data_5Y48 # _model_server_result.job_id 49wD3ld1T-NV3KkHhB7J-g _model_server_result.datetime_utc '2024-11-23 20:27:09' _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 5y48 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5Y48 # _exptl.entry_id 5Y48 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 112.087 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URACIL _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 5Y48 _cell.length_a 130.186 _cell.length_b 130.186 _cell.length_c 39.976 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y48 _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 ? _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id ND2 _struct_conn.ptnr1_label_comp_id ASN _struct_conn.ptnr1_label_seq_id 227 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ASN _struct_conn.ptnr1_auth_seq_id 227 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id C1 _struct_conn.ptnr2_label_comp_id NAG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id NAG _struct_conn.ptnr2_auth_seq_id 302 _struct_conn.ptnr2_symmetry 1_555 _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 1.458 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C4 H4 N2 O2' _chem_comp.formula_weight 112.087 _chem_comp.id URA _chem_comp.mon_nstd_flag . _chem_comp.name URACIL _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 N1 C2 URA sing 375 n n N1 C6 URA sing 376 n n N1 HN1 URA sing 377 n n C2 O2 URA doub 378 n n C2 N3 URA sing 379 n n N3 C4 URA sing 380 n n N3 HN3 URA sing 381 n n C4 O4 URA doub 382 n n C4 C5 URA sing 383 n n C5 C6 URA doub 384 n n C5 H5 URA sing 385 n n C6 H6 URA sing 386 n n # _atom_sites.entry_id 5Y48 _atom_sites.fract_transf_matrix[1][1] 0.007681 _atom_sites.fract_transf_matrix[1][2] 0.004435 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00887 _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] 0.025015 _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 URA A 1 301 301 URA URA . C 3 NAG A 1 302 302 NAG NAG . D 4 HOH A 1 401 401 HOH HOH . D 4 HOH A 2 402 403 HOH HOH . D 4 HOH A 3 403 404 HOH HOH . D 4 HOH A 4 404 409 HOH HOH . D 4 HOH A 5 405 406 HOH HOH . D 4 HOH A 6 406 402 HOH HOH . D 4 HOH A 7 407 410 HOH HOH . D 4 HOH A 8 408 412 HOH HOH . D 4 HOH A 9 409 408 HOH HOH . D 4 HOH A 10 410 405 HOH HOH . D 4 HOH A 11 411 413 HOH HOH . D 4 HOH A 12 412 418 HOH HOH . D 4 HOH A 13 413 420 HOH HOH . D 4 HOH A 14 414 414 HOH HOH . D 4 HOH A 15 415 443 HOH HOH . D 4 HOH A 16 416 416 HOH HOH . D 4 HOH A 17 417 419 HOH HOH . D 4 HOH A 18 418 431 HOH HOH . D 4 HOH A 19 419 422 HOH HOH . D 4 HOH A 20 420 441 HOH HOH . D 4 HOH A 21 421 425 HOH HOH . D 4 HOH A 22 422 423 HOH HOH . D 4 HOH A 23 423 453 HOH HOH . D 4 HOH A 24 424 434 HOH HOH . D 4 HOH A 25 425 436 HOH HOH . D 4 HOH A 26 426 428 HOH HOH . D 4 HOH A 27 427 433 HOH HOH . D 4 HOH A 28 428 427 HOH HOH . D 4 HOH A 29 429 426 HOH HOH . D 4 HOH A 30 430 435 HOH HOH . D 4 HOH A 31 431 432 HOH HOH . D 4 HOH A 32 432 437 HOH HOH . D 4 HOH A 33 433 447 HOH HOH . D 4 HOH A 34 434 444 HOH HOH . D 4 HOH A 35 435 454 HOH HOH . D 4 HOH A 36 436 445 HOH HOH . D 4 HOH A 37 437 460 HOH HOH . D 4 HOH A 38 438 442 HOH HOH . D 4 HOH A 39 439 440 HOH HOH . D 4 HOH A 40 440 450 HOH HOH . D 4 HOH A 41 441 451 HOH HOH . D 4 HOH A 42 442 452 HOH HOH . D 4 HOH A 43 443 438 HOH HOH . D 4 HOH A 44 444 456 HOH HOH . D 4 HOH A 45 445 446 HOH HOH . D 4 HOH A 46 446 464 HOH HOH . D 4 HOH A 47 447 455 HOH HOH . D 4 HOH A 48 448 457 HOH HOH . D 4 HOH A 49 449 439 HOH HOH . D 4 HOH A 50 450 2 HOH HOH . D 4 HOH A 51 451 448 HOH HOH . D 4 HOH A 52 452 461 HOH HOH . D 4 HOH A 53 453 463 HOH HOH . D 4 HOH A 54 454 459 HOH HOH . D 4 HOH A 55 455 477 HOH HOH . D 4 HOH A 56 456 473 HOH HOH . D 4 HOH A 57 457 462 HOH HOH . D 4 HOH A 58 458 495 HOH HOH . D 4 HOH A 59 459 483 HOH HOH . D 4 HOH A 60 460 465 HOH HOH . D 4 HOH A 61 461 534 HOH HOH . D 4 HOH A 62 462 478 HOH HOH . D 4 HOH A 63 463 469 HOH HOH . D 4 HOH A 64 464 516 HOH HOH . D 4 HOH A 65 465 482 HOH HOH . D 4 HOH A 66 466 479 HOH HOH . D 4 HOH A 67 467 472 HOH HOH . D 4 HOH A 68 468 500 HOH HOH . D 4 HOH A 69 469 485 HOH HOH . D 4 HOH A 70 470 471 HOH HOH . D 4 HOH A 71 471 480 HOH HOH . D 4 HOH A 72 472 481 HOH HOH . D 4 HOH A 73 473 488 HOH HOH . D 4 HOH A 74 474 474 HOH HOH . D 4 HOH A 75 475 487 HOH HOH . D 4 HOH A 76 476 484 HOH HOH . D 4 HOH A 77 477 493 HOH HOH . D 4 HOH A 78 478 505 HOH HOH . D 4 HOH A 79 479 491 HOH HOH . D 4 HOH A 80 480 467 HOH HOH . D 4 HOH A 81 481 489 HOH HOH . D 4 HOH A 82 482 499 HOH HOH . D 4 HOH A 83 483 486 HOH HOH . D 4 HOH A 84 484 498 HOH HOH . D 4 HOH A 85 485 490 HOH HOH . D 4 HOH A 86 486 515 HOH HOH . D 4 HOH A 87 487 494 HOH HOH . D 4 HOH A 88 488 510 HOH HOH . D 4 HOH A 89 489 492 HOH HOH . D 4 HOH A 90 490 497 HOH HOH . D 4 HOH A 91 491 496 HOH HOH . D 4 HOH A 92 492 526 HOH HOH . D 4 HOH A 93 493 528 HOH HOH . D 4 HOH A 94 494 501 HOH HOH . D 4 HOH A 95 495 521 HOH HOH . D 4 HOH A 96 496 520 HOH HOH . D 4 HOH A 97 497 508 HOH HOH . D 4 HOH A 98 498 518 HOH HOH . D 4 HOH A 99 499 506 HOH HOH . D 4 HOH A 100 500 519 HOH HOH . D 4 HOH A 101 501 527 HOH HOH . D 4 HOH A 102 502 513 HOH HOH . D 4 HOH A 103 503 502 HOH HOH . D 4 HOH A 104 504 509 HOH HOH . D 4 HOH A 105 505 524 HOH HOH . D 4 HOH A 106 506 517 HOH HOH . D 4 HOH A 107 507 504 HOH HOH . D 4 HOH A 108 508 523 HOH HOH . D 4 HOH A 109 509 514 HOH HOH . D 4 HOH A 110 510 522 HOH HOH . D 4 HOH A 111 511 530 HOH HOH . D 4 HOH A 112 512 525 HOH HOH . D 4 HOH A 113 513 529 HOH HOH . D 4 HOH A 114 514 562 HOH HOH . D 4 HOH A 115 515 533 HOH HOH . D 4 HOH A 116 516 547 HOH HOH . D 4 HOH A 117 517 542 HOH HOH . D 4 HOH A 118 518 536 HOH HOH . D 4 HOH A 119 519 541 HOH HOH . D 4 HOH A 120 520 544 HOH HOH . D 4 HOH A 121 521 549 HOH HOH . D 4 HOH A 122 522 540 HOH HOH . D 4 HOH A 123 523 561 HOH HOH . D 4 HOH A 124 524 546 HOH HOH . D 4 HOH A 125 525 539 HOH HOH . D 4 HOH A 126 526 555 HOH HOH . D 4 HOH A 127 527 556 HOH HOH . D 4 HOH A 128 528 553 HOH HOH . D 4 HOH A 129 529 537 HOH HOH . D 4 HOH A 130 530 543 HOH HOH . D 4 HOH A 131 531 557 HOH HOH . D 4 HOH A 132 532 560 HOH HOH . D 4 HOH A 133 533 558 HOH HOH . D 4 HOH A 134 534 550 HOH HOH . D 4 HOH A 135 535 559 HOH HOH . D 4 HOH A 136 536 532 HOH HOH . D 4 HOH A 137 537 554 HOH HOH . D 4 HOH A 138 538 563 HOH HOH . D 4 HOH A 139 539 566 HOH HOH . D 4 HOH A 140 540 568 HOH HOH . D 4 HOH A 141 541 571 HOH HOH . D 4 HOH A 142 542 565 HOH HOH . D 4 HOH A 143 543 567 HOH HOH . D 4 HOH A 144 544 572 HOH HOH . D 4 HOH A 145 545 564 HOH HOH . D 4 HOH A 146 546 569 HOH HOH . D 4 HOH A 147 547 570 HOH HOH . D 4 HOH A 148 548 575 HOH HOH . D 4 HOH A 149 549 577 HOH HOH . D 4 HOH A 150 550 579 HOH HOH . D 4 HOH A 151 551 574 HOH HOH . D 4 HOH A 152 552 576 HOH HOH . D 4 HOH A 153 553 589 HOH HOH . D 4 HOH A 154 554 581 HOH HOH . D 4 HOH A 155 555 578 HOH HOH . D 4 HOH A 156 556 582 HOH HOH . D 4 HOH A 157 557 595 HOH HOH . D 4 HOH A 158 558 584 HOH HOH . D 4 HOH A 159 559 587 HOH HOH . D 4 HOH A 160 560 586 HOH HOH . D 4 HOH A 161 561 598 HOH HOH . D 4 HOH A 162 562 585 HOH HOH . D 4 HOH A 163 563 592 HOH HOH . D 4 HOH A 164 564 594 HOH HOH . D 4 HOH A 165 565 531 HOH HOH . D 4 HOH A 166 566 593 HOH HOH . D 4 HOH A 167 567 596 HOH HOH . D 4 HOH A 168 568 601 HOH HOH . D 4 HOH A 169 569 600 HOH HOH . D 4 HOH A 170 570 604 HOH HOH . D 4 HOH A 171 571 611 HOH HOH . D 4 HOH A 172 572 603 HOH HOH . D 4 HOH A 173 573 612 HOH HOH . D 4 HOH A 174 574 606 HOH HOH . D 4 HOH A 175 575 613 HOH HOH . D 4 HOH A 176 576 621 HOH HOH . D 4 HOH A 177 577 610 HOH HOH . D 4 HOH A 178 578 618 HOH HOH . D 4 HOH A 179 579 616 HOH HOH . D 4 HOH A 180 580 619 HOH HOH . D 4 HOH A 181 581 615 HOH HOH . D 4 HOH A 182 582 623 HOH HOH . D 4 HOH A 183 583 607 HOH HOH . D 4 HOH A 184 584 617 HOH HOH . D 4 HOH A 185 585 1 HOH HOH . D 4 HOH A 186 586 407 HOH HOH . D 4 HOH A 187 587 622 HOH HOH . D 4 HOH A 188 588 624 HOH HOH . D 4 HOH A 189 589 630 HOH HOH . D 4 HOH A 190 590 628 HOH HOH . D 4 HOH A 191 591 629 HOH HOH . D 4 HOH A 192 592 625 HOH HOH . D 4 HOH A 193 593 627 HOH HOH . D 4 HOH A 194 594 633 HOH HOH . D 4 HOH A 195 595 637 HOH HOH . D 4 HOH A 196 596 638 HOH HOH . D 4 HOH A 197 597 632 HOH HOH . D 4 HOH A 198 598 634 HOH HOH . D 4 HOH A 199 599 639 HOH HOH . D 4 HOH A 200 600 641 HOH HOH . D 4 HOH A 201 601 646 HOH HOH . D 4 HOH A 202 602 645 HOH HOH . D 4 HOH A 203 603 652 HOH HOH . D 4 HOH A 204 604 644 HOH HOH . D 4 HOH A 205 605 643 HOH HOH . D 4 HOH A 206 606 649 HOH HOH . D 4 HOH A 207 607 656 HOH HOH . D 4 HOH A 208 608 636 HOH HOH . D 4 HOH A 209 609 655 HOH HOH . D 4 HOH A 210 610 651 HOH HOH . D 4 HOH A 211 611 650 HOH HOH . D 4 HOH A 212 612 654 HOH HOH . D 4 HOH A 213 613 657 HOH HOH . D 4 HOH A 214 614 658 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 N N1 URA . . . B 2 -8.094 -21.078 -1.559 1 28.5 ? N1 URA 301 A 1 HETATM 2 C C2 URA . . . B 2 -6.858 -21.48 -2.049 1 29.16 ? C2 URA 301 A 1 HETATM 3 O O2 URA . . . B 2 -5.851 -21.6 -1.247 1 22.99 ? O2 URA 301 A 1 HETATM 4 N N3 URA . . . B 2 -6.703 -21.772 -3.38 1 29.86 ? N3 URA 301 A 1 HETATM 5 C C4 URA . . . B 2 -7.778 -21.667 -4.229 1 31.89 ? C4 URA 301 A 1 HETATM 6 O O4 URA . . . B 2 -7.577 -21.961 -5.455 1 34.07 ? O4 URA 301 A 1 HETATM 7 C C5 URA . . . B 2 -9.033 -21.264 -3.726 1 28.5 ? C5 URA 301 A 1 HETATM 8 C C6 URA . . . B 2 -9.191 -20.962 -2.335 1 27.24 ? C6 URA 301 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #