data_1TR5 # _model_server_result.job_id -WZziToJ7Bf5dQC9pVJRMw _model_server_result.datetime_utc '2024-10-11 10:26:25' _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 1tr5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":300}' # _entry.id 1TR5 # _exptl.entry_id 1TR5 _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 96.1 _cell.angle_gamma 90 _cell.entry_id 1TR5 _cell.length_a 31.298 _cell.length_b 60.981 _cell.length_c 38.789 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TR5 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 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 A OD2 ASP 21 A ASP 21 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.911 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc4 A OE1 GLU 43 A GLU 43 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.377 ? metalc ? metalc5 C O4P THP . A THP 300 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? # _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 1TR5 _atom_sites.fract_transf_matrix[1][1] 0.031951 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003415 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016399 _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] 0.025927 _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 1 301 301 CA CA . C 3 THP A 1 300 300 THP THP . D 4 HOH A 1 201 201 HOH HOH . D 4 HOH A 2 202 202 HOH HOH . D 4 HOH A 3 203 203 HOH HOH . D 4 HOH A 4 204 204 HOH HOH . D 4 HOH A 5 205 205 HOH HOH . D 4 HOH A 6 206 206 HOH HOH . D 4 HOH A 7 207 207 HOH HOH . D 4 HOH A 8 208 208 HOH HOH . D 4 HOH A 9 209 209 HOH HOH . D 4 HOH A 10 210 210 HOH HOH . D 4 HOH A 11 211 211 HOH HOH . D 4 HOH A 12 212 212 HOH HOH . D 4 HOH A 13 213 213 HOH HOH . D 4 HOH A 14 214 214 HOH HOH . D 4 HOH A 15 215 215 HOH HOH . D 4 HOH A 16 216 216 HOH HOH . D 4 HOH A 17 217 217 HOH HOH . D 4 HOH A 18 218 218 HOH HOH . D 4 HOH A 19 219 219 HOH HOH . D 4 HOH A 20 220 220 HOH HOH . D 4 HOH A 21 221 221 HOH HOH . D 4 HOH A 22 222 222 HOH HOH . D 4 HOH A 23 223 223 HOH HOH . D 4 HOH A 24 224 224 HOH HOH . D 4 HOH A 25 225 225 HOH HOH . D 4 HOH A 26 226 226 HOH HOH . D 4 HOH A 27 227 227 HOH HOH . D 4 HOH A 28 228 228 HOH HOH . D 4 HOH A 29 229 229 HOH HOH . D 4 HOH A 30 230 230 HOH HOH . D 4 HOH A 31 231 231 HOH HOH . D 4 HOH A 32 232 232 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 18.043 7.126 4.989 1 47.46 ? P2 THP 300 A 1 HETATM 2 O O4P THP . . . C 3 16.941 7.999 5.472 1 48.2 ? O4P THP 300 A 1 HETATM 3 O O5P THP . . . C 3 18.112 5.709 5.4 1 46.63 ? O5P THP 300 A 1 HETATM 4 O O6P THP . . . C 3 19.408 7.815 5.353 1 46.43 ? O6P THP 300 A 1 HETATM 5 P P1 THP . . . C 3 21.014 10.995 0.552 1 60.09 ? P1 THP 300 A 1 HETATM 6 O O1P THP . . . C 3 20.021 12.074 0.695 1 61.66 ? O1P THP 300 A 1 HETATM 7 O O2P THP . . . C 3 22.215 10.973 -0.301 1 59.28 ? O2P THP 300 A 1 HETATM 8 O O3P THP . . . C 3 21.495 10.631 2.038 1 60.4 ? O3P THP 300 A 1 HETATM 9 O O5' THP . . . C 3 18.053 7.189 3.405 1 46.93 ? O5' THP 300 A 1 HETATM 10 C C5' THP . . . C 3 17.978 8.407 2.688 1 48.08 ? C5' THP 300 A 1 HETATM 11 C C4' THP . . . C 3 18.854 8.268 1.452 1 51.34 ? C4' THP 300 A 1 HETATM 12 O O4' THP . . . C 3 18.384 7.195 0.645 1 52.04 ? O4' THP 300 A 1 HETATM 13 C C3' THP . . . C 3 18.799 9.506 0.594 1 53.95 ? C3' THP 300 A 1 HETATM 14 O O3' THP . . . C 3 20.092 9.779 0.041 1 58.68 ? O3' THP 300 A 1 HETATM 15 C C2' THP . . . C 3 17.832 9.203 -0.498 1 51.88 ? C2' THP 300 A 1 HETATM 16 C C1' THP . . . C 3 18.013 7.692 -0.638 1 49.2 ? C1' THP 300 A 1 HETATM 17 N N1 THP . . . C 3 16.711 7.178 -1.07 1 47.86 ? N1 THP 300 A 1 HETATM 18 C C2 THP . . . C 3 16.518 6.997 -2.431 1 47.54 ? C2 THP 300 A 1 HETATM 19 O O2 THP . . . C 3 17.362 7.235 -3.267 1 47.91 ? O2 THP 300 A 1 HETATM 20 N N3 THP . . . C 3 15.3 6.525 -2.824 1 45.02 ? N3 THP 300 A 1 HETATM 21 C C4 THP . . . C 3 14.252 6.216 -1.987 1 45.25 ? C4 THP 300 A 1 HETATM 22 O O4 THP . . . C 3 13.229 5.806 -2.495 1 44.56 ? O4 THP 300 A 1 HETATM 23 C C5 THP . . . C 3 14.499 6.421 -0.556 1 44.54 ? C5 THP 300 A 1 HETATM 24 C C5M THP . . . C 3 13.403 6.116 0.48 1 43.01 ? C5M THP 300 A 1 HETATM 25 C C6 THP . . . C 3 15.704 6.89 -0.155 1 45.89 ? C6 THP 300 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #