data_4FRM # _model_server_result.job_id 7zK5ankB8jXCCHP9ZzfxFw _model_server_result.datetime_utc '2024-11-26 21:28:52' _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 4frm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4FRM # _exptl.entry_id 4FRM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 4FRM _cell.length_a 52.203 _cell.length_b 150.598 _cell.length_c 79.353 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FRM _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 52.203 0 39.6765 # _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 # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna 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 N1 C2 UDP sing 382 n n N1 C6 UDP sing 383 n n N1 C1' UDP sing 384 n n C2 N3 UDP sing 385 n n C2 O2 UDP doub 386 n n N3 C4 UDP sing 387 n n N3 HN3 UDP sing 388 n n C4 C5 UDP sing 389 n n C4 O4 UDP doub 390 n n C5 C6 UDP doub 391 n n C5 H5 UDP sing 392 n n C6 H6 UDP sing 393 n n C1' C2' UDP sing 394 n n C1' O4' UDP sing 395 n n C1' H1' UDP sing 396 n n C2' O2' UDP sing 397 n n C2' C3' UDP sing 398 n n C2' H2' UDP sing 399 n n O2' HO2' UDP sing 400 n n C3' C4' UDP sing 401 n n C3' O3' UDP sing 402 n n C3' H3' UDP sing 403 n n C4' O4' UDP sing 404 n n C4' C5' UDP sing 405 n n C4' H4' UDP sing 406 n n O3' HO3' UDP sing 407 n n C5' O5' UDP sing 408 n n C5' "H5'1" UDP sing 409 n n C5' "H5'2" UDP sing 410 n n O5' PA UDP sing 411 n n PA O1A UDP doub 412 n n PA O2A UDP sing 413 n n PA O3A UDP sing 414 n n O2A HOA2 UDP sing 415 n n O3A PB UDP sing 416 n n PB O1B UDP doub 417 n n PB O2B UDP sing 418 n n PB O3B UDP sing 419 n n O2B HOB2 UDP sing 420 n n O3B HOB3 UDP sing 421 n n # _atom_sites.entry_id 4FRM _atom_sites.fract_transf_matrix[1][1] 0.019156 _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] 0.00664 _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] 0.012602 _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 UDP A 1 401 1 UDP UDP . C 3 GAL A 1 402 2 GAL GAL . D 4 HOH A 1 501 1 HOH HOH . D 4 HOH A 2 502 2 HOH HOH . D 4 HOH A 3 503 3 HOH HOH . D 4 HOH A 4 504 4 HOH HOH . D 4 HOH A 5 505 5 HOH HOH . D 4 HOH A 6 506 6 HOH HOH . D 4 HOH A 7 507 7 HOH HOH . D 4 HOH A 8 508 8 HOH HOH . D 4 HOH A 9 509 9 HOH HOH . D 4 HOH A 10 510 10 HOH HOH . D 4 HOH A 11 511 11 HOH HOH . D 4 HOH A 12 512 12 HOH HOH . D 4 HOH A 13 513 13 HOH HOH . D 4 HOH A 14 514 14 HOH HOH . D 4 HOH A 15 515 15 HOH HOH . D 4 HOH A 16 516 16 HOH HOH . D 4 HOH A 17 517 17 HOH HOH . D 4 HOH A 18 518 18 HOH HOH . D 4 HOH A 19 519 19 HOH HOH . D 4 HOH A 20 520 20 HOH HOH . D 4 HOH A 21 521 21 HOH HOH . D 4 HOH A 22 522 22 HOH HOH . D 4 HOH A 23 523 23 HOH HOH . D 4 HOH A 24 524 24 HOH HOH . D 4 HOH A 25 525 25 HOH HOH . D 4 HOH A 26 526 26 HOH HOH . D 4 HOH A 27 527 27 HOH HOH . D 4 HOH A 28 528 28 HOH HOH . D 4 HOH A 29 529 29 HOH HOH . D 4 HOH A 30 530 30 HOH HOH . D 4 HOH A 31 531 31 HOH HOH . D 4 HOH A 32 532 32 HOH HOH . D 4 HOH A 33 533 33 HOH HOH . D 4 HOH A 34 534 34 HOH HOH . D 4 HOH A 35 535 35 HOH HOH . D 4 HOH A 36 536 36 HOH HOH . D 4 HOH A 37 537 37 HOH HOH . D 4 HOH A 38 538 38 HOH HOH . D 4 HOH A 39 539 39 HOH HOH . D 4 HOH A 40 540 40 HOH HOH . D 4 HOH A 41 541 41 HOH HOH . D 4 HOH A 42 542 42 HOH HOH . D 4 HOH A 43 543 43 HOH HOH . D 4 HOH A 44 544 44 HOH HOH . D 4 HOH A 45 545 45 HOH HOH . D 4 HOH A 46 546 46 HOH HOH . D 4 HOH A 47 547 47 HOH HOH . D 4 HOH A 48 548 48 HOH HOH . D 4 HOH A 49 549 49 HOH HOH . D 4 HOH A 50 550 50 HOH HOH . D 4 HOH A 51 551 51 HOH HOH . D 4 HOH A 52 552 52 HOH HOH . D 4 HOH A 53 553 53 HOH HOH . D 4 HOH A 54 554 54 HOH HOH . D 4 HOH A 55 555 55 HOH HOH . D 4 HOH A 56 556 56 HOH HOH . D 4 HOH A 57 557 57 HOH HOH . D 4 HOH A 58 558 58 HOH HOH . D 4 HOH A 59 559 59 HOH HOH . D 4 HOH A 60 560 60 HOH HOH . D 4 HOH A 61 561 61 HOH HOH . D 4 HOH A 62 562 62 HOH HOH . D 4 HOH A 63 563 63 HOH HOH . D 4 HOH A 64 564 64 HOH HOH . D 4 HOH A 65 565 65 HOH HOH . D 4 HOH A 66 566 66 HOH HOH . D 4 HOH A 67 567 67 HOH HOH . D 4 HOH A 68 568 68 HOH HOH . D 4 HOH A 69 569 69 HOH HOH . D 4 HOH A 70 570 70 HOH HOH . D 4 HOH A 71 571 71 HOH HOH . D 4 HOH A 72 572 72 HOH HOH . D 4 HOH A 73 573 73 HOH HOH . D 4 HOH A 74 574 74 HOH HOH . D 4 HOH A 75 575 75 HOH HOH . D 4 HOH A 76 576 76 HOH HOH . D 4 HOH A 77 577 77 HOH HOH . D 4 HOH A 78 578 78 HOH HOH . D 4 HOH A 79 579 79 HOH HOH . D 4 HOH A 80 580 80 HOH HOH . D 4 HOH A 81 581 81 HOH HOH . D 4 HOH A 82 582 82 HOH HOH . D 4 HOH A 83 583 83 HOH HOH . D 4 HOH A 84 584 84 HOH HOH . D 4 HOH A 85 585 85 HOH HOH . D 4 HOH A 86 586 86 HOH HOH . D 4 HOH A 87 587 87 HOH HOH . D 4 HOH A 88 588 88 HOH HOH . D 4 HOH A 89 589 89 HOH HOH . D 4 HOH A 90 590 90 HOH HOH . D 4 HOH A 91 591 91 HOH HOH . D 4 HOH A 92 592 92 HOH HOH . D 4 HOH A 93 593 93 HOH HOH . D 4 HOH A 94 594 94 HOH HOH . D 4 HOH A 95 595 95 HOH HOH . D 4 HOH A 96 596 96 HOH HOH . D 4 HOH A 97 597 97 HOH HOH . D 4 HOH A 98 598 98 HOH HOH . D 4 HOH A 99 599 99 HOH HOH . D 4 HOH A 100 600 100 HOH HOH . D 4 HOH A 101 601 101 HOH HOH . D 4 HOH A 102 602 102 HOH HOH . D 4 HOH A 103 603 103 HOH HOH . D 4 HOH A 104 604 104 HOH HOH . D 4 HOH A 105 605 105 HOH HOH . D 4 HOH A 106 606 106 HOH HOH . D 4 HOH A 107 607 107 HOH HOH . D 4 HOH A 108 608 108 HOH HOH . D 4 HOH A 109 609 109 HOH HOH . D 4 HOH A 110 610 110 HOH HOH . D 4 HOH A 111 611 111 HOH HOH . D 4 HOH A 112 612 112 HOH HOH . D 4 HOH A 113 613 113 HOH HOH . D 4 HOH A 114 614 114 HOH HOH . D 4 HOH A 115 615 115 HOH HOH . D 4 HOH A 116 616 116 HOH HOH . D 4 HOH A 117 617 117 HOH HOH . D 4 HOH A 118 618 118 HOH HOH . D 4 HOH A 119 619 119 HOH HOH . D 4 HOH A 120 620 120 HOH HOH . D 4 HOH A 121 621 121 HOH HOH . D 4 HOH A 122 622 122 HOH HOH . D 4 HOH A 123 623 123 HOH HOH . D 4 HOH A 124 624 124 HOH HOH . D 4 HOH A 125 625 125 HOH HOH . D 4 HOH A 126 626 126 HOH HOH . D 4 HOH A 127 627 127 HOH HOH . D 4 HOH A 128 628 128 HOH HOH . D 4 HOH A 129 629 129 HOH HOH . D 4 HOH A 130 630 130 HOH HOH . D 4 HOH A 131 631 131 HOH HOH . D 4 HOH A 132 632 132 HOH HOH . D 4 HOH A 133 633 133 HOH HOH . D 4 HOH A 134 634 134 HOH HOH . D 4 HOH A 135 635 135 HOH HOH . D 4 HOH A 136 636 136 HOH HOH . D 4 HOH A 137 637 137 HOH HOH . D 4 HOH A 138 638 138 HOH HOH . D 4 HOH A 139 639 139 HOH HOH . D 4 HOH A 140 640 140 HOH HOH . D 4 HOH A 141 641 141 HOH HOH . D 4 HOH A 142 642 142 HOH HOH . D 4 HOH A 143 643 143 HOH HOH . D 4 HOH A 144 644 144 HOH HOH . D 4 HOH A 145 645 145 HOH HOH . D 4 HOH A 146 646 146 HOH HOH . D 4 HOH A 147 647 147 HOH HOH . D 4 HOH A 148 648 148 HOH HOH . D 4 HOH A 149 649 149 HOH HOH . D 4 HOH A 150 650 150 HOH HOH . D 4 HOH A 151 651 151 HOH HOH . D 4 HOH A 152 652 152 HOH HOH . D 4 HOH A 153 653 153 HOH HOH . D 4 HOH A 154 654 154 HOH HOH . D 4 HOH A 155 655 155 HOH HOH . D 4 HOH A 156 656 156 HOH HOH . D 4 HOH A 157 657 157 HOH HOH . D 4 HOH A 158 658 158 HOH HOH . D 4 HOH A 159 659 159 HOH HOH . D 4 HOH A 160 660 160 HOH HOH . D 4 HOH A 161 661 161 HOH HOH . D 4 HOH A 162 662 162 HOH HOH . D 4 HOH A 163 663 163 HOH HOH . D 4 HOH A 164 664 164 HOH HOH . D 4 HOH A 165 665 165 HOH HOH . D 4 HOH A 166 666 166 HOH HOH . D 4 HOH A 167 667 167 HOH HOH . D 4 HOH A 168 668 168 HOH HOH . D 4 HOH A 169 669 169 HOH HOH . D 4 HOH A 170 670 170 HOH HOH . D 4 HOH A 171 671 171 HOH HOH . D 4 HOH A 172 672 172 HOH HOH . D 4 HOH A 173 673 173 HOH HOH . D 4 HOH A 174 674 174 HOH HOH . D 4 HOH A 175 675 175 HOH HOH . D 4 HOH A 176 676 176 HOH HOH . D 4 HOH A 177 677 177 HOH HOH . D 4 HOH A 178 678 178 HOH HOH . D 4 HOH A 179 679 179 HOH HOH . D 4 HOH A 180 680 180 HOH HOH . D 4 HOH A 181 681 181 HOH HOH . D 4 HOH A 182 682 182 HOH HOH . D 4 HOH A 183 683 183 HOH HOH . D 4 HOH A 184 684 184 HOH HOH . D 4 HOH A 185 685 185 HOH HOH . D 4 HOH A 186 686 186 HOH HOH . D 4 HOH A 187 687 187 HOH HOH . D 4 HOH A 188 688 188 HOH HOH . D 4 HOH A 189 689 189 HOH HOH . D 4 HOH A 190 690 190 HOH HOH . D 4 HOH A 191 691 191 HOH HOH . D 4 HOH A 192 692 192 HOH HOH . D 4 HOH A 193 693 193 HOH HOH . D 4 HOH A 194 694 194 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 UDP . . . B 2 9.938 23.511 -7.749 1 43.35 ? N1 UDP 401 A 1 HETATM 2 C C2 UDP . . . B 2 8.802 24.184 -8.041 1 46.37 ? C2 UDP 401 A 1 HETATM 3 N N3 UDP . . . B 2 8.328 24.193 -9.416 1 51.33 ? N3 UDP 401 A 1 HETATM 4 C C4 UDP . . . B 2 9.012 23.514 -10.496 1 56.97 ? C4 UDP 401 A 1 HETATM 5 C C5 UDP . . . B 2 10.189 22.803 -10.143 1 55.33 ? C5 UDP 401 A 1 HETATM 6 C C6 UDP . . . B 2 10.635 22.81 -8.793 1 49.5 ? C6 UDP 401 A 1 HETATM 7 O O2 UDP . . . B 2 8.175 24.803 -7.164 1 27.81 ? O2 UDP 401 A 1 HETATM 8 O O4 UDP . . . B 2 8.547 23.561 -11.665 1 49.26 ? O4 UDP 401 A 1 HETATM 9 C C1' UDP . . . B 2 10.406 23.516 -6.299 1 43.36 ? C1' UDP 401 A 1 HETATM 10 C C2' UDP . . . B 2 9.558 22.603 -5.475 1 34.99 ? C2' UDP 401 A 1 HETATM 11 O O2' UDP . . . B 2 9.712 22.652 -4.021 1 29.36 ? O2' UDP 401 A 1 HETATM 12 C C3' UDP . . . B 2 10.214 21.322 -5.791 1 37.84 ? C3' UDP 401 A 1 HETATM 13 C C4' UDP . . . B 2 11.72 21.527 -5.886 1 41.04 ? C4' UDP 401 A 1 HETATM 14 O O4' UDP . . . B 2 11.821 22.962 -6.232 1 46.74 ? O4' UDP 401 A 1 HETATM 15 O O3' UDP . . . B 2 10.017 20.577 -4.618 1 45.77 ? O3' UDP 401 A 1 HETATM 16 C C5' UDP . . . B 2 12.46 20.485 -6.806 1 35.96 ? C5' UDP 401 A 1 HETATM 17 O O5' UDP . . . B 2 11.575 19.609 -7.474 0.1 31.75 ? O5' UDP 401 A 1 HETATM 18 P PA UDP . . . B 2 12.241 18.431 -8.282 0.1 28.11 ? PA UDP 401 A 1 HETATM 19 O O1A UDP . . . B 2 13.672 18.742 -8.44 0.1 27.73 ? O1A UDP 401 A 1 HETATM 20 O O2A UDP . . . B 2 11.822 17.141 -7.706 0.1 27.67 ? O2A UDP 401 A 1 HETATM 21 O O3A UDP . . . B 2 11.598 18.618 -9.704 0.1 26.55 ? O3A UDP 401 A 1 HETATM 22 P PB UDP . . . B 2 12.623 19.068 -10.828 0.1 25.27 ? PB UDP 401 A 1 HETATM 23 O O1B UDP . . . B 2 12.926 17.707 -11.599 0.1 25.02 ? O1B UDP 401 A 1 HETATM 24 O O2B UDP . . . B 2 11.932 20.024 -11.722 0.1 24.44 ? O2B UDP 401 A 1 HETATM 25 O O3B UDP . . . B 2 13.842 19.485 -10.099 0.1 25 ? O3B UDP 401 A 1 HETATM 26 H HN3 UDP . . . B 2 7.495 24.69 -9.638 1 48.94 ? HN3 UDP 401 A 1 HETATM 27 H H5 UDP . . . B 2 10.755 22.269 -10.905 1 52.16 ? H5 UDP 401 A 1 HETATM 28 H H6 UDP . . . B 2 11.543 22.269 -8.566 1 48.17 ? H6 UDP 401 A 1 HETATM 29 H H1' UDP . . . B 2 10.389 24.522 -5.879 1 41.91 ? H1' UDP 401 A 1 HETATM 30 H H2' UDP . . . B 2 8.516 22.593 -5.792 1 35.78 ? H2' UDP 401 A 1 HETATM 31 H HO2' UDP . . . B 2 10.369 23.342 -4.015 0 27.66 ? HO2' UDP 401 A 1 HETATM 32 H H3' UDP . . . B 2 9.785 20.873 -6.683 1 39.03 ? H3' UDP 401 A 1 HETATM 33 H H4' UDP . . . B 2 12.143 21.436 -4.887 1 40.04 ? H4' UDP 401 A 1 HETATM 34 H HO3' UDP . . . B 2 9.496 21.186 -4.178 0 39.67 ? HO3' UDP 401 A 1 HETATM 35 H "H5'1" UDP . . . B 2 13.057 21.029 -7.537 1 36 ? "H5'1" UDP 401 A 1 HETATM 36 H "H5'2" UDP . . . B 2 13.13 19.899 -6.176 1 35.81 ? "H5'2" UDP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #