data_5D42 # _model_server_result.job_id CjKd0_CoL90CnkUcWVWUWg _model_server_result.datetime_utc '2024-10-20 19:01:23' _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 5d42 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 5D42 # _exptl.entry_id 5D42 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-PHOSPHATE" _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 5D42 _cell.length_a 74.084 _cell.length_b 74.084 _cell.length_c 130.312 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D42 _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _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 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 A NE2 HIS 41 A HIS 41 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc2 A OE2 GLU 61 A GLU 80 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc3 A OD2 ASP 89 A ASP 108 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? metalc ? metalc4 A OD1 ASP 89 A ASP 108 1_555 C MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc5 A OE2 GLU 100 A GLU 119 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc6 A O ILE 101 A ILE 120 1_555 B MN MN . A MN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc7 B MN MN . A MN 301 1_555 D O2P TMP . A TMP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc8 B MN MN . A MN 301 1_555 D O3P TMP . A TMP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc9 C MN MN . A MN 302 1_555 D O2P TMP . A TMP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc10 C MN MN . A MN 302 1_555 E O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc11 C MN MN . A MN 302 1_555 E O HOH . A HOH 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc12 C MN MN . A MN 302 1_555 E O HOH . A HOH 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-PHOSPHATE" _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 P O1P TMP doub 306 n n P O2P TMP sing 307 n n P O3P TMP sing 308 n n P O5' TMP sing 309 n n O2P HOP2 TMP sing 310 n n O3P HOP3 TMP sing 311 n n O5' C5' TMP sing 312 n n C5' C4' TMP sing 313 n n C5' "H5'1" TMP sing 314 n n C5' "H5'2" TMP sing 315 n n C4' O4' TMP sing 316 n n C4' C3' TMP sing 317 n n C4' H4' TMP sing 318 n n O4' C1' TMP sing 319 n n C3' O3' TMP sing 320 n n C3' C2' TMP sing 321 n n C3' H3' TMP sing 322 n n O3' HO3' TMP sing 323 n n C2' C1' TMP sing 324 n n C2' "H2'1" TMP sing 325 n n C2' "H2'2" TMP sing 326 n n C1' N1 TMP sing 327 n n C1' H1' TMP sing 328 n n N1 C2 TMP sing 329 n n N1 C6 TMP sing 330 n n C2 O2 TMP doub 331 n n C2 N3 TMP sing 332 n n N3 C4 TMP sing 333 n n N3 HN3 TMP sing 334 n n C4 O4 TMP doub 335 n n C4 C5 TMP sing 336 n n C5 C5M TMP sing 337 n n C5 C6 TMP doub 338 n n C5M H51 TMP sing 339 n n C5M H52 TMP sing 340 n n C5M H53 TMP sing 341 n n C6 H6 TMP sing 342 n n # _atom_sites.entry_id 5D42 _atom_sites.fract_transf_matrix[1][1] 0.013498 _atom_sites.fract_transf_matrix[1][2] 0.007793 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015586 _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] 0.007674 _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 MN A 1 301 201 MN MN . C 2 MN A 1 302 202 MN MN . D 3 TMP A 1 303 1 TMP TMP . E 4 HOH A 1 401 21 HOH HOH . E 4 HOH A 2 402 14 HOH HOH . E 4 HOH A 3 403 10 HOH HOH . E 4 HOH A 4 404 46 HOH HOH . E 4 HOH A 5 405 23 HOH HOH . E 4 HOH A 6 406 1 HOH HOH . E 4 HOH A 7 407 17 HOH HOH . E 4 HOH A 8 408 15 HOH HOH . E 4 HOH A 9 409 57 HOH HOH . E 4 HOH A 10 410 63 HOH HOH . E 4 HOH A 11 411 48 HOH HOH . E 4 HOH A 12 412 52 HOH HOH . E 4 HOH A 13 413 58 HOH HOH . E 4 HOH A 14 414 5 HOH HOH . E 4 HOH A 15 415 50 HOH HOH . E 4 HOH A 16 416 61 HOH HOH . E 4 HOH A 17 417 4 HOH HOH . E 4 HOH A 18 418 30 HOH HOH . E 4 HOH A 19 419 62 HOH HOH . E 4 HOH A 20 420 64 HOH HOH . E 4 HOH A 21 421 36 HOH HOH . E 4 HOH A 22 422 40 HOH HOH . E 4 HOH A 23 423 44 HOH HOH . E 4 HOH A 24 424 35 HOH HOH . E 4 HOH A 25 425 47 HOH HOH . E 4 HOH A 26 426 42 HOH HOH . E 4 HOH A 27 427 27 HOH HOH . E 4 HOH A 28 428 59 HOH HOH . E 4 HOH A 29 429 13 HOH HOH . E 4 HOH A 30 430 49 HOH HOH . E 4 HOH A 31 431 34 HOH HOH . E 4 HOH A 32 432 26 HOH HOH . E 4 HOH A 33 433 22 HOH HOH . E 4 HOH A 34 434 25 HOH HOH . E 4 HOH A 35 435 8 HOH HOH . E 4 HOH A 36 436 60 HOH HOH . E 4 HOH A 37 437 39 HOH HOH . E 4 HOH A 38 438 43 HOH HOH . E 4 HOH A 39 439 18 HOH HOH . E 4 HOH A 40 440 31 HOH HOH . E 4 HOH A 41 441 32 HOH HOH . E 4 HOH A 42 442 56 HOH HOH . E 4 HOH A 43 443 41 HOH HOH . E 4 HOH A 44 444 12 HOH HOH . E 4 HOH A 45 445 29 HOH HOH . E 4 HOH A 46 446 24 HOH HOH . E 4 HOH A 47 447 6 HOH HOH . E 4 HOH A 48 448 54 HOH HOH . E 4 HOH A 49 449 9 HOH HOH . E 4 HOH A 50 450 2 HOH HOH . E 4 HOH A 51 451 33 HOH HOH . E 4 HOH A 52 452 3 HOH HOH . E 4 HOH A 53 453 28 HOH HOH . E 4 HOH A 54 454 37 HOH HOH . E 4 HOH A 55 455 11 HOH HOH . E 4 HOH A 56 456 38 HOH HOH . E 4 HOH A 57 457 45 HOH HOH . E 4 HOH A 58 458 19 HOH HOH . E 4 HOH A 59 459 20 HOH HOH . E 4 HOH A 60 460 51 HOH HOH . E 4 HOH A 61 461 7 HOH HOH . E 4 HOH A 62 462 16 HOH HOH . E 4 HOH A 63 463 55 HOH HOH . E 4 HOH A 64 464 53 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 P TMP . . . D 3 25.91 16.514 4.786 1 41.55 ? P TMP 303 A 1 HETATM 2 O O1P TMP . . . D 3 26.767 17.484 3.998 1 39.76 ? O1P TMP 303 A 1 HETATM 3 O O2P TMP . . . D 3 25.159 15.433 4.047 1 36.56 ? O2P TMP 303 A 1 HETATM 4 O O3P TMP . . . D 3 24.719 17.134 5.595 1 37.21 ? O3P TMP 303 A 1 HETATM 5 O O5' TMP . . . D 3 26.812 15.907 5.975 1 42.36 ? O5' TMP 303 A 1 HETATM 6 C C5' TMP . . . D 3 26.304 14.893 6.839 1 45.05 ? C5' TMP 303 A 1 HETATM 7 C C4' TMP . . . D 3 27.156 14.738 8.111 1 49.22 ? C4' TMP 303 A 1 HETATM 8 O O4' TMP . . . D 3 28.47 14.4 7.637 1 51.05 ? O4' TMP 303 A 1 HETATM 9 C C3' TMP . . . D 3 27.283 16.048 8.927 1 47.1 ? C3' TMP 303 A 1 HETATM 10 O O3' TMP . . . D 3 27.332 15.818 10.336 1 51.7 ? O3' TMP 303 A 1 HETATM 11 C C2' TMP . . . D 3 28.627 16.614 8.593 1 47.46 ? C2' TMP 303 A 1 HETATM 12 C C1' TMP . . . D 3 29.406 15.388 8.123 1 52.09 ? C1' TMP 303 A 1 HETATM 13 N N1 TMP . . . D 3 30.419 15.685 7.086 1 56.18 ? N1 TMP 303 A 1 HETATM 14 C C2 TMP . . . D 3 31.815 15.882 7.475 1 60.99 ? C2 TMP 303 A 1 HETATM 15 O O2 TMP . . . D 3 32.217 15.785 8.661 1 61.5 ? O2 TMP 303 A 1 HETATM 16 N N3 TMP . . . D 3 32.741 16.165 6.533 1 60.66 ? N3 TMP 303 A 1 HETATM 17 C C4 TMP . . . D 3 32.373 16.277 5.251 1 59.92 ? C4 TMP 303 A 1 HETATM 18 O O4 TMP . . . D 3 33.246 16.497 4.424 1 64.39 ? O4 TMP 303 A 1 HETATM 19 C C5 TMP . . . D 3 30.97 16.091 4.796 1 58.42 ? C5 TMP 303 A 1 HETATM 20 C C5M TMP . . . D 3 30.571 16.258 3.331 1 60.97 ? C5M TMP 303 A 1 HETATM 21 C C6 TMP . . . D 3 30.028 15.83 5.774 1 55.87 ? C6 TMP 303 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 21 #