 HETATM 19 O O2A DUP . B . D 4 -8.616 61.741 30.874 0.2 9.59 ? O2A DUP 154 A 1 HETATM 20 N N3A DUP . B . D 4 -10.34 59.94 30.018 0.2 8.41 ? N3A DUP 154 A 1 HETATM 21 P PB DUP . B . D 4 -11.993 59.963 29.774 0.2 10.66 ? PB DUP 154 A 1 HETATM 22 O O1B DUP . B . D 4 -12.644 61.112 30.502 0.2 13.11 ? O1B DUP 154 A 1 HETATM 23 O O2B DUP . B . D 4 -12.181 60.065 28.282 0.2 12.51 ? O2B DUP 154 A 1 HETATM 24 O O3B DUP . B . D 4 -12.517 58.55 30.333 0.2 12.17 ? O3B DUP 154 A 1 HETATM 25 P PG DUP . B . D 4 -13.354 58.356 31.7 0.2 14.06 ? PG DUP 154 A 1 HETATM 26 O O2G DUP . B . D 4 -12.756 59.196 32.802 0.2 14.65 ? O2G DUP 154 A 1 HETATM 27 O O1G DUP . B . D 4 -14.715 58.931 31.408 0.2 17.02 ? O1G DUP 154 A 1 HETATM 28 O O3G DUP . B . D 4 -13.395 56.904 32.068 0.2 16.47 ? O3G DUP 154 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #