data_3NQT # _model_server_result.job_id bvxmKwTDX-LEAUypTQEOTg _model_server_result.datetime_utc '2024-11-10 01:25:02' _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 3nqt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":150}' # _entry.id 3NQT # _exptl.entry_id 3NQT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-3',5'-DIPHOSPHATE" _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 93.3 _cell.angle_gamma 90 _cell.entry_id 3NQT _cell.length_a 30.963 _cell.length_b 60.654 _cell.length_c 38.553 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NQT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 A OD2 ASP 21 A ASP 21 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc4 B O4P THP . A THP 150 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.145 ? metalc ? metalc5 C CA CA . A CA 151 1_555 D O HOH . A HOH 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.029 ? metalc ? metalc6 C CA CA . A CA 151 1_555 D O HOH . A HOH 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id THP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-3',5'-DIPHOSPHATE" _chem_comp.type 'dna 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 P2 O4P THP doub 277 n n P2 O5P THP sing 278 n n P2 O6P THP sing 279 n n P2 O5' THP sing 280 n n O5P HOP5 THP sing 281 n n O6P HOP6 THP sing 282 n n P1 O1P THP doub 283 n n P1 O2P THP sing 284 n n P1 O3P THP sing 285 n n P1 O3' THP sing 286 n n O2P HOP2 THP sing 287 n n O3P HOP3 THP sing 288 n n O5' C5' THP sing 289 n n C5' C4' THP sing 290 n n C5' "H5'1" THP sing 291 n n C5' "H5'2" THP sing 292 n n C4' O4' THP sing 293 n n C4' C3' THP sing 294 n n C4' H4' THP sing 295 n n O4' C1' THP sing 296 n n C3' O3' THP sing 297 n n C3' C2' THP sing 298 n n C3' H3' THP sing 299 n n C2' C1' THP sing 300 n n C2' "H2'1" THP sing 301 n n C2' "H2'2" THP sing 302 n n C1' N1 THP sing 303 n n C1' H1' THP sing 304 n n N1 C2 THP sing 305 n n N1 C6 THP sing 306 n n C2 O2 THP doub 307 n n C2 N3 THP sing 308 n n N3 C4 THP sing 309 n n N3 H3 THP sing 310 n n C4 O4 THP doub 311 n n C4 C5 THP sing 312 n n C5 C5M THP sing 313 n n C5 C6 THP doub 314 n n C5M H51 THP sing 315 n n C5M H52 THP sing 316 n n C5M H53 THP sing 317 n n C6 H6 THP sing 318 n n # _atom_sites.entry_id 3NQT _atom_sites.fract_transf_matrix[1][1] 0.032297 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001861 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016487 _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] 0.025981 _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 THP A 1 150 1 THP THP . C 3 CA A 1 151 1 CA CA . D 4 HOH A 1 152 1 HOH HOH . D 4 HOH A 2 153 1 HOH HOH . D 4 HOH A 3 154 2 HOH HOH . D 4 HOH A 4 155 3 HOH HOH . D 4 HOH A 5 156 4 HOH HOH . D 4 HOH A 6 157 5 HOH HOH . D 4 HOH A 7 158 6 HOH HOH . D 4 HOH A 8 159 7 HOH HOH . D 4 HOH A 9 160 8 HOH HOH . D 4 HOH A 10 161 9 HOH HOH . D 4 HOH A 11 162 11 HOH HOH . D 4 HOH A 12 163 12 HOH HOH . D 4 HOH A 13 164 14 HOH HOH . D 4 HOH A 14 165 16 HOH HOH . D 4 HOH A 15 166 18 HOH HOH . D 4 HOH A 16 167 19 HOH HOH . D 4 HOH A 17 168 1 HOH HOH . D 4 HOH A 18 169 1 HOH HOH . D 4 HOH A 19 170 2 HOH HOH . D 4 HOH A 20 171 3 HOH HOH . D 4 HOH A 21 172 4 HOH HOH . D 4 HOH A 22 173 5 HOH HOH . D 4 HOH A 23 174 6 HOH HOH . D 4 HOH A 24 175 7 HOH HOH . D 4 HOH A 25 176 9 HOH HOH . D 4 HOH A 26 177 10 HOH HOH . D 4 HOH A 27 178 16 HOH HOH . D 4 HOH A 28 179 17 HOH HOH . D 4 HOH A 29 180 19 HOH HOH . D 4 HOH A 30 181 21 HOH HOH . D 4 HOH A 31 182 23 HOH HOH . D 4 HOH A 32 183 26 HOH HOH . D 4 HOH A 33 184 30 HOH HOH . D 4 HOH A 34 185 32 HOH HOH . D 4 HOH A 35 186 35 HOH HOH . D 4 HOH A 36 187 39 HOH HOH . D 4 HOH A 37 188 40 HOH HOH . D 4 HOH A 38 189 41 HOH HOH . D 4 HOH A 39 190 42 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 P2 THP . . . B 2 17.923 10.872 5.016 1 27.39 ? P2 THP 150 A 1 HETATM 2 O O4P THP . . . B 2 16.687 11.549 5.476 1 27.13 ? O4P THP 150 A 1 HETATM 3 O O5P THP . . . B 2 17.918 9.336 5.296 1 21.9 ? O5P THP 150 A 1 HETATM 4 O O6P THP . . . B 2 19.226 11.534 5.599 1 28 ? O6P THP 150 A 1 HETATM 5 P P1 THP . . . B 2 21.056 14.602 1.05 1 34 ? P1 THP 150 A 1 HETATM 6 O O1P THP . . . B 2 22.091 15.121 0.167 1 37.67 ? O1P THP 150 A 1 HETATM 7 O O2P THP . . . B 2 20.441 15.662 2.039 1 34.97 ? O2P THP 150 A 1 HETATM 8 O O3P THP . . . B 2 21.768 13.467 1.964 1 37.51 ? O3P THP 150 A 1 HETATM 9 O O5' THP . . . B 2 18.023 10.966 3.396 1 25.97 ? O5' THP 150 A 1 HETATM 10 C C5' THP . . . B 2 17.978 12.306 2.899 1 25.13 ? C5' THP 150 A 1 HETATM 11 C C4' THP . . . B 2 18.825 12.306 1.615 1 22.73 ? C4' THP 150 A 1 HETATM 12 O O4' THP . . . B 2 18.463 11.184 0.808 1 22.96 ? O4' THP 150 A 1 HETATM 13 C C3' THP . . . B 2 18.77 13.57 0.706 1 25.2 ? C3' THP 150 A 1 HETATM 14 O O3' THP . . . B 2 20.022 13.868 0.045 1 33.01 ? O3' THP 150 A 1 HETATM 15 C C2' THP . . . B 2 17.827 13.127 -0.44 1 21.72 ? C2' THP 150 A 1 HETATM 16 C C1' THP . . . B 2 18.064 11.602 -0.512 1 22.11 ? C1' THP 150 A 1 HETATM 17 N N1 THP . . . B 2 16.774 10.992 -0.889 1 23.73 ? N1 THP 150 A 1 HETATM 18 C C2 THP . . . B 2 16.511 10.812 -2.204 1 27.51 ? C2 THP 150 A 1 HETATM 19 O O2 THP . . . B 2 17.34 11.158 -3.038 1 29.14 ? O2 THP 150 A 1 HETATM 20 N N3 THP . . . B 2 15.328 10.314 -2.635 1 25.62 ? N3 THP 150 A 1 HETATM 21 C C4 THP . . . B 2 14.364 10.001 -1.757 1 27.6 ? C4 THP 150 A 1 HETATM 22 O O4 THP . . . B 2 13.328 9.569 -2.227 1 26.6 ? O4 THP 150 A 1 HETATM 23 C C5 THP . . . B 2 14.619 10.169 -0.35 1 22.21 ? C5 THP 150 A 1 HETATM 24 C C5M THP . . . B 2 13.6 9.815 0.705 1 25.77 ? C5M THP 150 A 1 HETATM 25 C C6 THP . . . B 2 15.826 10.664 0.044 1 23.01 ? C6 THP 150 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #