data_7W1B # _model_server_result.job_id NWubaXxe9WnZUI_R1DpdNQ _model_server_result.datetime_utc '2024-11-05 19:31:53' _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 7w1b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7W1B # _exptl.entry_id 7W1B _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 95.76 _cell.angle_gamma 90 _cell.entry_id 7W1B _cell.length_a 53.351 _cell.length_b 74.141 _cell.length_c 63.588 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W1B _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _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 # _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 442 n n N1 C6 UDP sing 443 n n N1 C1' UDP sing 444 n n C2 N3 UDP sing 445 n n C2 O2 UDP doub 446 n n N3 C4 UDP sing 447 n n N3 HN3 UDP sing 448 n n C4 C5 UDP sing 449 n n C4 O4 UDP doub 450 n n C5 C6 UDP doub 451 n n C5 H5 UDP sing 452 n n C6 H6 UDP sing 453 n n C1' C2' UDP sing 454 n n C1' O4' UDP sing 455 n n C1' H1' UDP sing 456 n n C2' O2' UDP sing 457 n n C2' C3' UDP sing 458 n n C2' H2' UDP sing 459 n n O2' HO2' UDP sing 460 n n C3' C4' UDP sing 461 n n C3' O3' UDP sing 462 n n C3' H3' UDP sing 463 n n C4' O4' UDP sing 464 n n C4' C5' UDP sing 465 n n C4' H4' UDP sing 466 n n O3' HO3' UDP sing 467 n n C5' O5' UDP sing 468 n n C5' "H5'1" UDP sing 469 n n C5' "H5'2" UDP sing 470 n n O5' PA UDP sing 471 n n PA O1A UDP doub 472 n n PA O2A UDP sing 473 n n PA O3A UDP sing 474 n n O2A HOA2 UDP sing 475 n n O3A PB UDP sing 476 n n PB O1B UDP doub 477 n n PB O2B UDP sing 478 n n PB O3B UDP sing 479 n n O2B HOB2 UDP sing 480 n n O3B HOB3 UDP sing 481 n n # _atom_sites.entry_id 7W1B _atom_sites.fract_transf_matrix[1][1] 0.018744 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001891 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013488 _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] 0.015806 _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 1 501 501 UDP UDP . C 3 TRS A 1 502 701 TRS TRS . D 4 DTX A 1 503 702 DTX DRG . E 5 HOH A 1 601 23 HOH HOH . E 5 HOH A 2 602 69 HOH HOH . E 5 HOH A 3 603 62 HOH HOH . E 5 HOH A 4 604 70 HOH HOH . E 5 HOH A 5 605 75 HOH HOH . E 5 HOH A 6 606 97 HOH HOH . E 5 HOH A 7 607 90 HOH HOH . E 5 HOH A 8 608 56 HOH HOH . E 5 HOH A 9 609 3 HOH HOH . E 5 HOH A 10 610 79 HOH HOH . E 5 HOH A 11 611 6 HOH HOH . E 5 HOH A 12 612 8 HOH HOH . E 5 HOH A 13 613 108 HOH HOH . E 5 HOH A 14 614 1 HOH HOH . E 5 HOH A 15 615 19 HOH HOH . E 5 HOH A 16 616 36 HOH HOH . E 5 HOH A 17 617 64 HOH HOH . E 5 HOH A 18 618 16 HOH HOH . E 5 HOH A 19 619 13 HOH HOH . E 5 HOH A 20 620 91 HOH HOH . E 5 HOH A 21 621 163 HOH HOH . E 5 HOH A 22 622 121 HOH HOH . E 5 HOH A 23 623 25 HOH HOH . E 5 HOH A 24 624 51 HOH HOH . E 5 HOH A 25 625 54 HOH HOH . E 5 HOH A 26 626 2 HOH HOH . E 5 HOH A 27 627 77 HOH HOH . E 5 HOH A 28 628 27 HOH HOH . E 5 HOH A 29 629 9 HOH HOH . E 5 HOH A 30 630 112 HOH HOH . E 5 HOH A 31 631 61 HOH HOH . E 5 HOH A 32 632 71 HOH HOH . E 5 HOH A 33 633 200 HOH HOH . E 5 HOH A 34 634 101 HOH HOH . E 5 HOH A 35 635 38 HOH HOH . E 5 HOH A 36 636 29 HOH HOH . E 5 HOH A 37 637 12 HOH HOH . E 5 HOH A 38 638 257 HOH HOH . E 5 HOH A 39 639 7 HOH HOH . E 5 HOH A 40 640 24 HOH HOH . E 5 HOH A 41 641 14 HOH HOH . E 5 HOH A 42 642 55 HOH HOH . E 5 HOH A 43 643 17 HOH HOH . E 5 HOH A 44 644 110 HOH HOH . E 5 HOH A 45 645 81 HOH HOH . E 5 HOH A 46 646 84 HOH HOH . E 5 HOH A 47 647 20 HOH HOH . E 5 HOH A 48 648 39 HOH HOH . E 5 HOH A 49 649 18 HOH HOH . E 5 HOH A 50 650 45 HOH HOH . E 5 HOH A 51 651 57 HOH HOH . E 5 HOH A 52 652 149 HOH HOH . E 5 HOH A 53 653 256 HOH HOH . E 5 HOH A 54 654 114 HOH HOH . E 5 HOH A 55 655 83 HOH HOH . E 5 HOH A 56 656 5 HOH HOH . E 5 HOH A 57 657 33 HOH HOH . E 5 HOH A 58 658 52 HOH HOH . E 5 HOH A 59 659 161 HOH HOH . E 5 HOH A 60 660 15 HOH HOH . E 5 HOH A 61 661 196 HOH HOH . E 5 HOH A 62 662 46 HOH HOH . E 5 HOH A 63 663 255 HOH HOH . E 5 HOH A 64 664 74 HOH HOH . E 5 HOH A 65 665 173 HOH HOH . E 5 HOH A 66 666 78 HOH HOH . E 5 HOH A 67 667 21 HOH HOH . E 5 HOH A 68 668 229 HOH HOH . E 5 HOH A 69 669 44 HOH HOH . E 5 HOH A 70 670 194 HOH HOH . E 5 HOH A 71 671 76 HOH HOH . E 5 HOH A 72 672 48 HOH HOH . E 5 HOH A 73 673 107 HOH HOH . E 5 HOH A 74 674 10 HOH HOH . E 5 HOH A 75 675 42 HOH HOH . E 5 HOH A 76 676 49 HOH HOH . E 5 HOH A 77 677 182 HOH HOH . E 5 HOH A 78 678 47 HOH HOH . E 5 HOH A 79 679 158 HOH HOH . E 5 HOH A 80 680 22 HOH HOH . E 5 HOH A 81 681 41 HOH HOH . E 5 HOH A 82 682 65 HOH HOH . E 5 HOH A 83 683 167 HOH HOH . E 5 HOH A 84 684 4 HOH HOH . E 5 HOH A 85 685 26 HOH HOH . E 5 HOH A 86 686 72 HOH HOH . E 5 HOH A 87 687 37 HOH HOH . E 5 HOH A 88 688 249 HOH HOH . E 5 HOH A 89 689 35 HOH HOH . E 5 HOH A 90 690 227 HOH HOH . E 5 HOH A 91 691 98 HOH HOH . E 5 HOH A 92 692 53 HOH HOH . E 5 HOH A 93 693 63 HOH HOH . E 5 HOH A 94 694 50 HOH HOH . E 5 HOH A 95 695 119 HOH HOH . E 5 HOH A 96 696 187 HOH HOH . E 5 HOH A 97 697 164 HOH HOH . E 5 HOH A 98 698 208 HOH HOH . E 5 HOH A 99 699 150 HOH HOH . E 5 HOH A 100 700 237 HOH HOH . E 5 HOH A 101 701 43 HOH HOH . E 5 HOH A 102 702 138 HOH HOH . E 5 HOH A 103 703 11 HOH HOH . E 5 HOH A 104 704 32 HOH HOH . E 5 HOH A 105 705 31 HOH HOH . E 5 HOH A 106 706 30 HOH HOH . E 5 HOH A 107 707 59 HOH HOH . E 5 HOH A 108 708 67 HOH HOH . E 5 HOH A 109 709 314 HOH HOH . E 5 HOH A 110 710 106 HOH HOH . E 5 HOH A 111 711 82 HOH HOH . E 5 HOH A 112 712 128 HOH HOH . E 5 HOH A 113 713 28 HOH HOH . E 5 HOH A 114 714 272 HOH HOH . E 5 HOH A 115 715 133 HOH HOH . E 5 HOH A 116 716 40 HOH HOH . E 5 HOH A 117 717 254 HOH HOH . E 5 HOH A 118 718 34 HOH HOH . E 5 HOH A 119 719 60 HOH HOH . E 5 HOH A 120 720 66 HOH HOH . E 5 HOH A 121 721 213 HOH HOH . E 5 HOH A 122 722 152 HOH HOH . E 5 HOH A 123 723 202 HOH HOH . E 5 HOH A 124 724 118 HOH HOH . E 5 HOH A 125 725 278 HOH HOH . E 5 HOH A 126 726 294 HOH HOH . E 5 HOH A 127 727 240 HOH HOH . E 5 HOH A 128 728 260 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 -24.478 -2.556 -10.205 1 13.59 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 -25.435 -1.904 -9.558 1 15.72 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 -26.155 -0.962 -10.143 1 17.2 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 -25.929 -0.657 -11.408 1 13.35 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 -24.941 -1.314 -12.139 1 17.07 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 -24.207 -2.291 -11.471 1 13.86 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 -25.704 -2.221 -8.218 1 14.82 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 -26.681 0.334 -11.994 1 15.35 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 -23.695 -3.59 -9.489 1 15.74 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 -23.975 -5.016 -10 1 16.18 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 -24.948 -5.528 -9.215 1 10.25 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 -22.625 -5.734 -9.768 1 15.6 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 -21.699 -4.804 -9.952 1 15.16 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 -22.417 -3.383 -9.699 1 15.28 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 -22.609 -6.206 -8.338 1 13.65 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 -21.118 -4.81 -11.356 1 14.57 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 -20.18 -5.844 -11.396 1 15.27 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 -19.848 -6.719 -12.746 1 15.88 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 -21.102 -7.205 -13.426 1 15.8 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 -19.007 -7.939 -12.38 1 18.34 -1 O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 -19.002 -5.8 -13.827 1 17.71 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 -17.878 -4.614 -13.558 1 14.5 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 -17.326 -4.327 -14.942 1 20.38 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 -18.501 -3.396 -12.963 1 15.39 -1 O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 -16.776 -5.071 -12.645 1 16.66 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #