data_7TXQ # _model_server_result.job_id ZeFl1lzomyUsW3RjmEoLIg _model_server_result.datetime_utc '2024-12-21 16:43:20' _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 7txq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7TXQ # _exptl.entry_id 7TXQ _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-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 120 _cell.entry_id 7TXQ _cell.length_a 97.413 _cell.length_b 97.413 _cell.length_c 72.842 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7TXQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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 ASN 130 A ASN 130 1_555 D NA NA . A NA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc2 A OD1 ASN 130 A ASN 130 1_555 D NA NA . A NA 303 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc3 A OD1 ASN 166 A ASN 166 1_555 E NA NA . A NA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc4 A OD1 ASN 166 A ASN 166 1_555 E NA NA . A NA 304 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc5 D NA NA . A NA 303 1_555 F O HOH . A HOH 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc6 D NA NA . A NA 303 1_555 F O HOH . A HOH 434 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc7 E NA NA . A NA 304 1_555 F O HOH . A HOH 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc8 E NA NA . A NA 304 1_555 F O HOH . A HOH 448 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _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 PA O1A TYD doub 425 n n PA O2A TYD sing 426 n n PA O3A TYD sing 427 n n PA O5' TYD sing 428 n n O2A HOA2 TYD sing 429 n n O3A PB TYD sing 430 n n PB O1B TYD doub 431 n n PB O2B TYD sing 432 n n PB O3B TYD sing 433 n n O2B HOB2 TYD sing 434 n n O3B HOB3 TYD sing 435 n n O5' C5' TYD sing 436 n n C5' C4' TYD sing 437 n n C5' "H5'1" TYD sing 438 n n C5' "H5'2" TYD sing 439 n n C4' O4' TYD sing 440 n n C4' C3' TYD sing 441 n n C4' H4' TYD sing 442 n n O4' C1' TYD sing 443 n n C3' O3' TYD sing 444 n n C3' C2' TYD sing 445 n n C3' H3' TYD sing 446 n n O3' HO3' TYD sing 447 n n C2' C1' TYD sing 448 n n C2' "H2'1" TYD sing 449 n n C2' "H2'2" TYD sing 450 n n C1' N1 TYD sing 451 n n C1' H1' TYD sing 452 n n N1 C2 TYD sing 453 n y N1 C6 TYD sing 454 n y C2 O2 TYD doub 455 n n C2 N3 TYD sing 456 n y N3 C4 TYD sing 457 n y N3 HN3 TYD sing 458 n n C4 O4 TYD doub 459 n n C4 C5 TYD sing 460 n y C5 C5M TYD sing 461 n n C5 C6 TYD doub 462 n y C5M H51 TYD sing 463 n n C5M H52 TYD sing 464 n n C5M H53 TYD sing 465 n n C6 H6 TYD sing 466 n n # _atom_sites.entry_id 7TXQ _atom_sites.fract_transf_matrix[1][1] 0.010266 _atom_sites.fract_transf_matrix[1][2] 0.005927 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011854 _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] 0.013728 _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 TYD A 1 301 250 TYD TYD . C 3 ACO A 1 302 251 ACO ACO . D 4 NA A 1 303 1 NA NA . E 4 NA A 1 304 2 NA NA . F 5 HOH A 1 401 202 HOH HOH . F 5 HOH A 2 402 168 HOH HOH . F 5 HOH A 3 403 172 HOH HOH . F 5 HOH A 4 404 30 HOH HOH . F 5 HOH A 5 405 169 HOH HOH . F 5 HOH A 6 406 164 HOH HOH . F 5 HOH A 7 407 129 HOH HOH . F 5 HOH A 8 408 187 HOH HOH . F 5 HOH A 9 409 120 HOH HOH . F 5 HOH A 10 410 165 HOH HOH . F 5 HOH A 11 411 56 HOH HOH . F 5 HOH A 12 412 118 HOH HOH . F 5 HOH A 13 413 105 HOH HOH . F 5 HOH A 14 414 87 HOH HOH . F 5 HOH A 15 415 98 HOH HOH . F 5 HOH A 16 416 3 HOH HOH . F 5 HOH A 17 417 27 HOH HOH . F 5 HOH A 18 418 31 HOH HOH . F 5 HOH A 19 419 101 HOH HOH . F 5 HOH A 20 420 69 HOH HOH . F 5 HOH A 21 421 104 HOH HOH . F 5 HOH A 22 422 190 HOH HOH . F 5 HOH A 23 423 106 HOH HOH . F 5 HOH A 24 424 21 HOH HOH . F 5 HOH A 25 425 96 HOH HOH . F 5 HOH A 26 426 72 HOH HOH . F 5 HOH A 27 427 20 HOH HOH . F 5 HOH A 28 428 121 HOH HOH . F 5 HOH A 29 429 128 HOH HOH . F 5 HOH A 30 430 66 HOH HOH . F 5 HOH A 31 431 93 HOH HOH . F 5 HOH A 32 432 16 HOH HOH . F 5 HOH A 33 433 63 HOH HOH . F 5 HOH A 34 434 154 HOH HOH . F 5 HOH A 35 435 33 HOH HOH . F 5 HOH A 36 436 35 HOH HOH . F 5 HOH A 37 437 12 HOH HOH . F 5 HOH A 38 438 143 HOH HOH . F 5 HOH A 39 439 54 HOH HOH . F 5 HOH A 40 440 50 HOH HOH . F 5 HOH A 41 441 10 HOH HOH . F 5 HOH A 42 442 41 HOH HOH . F 5 HOH A 43 443 29 HOH HOH . F 5 HOH A 44 444 34 HOH HOH . F 5 HOH A 45 445 114 HOH HOH . F 5 HOH A 46 446 201 HOH HOH . F 5 HOH A 47 447 89 HOH HOH . F 5 HOH A 48 448 4 HOH HOH . F 5 HOH A 49 449 43 HOH HOH . F 5 HOH A 50 450 127 HOH HOH . F 5 HOH A 51 451 15 HOH HOH . F 5 HOH A 52 452 23 HOH HOH . F 5 HOH A 53 453 107 HOH HOH . F 5 HOH A 54 454 59 HOH HOH . F 5 HOH A 55 455 5 HOH HOH . F 5 HOH A 56 456 88 HOH HOH . F 5 HOH A 57 457 71 HOH HOH . F 5 HOH A 58 458 52 HOH HOH . F 5 HOH A 59 459 61 HOH HOH . F 5 HOH A 60 460 75 HOH HOH . F 5 HOH A 61 461 67 HOH HOH . F 5 HOH A 62 462 58 HOH HOH . F 5 HOH A 63 463 11 HOH HOH . F 5 HOH A 64 464 81 HOH HOH . F 5 HOH A 65 465 163 HOH HOH . F 5 HOH A 66 466 86 HOH HOH . F 5 HOH A 67 467 46 HOH HOH . F 5 HOH A 68 468 179 HOH HOH . F 5 HOH A 69 469 70 HOH HOH . F 5 HOH A 70 470 112 HOH HOH . F 5 HOH A 71 471 38 HOH HOH . F 5 HOH A 72 472 48 HOH HOH . F 5 HOH A 73 473 57 HOH HOH . F 5 HOH A 74 474 80 HOH HOH . F 5 HOH A 75 475 60 HOH HOH . F 5 HOH A 76 476 130 HOH HOH . F 5 HOH A 77 477 2 HOH HOH . F 5 HOH A 78 478 198 HOH HOH . F 5 HOH A 79 479 203 HOH HOH . F 5 HOH A 80 480 7 HOH HOH . F 5 HOH A 81 481 1 HOH HOH . F 5 HOH A 82 482 90 HOH HOH . F 5 HOH A 83 483 49 HOH HOH . F 5 HOH A 84 484 92 HOH HOH . F 5 HOH A 85 485 82 HOH HOH . F 5 HOH A 86 486 62 HOH HOH . F 5 HOH A 87 487 22 HOH HOH . F 5 HOH A 88 488 8 HOH HOH . F 5 HOH A 89 489 102 HOH HOH . F 5 HOH A 90 490 124 HOH HOH . F 5 HOH A 91 491 84 HOH HOH . F 5 HOH A 92 492 142 HOH HOH . F 5 HOH A 93 493 166 HOH HOH . F 5 HOH A 94 494 119 HOH HOH . F 5 HOH A 95 495 193 HOH HOH . F 5 HOH A 96 496 174 HOH HOH . F 5 HOH A 97 497 17 HOH HOH . F 5 HOH A 98 498 64 HOH HOH . F 5 HOH A 99 499 40 HOH HOH . F 5 HOH A 100 500 110 HOH HOH . F 5 HOH A 101 501 44 HOH HOH . F 5 HOH A 102 502 144 HOH HOH . F 5 HOH A 103 503 32 HOH HOH . F 5 HOH A 104 504 85 HOH HOH . F 5 HOH A 105 505 123 HOH HOH . F 5 HOH A 106 506 37 HOH HOH . F 5 HOH A 107 507 175 HOH HOH . F 5 HOH A 108 508 51 HOH HOH . F 5 HOH A 109 509 151 HOH HOH . F 5 HOH A 110 510 184 HOH HOH . F 5 HOH A 111 511 68 HOH HOH . F 5 HOH A 112 512 94 HOH HOH . F 5 HOH A 113 513 24 HOH HOH . F 5 HOH A 114 514 197 HOH HOH . F 5 HOH A 115 515 195 HOH HOH . F 5 HOH A 116 516 26 HOH HOH . F 5 HOH A 117 517 115 HOH HOH . F 5 HOH A 118 518 9 HOH HOH . F 5 HOH A 119 519 134 HOH HOH . F 5 HOH A 120 520 125 HOH HOH . F 5 HOH A 121 521 45 HOH HOH . F 5 HOH A 122 522 170 HOH HOH . F 5 HOH A 123 523 18 HOH HOH . F 5 HOH A 124 524 192 HOH HOH . F 5 HOH A 125 525 103 HOH HOH . F 5 HOH A 126 526 25 HOH HOH . F 5 HOH A 127 527 6 HOH HOH . F 5 HOH A 128 528 76 HOH HOH . F 5 HOH A 129 529 77 HOH HOH . F 5 HOH A 130 530 19 HOH HOH . F 5 HOH A 131 531 28 HOH HOH . F 5 HOH A 132 532 65 HOH HOH . F 5 HOH A 133 533 13 HOH HOH . F 5 HOH A 134 534 83 HOH HOH . F 5 HOH A 135 535 73 HOH HOH . F 5 HOH A 136 536 39 HOH HOH . F 5 HOH A 137 537 47 HOH HOH . F 5 HOH A 138 538 108 HOH HOH . F 5 HOH A 139 539 14 HOH HOH . F 5 HOH A 140 540 53 HOH HOH . F 5 HOH A 141 541 171 HOH HOH . F 5 HOH A 142 542 183 HOH HOH . F 5 HOH A 143 543 131 HOH HOH . F 5 HOH A 144 544 147 HOH HOH . F 5 HOH A 145 545 160 HOH HOH . F 5 HOH A 146 546 191 HOH HOH . F 5 HOH A 147 547 100 HOH HOH . F 5 HOH A 148 548 199 HOH HOH . F 5 HOH A 149 549 181 HOH HOH . F 5 HOH A 150 550 145 HOH HOH . F 5 HOH A 151 551 157 HOH HOH . F 5 HOH A 152 552 74 HOH HOH . F 5 HOH A 153 553 159 HOH HOH . F 5 HOH A 154 554 173 HOH HOH . F 5 HOH A 155 555 189 HOH HOH . F 5 HOH A 156 556 185 HOH HOH . F 5 HOH A 157 557 97 HOH HOH . F 5 HOH A 158 558 162 HOH HOH . F 5 HOH A 159 559 42 HOH HOH . F 5 HOH A 160 560 111 HOH HOH . F 5 HOH A 161 561 180 HOH HOH . F 5 HOH A 162 562 196 HOH HOH . F 5 HOH A 163 563 200 HOH HOH . F 5 HOH A 164 564 150 HOH HOH . F 5 HOH A 165 565 158 HOH HOH . F 5 HOH A 166 566 167 HOH HOH . F 5 HOH A 167 567 139 HOH HOH . F 5 HOH A 168 568 186 HOH HOH . F 5 HOH A 169 569 117 HOH HOH . F 5 HOH A 170 570 188 HOH HOH . F 5 HOH A 171 571 113 HOH HOH . F 5 HOH A 172 572 95 HOH HOH . F 5 HOH A 173 573 78 HOH HOH . F 5 HOH A 174 574 55 HOH HOH . F 5 HOH A 175 575 155 HOH HOH . F 5 HOH A 176 576 161 HOH HOH . F 5 HOH A 177 577 182 HOH HOH . F 5 HOH A 178 578 176 HOH HOH . F 5 HOH A 179 579 177 HOH HOH . F 5 HOH A 180 580 116 HOH HOH . F 5 HOH A 181 581 194 HOH HOH . F 5 HOH A 182 582 178 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 PA TYD . . . B 2 -8.989 21.808 28.801 1 40.71 ? PA TYD 301 A 1 HETATM 2 O O1A TYD . . . B 2 -7.566 21.726 28.327 1 33.7 ? O1A TYD 301 A 1 HETATM 3 O O2A TYD . . . B 2 -9.316 22.516 30.076 1 43.53 ? O2A TYD 301 A 1 HETATM 4 O O3A TYD . . . B 2 -9.607 20.326 28.888 1 35.43 ? O3A TYD 301 A 1 HETATM 5 P PB TYD . . . B 2 -9.87 19.244 27.707 1 32.82 ? PB TYD 301 A 1 HETATM 6 O O1B TYD . . . B 2 -9.544 19.99 26.422 1 30.28 ? O1B TYD 301 A 1 HETATM 7 O O2B TYD . . . B 2 -11.3 18.778 27.769 1 28.78 ? O2B TYD 301 A 1 HETATM 8 O O3B TYD . . . B 2 -8.872 18.146 27.999 1 37.25 ? O3B TYD 301 A 1 HETATM 9 O O5' TYD . . . B 2 -9.882 22.419 27.617 1 41.33 ? O5' TYD 301 A 1 HETATM 10 C C5' TYD . . . B 2 -11.308 22.538 27.802 1 36.33 ? C5' TYD 301 A 1 HETATM 11 C C4' TYD . . . B 2 -11.78 23.686 26.95 1 36.49 ? C4' TYD 301 A 1 HETATM 12 O O4' TYD . . . B 2 -13.209 23.601 26.814 1 40.2 ? O4' TYD 301 A 1 HETATM 13 C C3' TYD . . . B 2 -11.465 25.079 27.497 1 37.81 ? C3' TYD 301 A 1 HETATM 14 O O3' TYD . . . B 2 -10.77 25.837 26.516 1 29.75 ? O3' TYD 301 A 1 HETATM 15 C C2' TYD . . . B 2 -12.833 25.699 27.776 1 37.65 ? C2' TYD 301 A 1 HETATM 16 C C1' TYD . . . B 2 -13.743 24.914 26.848 1 40.82 ? C1' TYD 301 A 1 HETATM 17 N N1 TYD . . . B 2 -15.14 24.806 27.295 1 42.59 ? N1 TYD 301 A 1 HETATM 18 C C2 TYD . . . B 2 -16.076 25.586 26.653 1 45.98 ? C2 TYD 301 A 1 HETATM 19 O O2 TYD . . . B 2 -15.778 26.344 25.737 1 37.48 ? O2 TYD 301 A 1 HETATM 20 N N3 TYD . . . B 2 -17.355 25.463 27.14 1 44.9 ? N3 TYD 301 A 1 HETATM 21 C C4 TYD . . . B 2 -17.781 24.624 28.157 1 49.46 ? C4 TYD 301 A 1 HETATM 22 O O4 TYD . . . B 2 -18.977 24.6 28.473 1 62.79 ? O4 TYD 301 A 1 HETATM 23 C C5 TYD . . . B 2 -16.744 23.829 28.779 1 44.3 ? C5 TYD 301 A 1 HETATM 24 C C5M TYD . . . B 2 -17.113 22.893 29.887 1 39.44 ? C5M TYD 301 A 1 HETATM 25 C C6 TYD . . . B 2 -15.485 23.96 28.329 1 46.58 ? C6 TYD 301 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #