data_4ODG # _model_server_result.job_id Qwy1QkbjCOeh6E9-6CNbPQ _model_server_result.datetime_utc '2024-10-11 10:26:47' _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 4odg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4ODG # _exptl.entry_id 4ODG _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 90 _cell.angle_gamma 90 _cell.entry_id 4ODG _cell.length_a 47.786 _cell.length_b 47.786 _cell.length_c 63.31 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ODG _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _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 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 OD1 ASP 21 A ASP 21 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc4 B O5P THP . A THP 201 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? metalc ? metalc5 C CA CA . A CA 202 1_555 E O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc6 C CA CA . A CA 202 1_555 E O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc7 C CA CA . A CA 202 1_555 E O HOH . A HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? # _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 281 n n P2 O5P THP sing 282 n n P2 O6P THP sing 283 n n P2 O5' THP sing 284 n n O5P HOP5 THP sing 285 n n O6P HOP6 THP sing 286 n n P1 O1P THP doub 287 n n P1 O2P THP sing 288 n n P1 O3P THP sing 289 n n P1 O3' THP sing 290 n n O2P HOP2 THP sing 291 n n O3P HOP3 THP sing 292 n n O5' C5' THP sing 293 n n C5' C4' THP sing 294 n n C5' "H5'1" THP sing 295 n n C5' "H5'2" THP sing 296 n n C4' O4' THP sing 297 n n C4' C3' THP sing 298 n n C4' H4' THP sing 299 n n O4' C1' THP sing 300 n n C3' O3' THP sing 301 n n C3' C2' THP sing 302 n n C3' H3' THP sing 303 n n C2' C1' THP sing 304 n n C2' "H2'1" THP sing 305 n n C2' "H2'2" THP sing 306 n n C1' N1 THP sing 307 n n C1' H1' THP sing 308 n n N1 C2 THP sing 309 n n N1 C6 THP sing 310 n n C2 O2 THP doub 311 n n C2 N3 THP sing 312 n n N3 C4 THP sing 313 n n N3 H3 THP sing 314 n n C4 O4 THP doub 315 n n C4 C5 THP sing 316 n n C5 C5M THP sing 317 n n C5 C6 THP doub 318 n n C5M H51 THP sing 319 n n C5M H52 THP sing 320 n n C5M H53 THP sing 321 n n C6 H6 THP sing 322 n n # _atom_sites.entry_id 4ODG _atom_sites.fract_transf_matrix[1][1] 0.020927 _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] 0.020927 _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] 0.015795 _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 1 201 1 THP THP . C 3 CA A 1 202 1 CA CA . D 4 PO4 A 1 203 1 PO4 PO4 . E 5 HOH A 1 301 1 HOH HOH . E 5 HOH A 2 302 2 HOH HOH . E 5 HOH A 3 303 3 HOH HOH . E 5 HOH A 4 304 4 HOH HOH . E 5 HOH A 5 305 5 HOH HOH . E 5 HOH A 6 306 6 HOH HOH . E 5 HOH A 7 307 7 HOH HOH . E 5 HOH A 8 308 8 HOH HOH . E 5 HOH A 9 309 9 HOH HOH . E 5 HOH A 10 310 10 HOH HOH . E 5 HOH A 11 311 11 HOH HOH . E 5 HOH A 12 312 12 HOH HOH . E 5 HOH A 13 313 13 HOH HOH . E 5 HOH A 14 314 14 HOH HOH . E 5 HOH A 15 315 15 HOH HOH . E 5 HOH A 16 316 16 HOH HOH . E 5 HOH A 17 317 17 HOH HOH . E 5 HOH A 18 318 18 HOH HOH . E 5 HOH A 19 319 19 HOH HOH . E 5 HOH A 20 320 21 HOH HOH . E 5 HOH A 21 321 22 HOH HOH . E 5 HOH A 22 322 24 HOH HOH . E 5 HOH A 23 323 26 HOH HOH . E 5 HOH A 24 324 27 HOH HOH . E 5 HOH A 25 325 28 HOH HOH . E 5 HOH A 26 326 29 HOH HOH . E 5 HOH A 27 327 30 HOH HOH . E 5 HOH A 28 328 31 HOH HOH . E 5 HOH A 29 329 33 HOH HOH . E 5 HOH A 30 330 34 HOH HOH . E 5 HOH A 31 331 35 HOH HOH . E 5 HOH A 32 332 36 HOH HOH . E 5 HOH A 33 333 37 HOH HOH . E 5 HOH A 34 334 38 HOH HOH . E 5 HOH A 35 335 39 HOH HOH . E 5 HOH A 36 336 40 HOH HOH . E 5 HOH A 37 337 41 HOH HOH . E 5 HOH A 38 338 42 HOH HOH . E 5 HOH A 39 339 43 HOH HOH . E 5 HOH A 40 340 44 HOH HOH . E 5 HOH A 41 341 45 HOH HOH . E 5 HOH A 42 342 46 HOH HOH . E 5 HOH A 43 343 47 HOH HOH . E 5 HOH A 44 344 48 HOH HOH . E 5 HOH A 45 345 49 HOH HOH . E 5 HOH A 46 346 50 HOH HOH . E 5 HOH A 47 347 51 HOH HOH . E 5 HOH A 48 348 52 HOH HOH . E 5 HOH A 49 349 53 HOH HOH . E 5 HOH A 50 350 54 HOH HOH . E 5 HOH A 51 351 55 HOH HOH . E 5 HOH A 52 352 56 HOH HOH . E 5 HOH A 53 353 57 HOH HOH . E 5 HOH A 54 354 58 HOH HOH . E 5 HOH A 55 355 59 HOH HOH . E 5 HOH A 56 356 60 HOH HOH . E 5 HOH A 57 357 61 HOH HOH . E 5 HOH A 58 358 62 HOH HOH . E 5 HOH A 59 359 63 HOH HOH . E 5 HOH A 60 360 64 HOH HOH . E 5 HOH A 61 361 65 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 13.791 5.94 -2.167 1 35.59 ? P2 THP 201 A 1 HETATM 2 O O4P THP . . . B 2 12.341 6.031 -2.692 1 36.43 ? O4P THP 201 A 1 HETATM 3 O O5P THP . . . B 2 13.74 4.844 -1.136 1 36.28 ? O5P THP 201 A 1 HETATM 4 O O6P THP . . . B 2 14.445 7.241 -1.902 1 28.93 ? O6P THP 201 A 1 HETATM 5 P P1 THP . . . B 2 11.702 4.515 -7.986 1 41.22 ? P1 THP 201 A 1 HETATM 6 O O1P THP . . . B 2 11.544 5.192 -9.326 1 53.17 ? O1P THP 201 A 1 HETATM 7 O O2P THP . . . B 2 11.178 5.373 -6.916 1 35.27 ? O2P THP 201 A 1 HETATM 8 O O3P THP . . . B 2 11.432 3.038 -8.023 1 37.5 ? O3P THP 201 A 1 HETATM 9 O O5' THP . . . B 2 14.562 5.344 -3.423 1 35.66 ? O5' THP 201 A 1 HETATM 10 C C5' THP . . . B 2 14.215 4.16 -4.125 1 36.96 ? C5' THP 201 A 1 HETATM 11 C C4' THP . . . B 2 14.248 4.609 -5.59 1 42.24 ? C4' THP 201 A 1 HETATM 12 O O4' THP . . . B 2 15.571 5.037 -5.951 1 40.44 ? O4' THP 201 A 1 HETATM 13 C C3' THP . . . B 2 13.866 3.592 -6.635 1 36.43 ? C3' THP 201 A 1 HETATM 14 O O3' THP . . . B 2 13.316 4.408 -7.691 1 47.65 ? O3' THP 201 A 1 HETATM 15 C C2' THP . . . B 2 15.192 2.983 -7.059 1 42.72 ? C2' THP 201 A 1 HETATM 16 C C1' THP . . . B 2 16.165 4.137 -6.871 1 39.44 ? C1' THP 201 A 1 HETATM 17 N N1 THP . . . B 2 17.446 3.624 -6.38 1 41.76 ? N1 THP 201 A 1 HETATM 18 C C2 THP . . . B 2 18.355 3.173 -7.355 1 37.05 ? C2 THP 201 A 1 HETATM 19 O O2 THP . . . B 2 18.067 3.308 -8.585 1 36.31 ? O2 THP 201 A 1 HETATM 20 N N3 THP . . . B 2 19.525 2.627 -7.032 1 32.09 ? N3 THP 201 A 1 HETATM 21 C C4 THP . . . B 2 19.875 2.517 -5.734 1 29.09 ? C4 THP 201 A 1 HETATM 22 O O4 THP . . . B 2 20.948 1.939 -5.5 1 29.27 ? O4 THP 201 A 1 HETATM 23 C C5 THP . . . B 2 18.927 2.913 -4.686 1 31.42 ? C5 THP 201 A 1 HETATM 24 C C5M THP . . . B 2 19.317 2.752 -3.214 1 28.31 ? C5M THP 201 A 1 HETATM 25 C C6 THP . . . B 2 17.732 3.524 -5.061 1 39.94 ? C6 THP 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #