data_8J66 # _model_server_result.job_id XUP-3VLS0oTAit04_EieXg _model_server_result.datetime_utc '2024-11-28 02:34:40' _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 8j66 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 8J66 # _exptl.entry_id 8J66 _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 8J66 _cell.length_a 72.068 _cell.length_b 78.127 _cell.length_c 94.653 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8J66 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _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 513 n n N1 C6 UDP sing 514 n n N1 C1' UDP sing 515 n n C2 N3 UDP sing 516 n n C2 O2 UDP doub 517 n n N3 C4 UDP sing 518 n n N3 HN3 UDP sing 519 n n C4 C5 UDP sing 520 n n C4 O4 UDP doub 521 n n C5 C6 UDP doub 522 n n C5 H5 UDP sing 523 n n C6 H6 UDP sing 524 n n C1' C2' UDP sing 525 n n C1' O4' UDP sing 526 n n C1' H1' UDP sing 527 n n C2' O2' UDP sing 528 n n C2' C3' UDP sing 529 n n C2' H2' UDP sing 530 n n O2' HO2' UDP sing 531 n n C3' C4' UDP sing 532 n n C3' O3' UDP sing 533 n n C3' H3' UDP sing 534 n n C4' O4' UDP sing 535 n n C4' C5' UDP sing 536 n n C4' H4' UDP sing 537 n n O3' HO3' UDP sing 538 n n C5' O5' UDP sing 539 n n C5' "H5'1" UDP sing 540 n n C5' "H5'2" UDP sing 541 n n O5' PA UDP sing 542 n n PA O1A UDP doub 543 n n PA O2A UDP sing 544 n n PA O3A UDP sing 545 n n O2A HOA2 UDP sing 546 n n O3A PB UDP sing 547 n n PB O1B UDP doub 548 n n PB O2B UDP sing 549 n n PB O3B UDP sing 550 n n O2B HOB2 UDP sing 551 n n O3B HOB3 UDP sing 552 n n # _atom_sites.entry_id 8J66 _atom_sites.fract_transf_matrix[1][1] 0.013876 _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] 0.0128 _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] 0.010565 _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 M2Q A 1 502 503 M2Q OGT . D 3 M2Q A 1 503 504 M2Q OGT . E 4 HOH A 1 601 60 HOH HOH . E 4 HOH A 2 602 6 HOH HOH . E 4 HOH A 3 603 77 HOH HOH . E 4 HOH A 4 604 158 HOH HOH . E 4 HOH A 5 605 178 HOH HOH . E 4 HOH A 6 606 68 HOH HOH . E 4 HOH A 7 607 88 HOH HOH . E 4 HOH A 8 608 25 HOH HOH . E 4 HOH A 9 609 119 HOH HOH . E 4 HOH A 10 610 149 HOH HOH . E 4 HOH A 11 611 166 HOH HOH . E 4 HOH A 12 612 37 HOH HOH . E 4 HOH A 13 613 18 HOH HOH . E 4 HOH A 14 614 201 HOH HOH . E 4 HOH A 15 615 167 HOH HOH . E 4 HOH A 16 616 183 HOH HOH . E 4 HOH A 17 617 67 HOH HOH . E 4 HOH A 18 618 103 HOH HOH . E 4 HOH A 19 619 33 HOH HOH . E 4 HOH A 20 620 156 HOH HOH . E 4 HOH A 21 621 90 HOH HOH . E 4 HOH A 22 622 50 HOH HOH . E 4 HOH A 23 623 98 HOH HOH . E 4 HOH A 24 624 47 HOH HOH . E 4 HOH A 25 625 87 HOH HOH . E 4 HOH A 26 626 200 HOH HOH . E 4 HOH A 27 627 94 HOH HOH . E 4 HOH A 28 628 31 HOH HOH . E 4 HOH A 29 629 5 HOH HOH . E 4 HOH A 30 630 162 HOH HOH . E 4 HOH A 31 631 32 HOH HOH . E 4 HOH A 32 632 85 HOH HOH . E 4 HOH A 33 633 198 HOH HOH . E 4 HOH A 34 634 193 HOH HOH . E 4 HOH A 35 635 11 HOH HOH . E 4 HOH A 36 636 34 HOH HOH . E 4 HOH A 37 637 69 HOH HOH . E 4 HOH A 38 638 165 HOH HOH . E 4 HOH A 39 639 48 HOH HOH . E 4 HOH A 40 640 93 HOH HOH . E 4 HOH A 41 641 36 HOH HOH . E 4 HOH A 42 642 8 HOH HOH . E 4 HOH A 43 643 109 HOH HOH . E 4 HOH A 44 644 15 HOH HOH . E 4 HOH A 45 645 2 HOH HOH . E 4 HOH A 46 646 3 HOH HOH . E 4 HOH A 47 647 81 HOH HOH . E 4 HOH A 48 648 38 HOH HOH . E 4 HOH A 49 649 4 HOH HOH . E 4 HOH A 50 650 35 HOH HOH . E 4 HOH A 51 651 140 HOH HOH . E 4 HOH A 52 652 148 HOH HOH . E 4 HOH A 53 653 14 HOH HOH . E 4 HOH A 54 654 154 HOH HOH . E 4 HOH A 55 655 63 HOH HOH . E 4 HOH A 56 656 13 HOH HOH . E 4 HOH A 57 657 130 HOH HOH . E 4 HOH A 58 658 21 HOH HOH . E 4 HOH A 59 659 65 HOH HOH . E 4 HOH A 60 660 40 HOH HOH . E 4 HOH A 61 661 43 HOH HOH . E 4 HOH A 62 662 26 HOH HOH . E 4 HOH A 63 663 41 HOH HOH . E 4 HOH A 64 664 101 HOH HOH . E 4 HOH A 65 665 1 HOH HOH . E 4 HOH A 66 666 190 HOH HOH . E 4 HOH A 67 667 100 HOH HOH . E 4 HOH A 68 668 105 HOH HOH . E 4 HOH A 69 669 79 HOH HOH . E 4 HOH A 70 670 55 HOH HOH . E 4 HOH A 71 671 10 HOH HOH . E 4 HOH A 72 672 97 HOH HOH . E 4 HOH A 73 673 74 HOH HOH . E 4 HOH A 74 674 89 HOH HOH . E 4 HOH A 75 675 29 HOH HOH . E 4 HOH A 76 676 80 HOH HOH . E 4 HOH A 77 677 16 HOH HOH . E 4 HOH A 78 678 163 HOH HOH . E 4 HOH A 79 679 113 HOH HOH . E 4 HOH A 80 680 133 HOH HOH . E 4 HOH A 81 681 45 HOH HOH . E 4 HOH A 82 682 78 HOH HOH . E 4 HOH A 83 683 27 HOH HOH . E 4 HOH A 84 684 157 HOH HOH . E 4 HOH A 85 685 137 HOH HOH . E 4 HOH A 86 686 180 HOH HOH . E 4 HOH A 87 687 7 HOH HOH . E 4 HOH A 88 688 73 HOH HOH . E 4 HOH A 89 689 64 HOH HOH . E 4 HOH A 90 690 23 HOH HOH . E 4 HOH A 91 691 116 HOH HOH . E 4 HOH A 92 692 20 HOH HOH . E 4 HOH A 93 693 117 HOH HOH . E 4 HOH A 94 694 195 HOH HOH . E 4 HOH A 95 695 159 HOH HOH . E 4 HOH A 96 696 127 HOH HOH . E 4 HOH A 97 697 22 HOH HOH . E 4 HOH A 98 698 185 HOH HOH . E 4 HOH A 99 699 62 HOH HOH . E 4 HOH A 100 700 145 HOH HOH . E 4 HOH A 101 701 126 HOH HOH . E 4 HOH A 102 702 12 HOH HOH . E 4 HOH A 103 703 99 HOH HOH . E 4 HOH A 104 704 114 HOH HOH . E 4 HOH A 105 705 30 HOH HOH . E 4 HOH A 106 706 108 HOH HOH . E 4 HOH A 107 707 192 HOH HOH . E 4 HOH A 108 708 70 HOH HOH . E 4 HOH A 109 709 53 HOH HOH . E 4 HOH A 110 710 54 HOH HOH . E 4 HOH A 111 711 56 HOH HOH . E 4 HOH A 112 712 147 HOH HOH . E 4 HOH A 113 713 150 HOH HOH . E 4 HOH A 114 714 188 HOH HOH . E 4 HOH A 115 715 82 HOH HOH . E 4 HOH A 116 716 42 HOH HOH . E 4 HOH A 117 717 19 HOH HOH . E 4 HOH A 118 718 111 HOH HOH . E 4 HOH A 119 719 128 HOH HOH . E 4 HOH A 120 720 141 HOH HOH . E 4 HOH A 121 721 91 HOH HOH . E 4 HOH A 122 722 202 HOH HOH . E 4 HOH A 123 723 143 HOH HOH . E 4 HOH A 124 724 112 HOH HOH . E 4 HOH A 125 725 51 HOH HOH . E 4 HOH A 126 726 107 HOH HOH . E 4 HOH A 127 727 168 HOH HOH . E 4 HOH A 128 728 123 HOH HOH . E 4 HOH A 129 729 17 HOH HOH . E 4 HOH A 130 730 39 HOH HOH . E 4 HOH A 131 731 57 HOH HOH . E 4 HOH A 132 732 115 HOH HOH . E 4 HOH A 133 733 86 HOH HOH . E 4 HOH A 134 734 132 HOH HOH . E 4 HOH A 135 735 121 HOH HOH . E 4 HOH A 136 736 24 HOH HOH . E 4 HOH A 137 737 72 HOH HOH . E 4 HOH A 138 738 174 HOH HOH . E 4 HOH A 139 739 61 HOH HOH . E 4 HOH A 140 740 189 HOH HOH . E 4 HOH A 141 741 129 HOH HOH . E 4 HOH A 142 742 124 HOH HOH . E 4 HOH A 143 743 104 HOH HOH . E 4 HOH A 144 744 9 HOH HOH . E 4 HOH A 145 745 66 HOH HOH . E 4 HOH A 146 746 71 HOH HOH . E 4 HOH A 147 747 118 HOH HOH . E 4 HOH A 148 748 196 HOH HOH . E 4 HOH A 149 749 110 HOH HOH . E 4 HOH A 150 750 152 HOH HOH . E 4 HOH A 151 751 151 HOH HOH . E 4 HOH A 152 752 176 HOH HOH . E 4 HOH A 153 753 160 HOH HOH . E 4 HOH A 154 754 125 HOH HOH . E 4 HOH A 155 755 197 HOH HOH . E 4 HOH A 156 756 182 HOH HOH . E 4 HOH A 157 757 120 HOH HOH . E 4 HOH A 158 758 59 HOH HOH . E 4 HOH A 159 759 138 HOH HOH . E 4 HOH A 160 760 58 HOH HOH . E 4 HOH A 161 761 95 HOH HOH . E 4 HOH A 162 762 153 HOH HOH . E 4 HOH A 163 763 199 HOH HOH . E 4 HOH A 164 764 84 HOH HOH . E 4 HOH A 165 765 134 HOH HOH . E 4 HOH A 166 766 191 HOH HOH . E 4 HOH A 167 767 170 HOH HOH . E 4 HOH A 168 768 144 HOH HOH . E 4 HOH A 169 769 135 HOH HOH . E 4 HOH A 170 770 155 HOH HOH . E 4 HOH A 171 771 184 HOH HOH . E 4 HOH A 172 772 187 HOH HOH . E 4 HOH A 173 773 44 HOH HOH . E 4 HOH A 174 774 186 HOH HOH . E 4 HOH A 175 775 194 HOH HOH . E 4 HOH A 176 776 171 HOH HOH . E 4 HOH A 177 777 75 HOH HOH . E 4 HOH A 178 778 122 HOH HOH . E 4 HOH A 179 779 46 HOH HOH . E 4 HOH A 180 780 164 HOH HOH . E 4 HOH A 181 781 179 HOH HOH . E 4 HOH A 182 782 181 HOH HOH . E 4 HOH A 183 783 173 HOH HOH . E 4 HOH A 184 784 142 HOH HOH . E 4 HOH A 185 785 131 HOH HOH . E 4 HOH A 186 786 172 HOH HOH . E 4 HOH A 187 787 175 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 25.48 -5.236 -23.103 1 24.98 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 26.499 -5.388 -24.016 1 19.73 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 27.557 -4.516 -23.89 1 23.07 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 27.682 -3.525 -22.94 1 24.67 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 26.589 -3.427 -22.024 1 24.49 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 25.534 -4.264 -22.12 1 19.82 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 26.47 -6.243 -24.901 1 22.32 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 28.688 -2.8 -22.925 1 23.58 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 24.32 -6.133 -23.19 1 22.06 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 24.463 -7.308 -22.157 1 25.95 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 25.107 -8.43 -22.764 1 26.32 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 23.035 -7.635 -21.834 1 23.53 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 22.291 -6.316 -22.043 1 19.87 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 23.136 -5.427 -22.831 1 26.52 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 22.537 -8.62 -22.742 1 26.66 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 22.015 -5.693 -20.715 1 21.42 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 20.865 -6.3 -20.205 1 31.17 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 20.686 -6.412 -18.574 1 22.43 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 19.361 -7.068 -18.278 1 21.98 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 21.811 -7.222 -17.975 1 25.51 -1 O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 20.695 -4.885 -17.955 1 29.66 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 19.927 -3.524 -18.468 1 20.69 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 18.641 -3.919 -19.15 1 25.81 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 20.802 -2.783 -19.449 1 22.56 -1 O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 19.62 -2.645 -17.28 1 25.41 -1 O3B UDP 501 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 48 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 434 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #