data_3P75 # _model_server_result.job_id GZDSpTU6KhkdpFua_jL7Hg _model_server_result.datetime_utc '2024-10-20 03:53:06' _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 3p75 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":142}' # _entry.id 3P75 # _exptl.entry_id 3P75 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 3 _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 93.45 _cell.angle_gamma 90 _cell.entry_id 3P75 _cell.length_a 31 _cell.length_b 60.791 _cell.length_c 36.838 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3P75 _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,E _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 3 _struct_asym.id C _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 B CA CA . A CA 1 1_555 A OD2 ASP 15 A ASP 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc2 B CA CA . A CA 1 1_555 A OD1 ASP 34 A ASP 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc3 B CA CA . A CA 1 1_555 A O THR 35 A THR 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc4 B CA CA . A CA 1 1_555 E O HOH . A HOH 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc5 B CA CA . A CA 1 1_555 E O HOH . A HOH 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc6 B CA CA . A CA 1 1_555 E O HOH . A HOH 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc7 B CA CA . A CA 1 1_555 E O HOH . A HOH 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc8 A OD2 ASP 13 A ASP 19 1_555 D CA CA . A CA 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc9 A OD1 ASP 13 A ASP 19 1_555 D CA CA . A CA 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc10 A OD1 ASP 15 A ASP 21 1_555 D CA CA . A CA 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc11 A OG1 THR 16 A THR 22 1_555 D CA CA . A CA 143 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc12 C O5P THP . A THP 142 1_555 D CA CA . A CA 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc13 D CA CA . A CA 143 1_555 E O HOH . A HOH 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc14 D CA CA . A CA 143 1_555 E O HOH . A HOH 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? # _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 3P75 _atom_sites.fract_transf_matrix[1][1] 0.032258 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001944 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01645 _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] 0.027195 _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 CA A 1 1 1 CA CA . C 3 THP A 1 142 1 THP THP . D 2 CA A 1 143 1 CA CA . E 4 HOH A 1 2 2 HOH HOH . E 4 HOH A 2 3 3 HOH HOH . E 4 HOH A 3 4 4 HOH HOH . E 4 HOH A 4 5 5 HOH HOH . E 4 HOH A 5 6 6 HOH HOH . E 4 HOH A 6 144 1 HOH HOH . E 4 HOH A 7 145 7 HOH HOH . E 4 HOH A 8 146 8 HOH HOH . E 4 HOH A 9 147 9 HOH HOH . E 4 HOH A 10 148 10 HOH HOH . E 4 HOH A 11 149 11 HOH HOH . E 4 HOH A 12 150 12 HOH HOH . E 4 HOH A 13 151 13 HOH HOH . E 4 HOH A 14 152 14 HOH HOH . E 4 HOH A 15 153 1 HOH HOH . E 4 HOH A 16 154 3 HOH HOH . E 4 HOH A 17 155 4 HOH HOH . E 4 HOH A 18 156 6 HOH HOH . E 4 HOH A 19 157 7 HOH HOH . E 4 HOH A 20 158 8 HOH HOH . E 4 HOH A 21 159 10 HOH HOH . E 4 HOH A 22 160 11 HOH HOH . E 4 HOH A 23 161 12 HOH HOH . E 4 HOH A 24 162 2 HOH HOH . E 4 HOH A 25 163 3 HOH HOH . E 4 HOH A 26 164 4 HOH HOH . E 4 HOH A 27 165 5 HOH HOH . E 4 HOH A 28 166 6 HOH HOH . E 4 HOH A 29 167 7 HOH HOH . E 4 HOH A 30 168 8 HOH HOH . E 4 HOH A 31 169 9 HOH HOH . E 4 HOH A 32 170 10 HOH HOH . E 4 HOH A 33 171 12 HOH HOH . E 4 HOH A 34 172 13 HOH HOH . E 4 HOH A 35 173 14 HOH HOH . E 4 HOH A 36 174 15 HOH HOH . E 4 HOH A 37 175 16 HOH HOH . E 4 HOH A 38 176 17 HOH HOH . E 4 HOH A 39 177 18 HOH HOH . E 4 HOH A 40 178 19 HOH HOH . E 4 HOH A 41 179 20 HOH HOH . E 4 HOH A 42 180 21 HOH HOH . E 4 HOH A 43 181 22 HOH HOH . E 4 HOH A 44 182 24 HOH HOH . E 4 HOH A 45 183 25 HOH HOH . E 4 HOH A 46 184 26 HOH HOH . E 4 HOH A 47 185 27 HOH HOH . E 4 HOH A 48 186 29 HOH HOH . E 4 HOH A 49 187 30 HOH HOH . E 4 HOH A 50 188 32 HOH HOH . E 4 HOH A 51 189 1 HOH HOH . E 4 HOH A 52 190 2 HOH HOH . E 4 HOH A 53 191 2 HOH HOH . E 4 HOH A 54 192 3 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 . . . C 3 18.319 9.611 4.453 1 36.79 ? P2 THP 142 A 1 HETATM 2 O O4P THP . . . C 3 18.35 10.816 5.296 1 36.9 ? O4P THP 142 A 1 HETATM 3 O O5P THP . . . C 3 17.691 8.344 5.219 1 38.05 ? O5P THP 142 A 1 HETATM 4 O O6P THP . . . C 3 19.833 9.229 4.037 1 41.43 ? O6P THP 142 A 1 HETATM 5 P P1 THP . . . C 3 20.86 13.295 0.011 1 42.29 ? P1 THP 142 A 1 HETATM 6 O O1P THP . . . C 3 20.158 14.53 -0.351 1 44.79 ? O1P THP 142 A 1 HETATM 7 O O2P THP . . . C 3 21.246 13.302 1.564 1 43.61 ? O2P THP 142 A 1 HETATM 8 O O3P THP . . . C 3 22.183 13.122 -0.904 1 46.38 ? O3P THP 142 A 1 HETATM 9 O O5' THP . . . C 3 17.447 9.96 3.143 1 33.68 ? O5' THP 142 A 1 HETATM 10 C C5' THP . . . C 3 17.817 11.189 2.535 1 31.17 ? C5' THP 142 A 1 HETATM 11 C C4' THP . . . C 3 18.494 10.846 1.201 1 34.16 ? C4' THP 142 A 1 HETATM 12 O O4' THP . . . C 3 17.742 9.861 0.448 1 34.3 ? O4' THP 142 A 1 HETATM 13 C C3' THP . . . C 3 18.69 12.069 0.275 1 33.37 ? C3' THP 142 A 1 HETATM 14 O O3' THP . . . C 3 20.001 11.965 -0.277 1 42.55 ? O3' THP 142 A 1 HETATM 15 C C2' THP . . . C 3 17.719 11.804 -0.9 1 34.42 ? C2' THP 142 A 1 HETATM 16 C C1' THP . . . C 3 17.618 10.271 -0.915 1 32.14 ? C1' THP 142 A 1 HETATM 17 N N1 THP . . . C 3 16.275 9.884 -1.376 1 30.03 ? N1 THP 142 A 1 HETATM 18 C C2 THP . . . C 3 16.067 9.77 -2.699 1 32.7 ? C2 THP 142 A 1 HETATM 19 O O2 THP . . . C 3 17.005 9.921 -3.475 1 33.64 ? O2 THP 142 A 1 HETATM 20 N N3 THP . . . C 3 14.849 9.45 -3.171 1 31.92 ? N3 THP 142 A 1 HETATM 21 C C4 THP . . . C 3 13.812 9.241 -2.308 1 29.08 ? C4 THP 142 A 1 HETATM 22 O O4 THP . . . C 3 12.709 8.953 -2.723 1 30.6 ? O4 THP 142 A 1 HETATM 23 C C5 THP . . . C 3 14.01 9.362 -0.915 1 30.91 ? C5 THP 142 A 1 HETATM 24 C C5M THP . . . C 3 12.835 9.133 0.011 1 25.37 ? C5M THP 142 A 1 HETATM 25 C C6 THP . . . C 3 15.245 9.709 -0.472 1 30.62 ? C6 THP 142 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #