data_6LF6 # _model_server_result.job_id I6MdeWyTc8n9UZFeKeZfiw _model_server_result.datetime_utc '2024-11-22 17:47:42' _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 6lf6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6LF6 # _exptl.entry_id 6LF6 _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 105.53 _cell.angle_gamma 90 _cell.entry_id 6LF6 _cell.length_a 51.85 _cell.length_b 82.696 _cell.length_c 58.693 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LF6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _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 _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 358 n n N1 C6 UDP sing 359 n n N1 C1' UDP sing 360 n n C2 N3 UDP sing 361 n n C2 O2 UDP doub 362 n n N3 C4 UDP sing 363 n n N3 HN3 UDP sing 364 n n C4 C5 UDP sing 365 n n C4 O4 UDP doub 366 n n C5 C6 UDP doub 367 n n C5 H5 UDP sing 368 n n C6 H6 UDP sing 369 n n C1' C2' UDP sing 370 n n C1' O4' UDP sing 371 n n C1' H1' UDP sing 372 n n C2' O2' UDP sing 373 n n C2' C3' UDP sing 374 n n C2' H2' UDP sing 375 n n O2' HO2' UDP sing 376 n n C3' C4' UDP sing 377 n n C3' O3' UDP sing 378 n n C3' H3' UDP sing 379 n n C4' O4' UDP sing 380 n n C4' C5' UDP sing 381 n n C4' H4' UDP sing 382 n n O3' HO3' UDP sing 383 n n C5' O5' UDP sing 384 n n C5' "H5'1" UDP sing 385 n n C5' "H5'2" UDP sing 386 n n O5' PA UDP sing 387 n n PA O1A UDP doub 388 n n PA O2A UDP sing 389 n n PA O3A UDP sing 390 n n O2A HOA2 UDP sing 391 n n O3A PB UDP sing 392 n n PB O1B UDP doub 393 n n PB O2B UDP sing 394 n n PB O3B UDP sing 395 n n O2B HOB2 UDP sing 396 n n O3B HOB3 UDP sing 397 n n # _atom_sites.entry_id 6LF6 _atom_sites.fract_transf_matrix[1][1] 0.019286 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00536 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012092 _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] 0.017684 _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 UPG . C 3 HOH A 1 601 45 HOH WAT . C 3 HOH A 2 602 104 HOH WAT . C 3 HOH A 3 603 170 HOH WAT . C 3 HOH A 4 604 8 HOH WAT . C 3 HOH A 5 605 81 HOH WAT . C 3 HOH A 6 606 102 HOH WAT . C 3 HOH A 7 607 47 HOH WAT . C 3 HOH A 8 608 20 HOH WAT . C 3 HOH A 9 609 100 HOH WAT . C 3 HOH A 10 610 164 HOH WAT . C 3 HOH A 11 611 65 HOH WAT . C 3 HOH A 12 612 38 HOH WAT . C 3 HOH A 13 613 14 HOH WAT . C 3 HOH A 14 614 166 HOH WAT . C 3 HOH A 15 615 108 HOH WAT . C 3 HOH A 16 616 26 HOH WAT . C 3 HOH A 17 617 68 HOH WAT . C 3 HOH A 18 618 34 HOH WAT . C 3 HOH A 19 619 41 HOH WAT . C 3 HOH A 20 620 67 HOH WAT . C 3 HOH A 21 621 2 HOH WAT . C 3 HOH A 22 622 27 HOH WAT . C 3 HOH A 23 623 18 HOH WAT . C 3 HOH A 24 624 46 HOH WAT . C 3 HOH A 25 625 86 HOH WAT . C 3 HOH A 26 626 176 HOH WAT . C 3 HOH A 27 627 30 HOH WAT . C 3 HOH A 28 628 28 HOH WAT . C 3 HOH A 29 629 5 HOH WAT . C 3 HOH A 30 630 79 HOH WAT . C 3 HOH A 31 631 66 HOH WAT . C 3 HOH A 32 632 4 HOH WAT . C 3 HOH A 33 633 184 HOH WAT . C 3 HOH A 34 634 57 HOH WAT . C 3 HOH A 35 635 179 HOH WAT . C 3 HOH A 36 636 23 HOH WAT . C 3 HOH A 37 637 22 HOH WAT . C 3 HOH A 38 638 82 HOH WAT . C 3 HOH A 39 639 143 HOH WAT . C 3 HOH A 40 640 31 HOH WAT . C 3 HOH A 41 641 138 HOH WAT . C 3 HOH A 42 642 157 HOH WAT . C 3 HOH A 43 643 125 HOH WAT . C 3 HOH A 44 644 163 HOH WAT . C 3 HOH A 45 645 54 HOH WAT . C 3 HOH A 46 646 95 HOH WAT . C 3 HOH A 47 647 78 HOH WAT . C 3 HOH A 48 648 9 HOH WAT . C 3 HOH A 49 649 19 HOH WAT . C 3 HOH A 50 650 105 HOH WAT . C 3 HOH A 51 651 107 HOH WAT . C 3 HOH A 52 652 96 HOH WAT . C 3 HOH A 53 653 56 HOH WAT . C 3 HOH A 54 654 13 HOH WAT . C 3 HOH A 55 655 173 HOH WAT . C 3 HOH A 56 656 87 HOH WAT . C 3 HOH A 57 657 178 HOH WAT . C 3 HOH A 58 658 32 HOH WAT . C 3 HOH A 59 659 73 HOH WAT . C 3 HOH A 60 660 137 HOH WAT . C 3 HOH A 61 661 29 HOH WAT . C 3 HOH A 62 662 72 HOH WAT . C 3 HOH A 63 663 40 HOH WAT . C 3 HOH A 64 664 162 HOH WAT . C 3 HOH A 65 665 168 HOH WAT . C 3 HOH A 66 666 124 HOH WAT . C 3 HOH A 67 667 64 HOH WAT . C 3 HOH A 68 668 185 HOH WAT . C 3 HOH A 69 669 180 HOH WAT . C 3 HOH A 70 670 113 HOH WAT . C 3 HOH A 71 671 36 HOH WAT . C 3 HOH A 72 672 77 HOH WAT . C 3 HOH A 73 673 49 HOH WAT . C 3 HOH A 74 674 128 HOH WAT . C 3 HOH A 75 675 21 HOH WAT . C 3 HOH A 76 676 172 HOH WAT . C 3 HOH A 77 677 88 HOH WAT . C 3 HOH A 78 678 37 HOH WAT . C 3 HOH A 79 679 52 HOH WAT . C 3 HOH A 80 680 83 HOH WAT . C 3 HOH A 81 681 89 HOH WAT . C 3 HOH A 82 682 131 HOH WAT . C 3 HOH A 83 683 160 HOH WAT . C 3 HOH A 84 684 43 HOH WAT . C 3 HOH A 85 685 70 HOH WAT . C 3 HOH A 86 686 127 HOH WAT . C 3 HOH A 87 687 85 HOH WAT . C 3 HOH A 88 688 177 HOH WAT . C 3 HOH A 89 689 153 HOH WAT . C 3 HOH A 90 690 98 HOH WAT . C 3 HOH A 91 691 112 HOH WAT . C 3 HOH A 92 692 60 HOH WAT . C 3 HOH A 93 693 174 HOH WAT . C 3 HOH A 94 694 117 HOH WAT . C 3 HOH A 95 695 91 HOH WAT . C 3 HOH A 96 696 120 HOH WAT . C 3 HOH A 97 697 114 HOH WAT . C 3 HOH A 98 698 148 HOH WAT . C 3 HOH A 99 699 186 HOH WAT . C 3 HOH A 100 700 109 HOH WAT . C 3 HOH A 101 701 74 HOH WAT . C 3 HOH A 102 702 50 HOH WAT . C 3 HOH A 103 703 134 HOH WAT . C 3 HOH A 104 704 150 HOH WAT . C 3 HOH A 105 705 110 HOH WAT . C 3 HOH A 106 706 59 HOH WAT . C 3 HOH A 107 707 136 HOH WAT . C 3 HOH A 108 708 106 HOH WAT . C 3 HOH A 109 709 39 HOH WAT . C 3 HOH A 110 710 123 HOH WAT . C 3 HOH A 111 711 135 HOH WAT . C 3 HOH A 112 712 61 HOH WAT . C 3 HOH A 113 713 156 HOH WAT . C 3 HOH A 114 714 80 HOH WAT . C 3 HOH A 115 715 93 HOH WAT . C 3 HOH A 116 716 167 HOH WAT . C 3 HOH A 117 717 94 HOH WAT . C 3 HOH A 118 718 159 HOH WAT . C 3 HOH A 119 719 11 HOH WAT . C 3 HOH A 120 720 149 HOH WAT . C 3 HOH A 121 721 24 HOH WAT . C 3 HOH A 122 722 129 HOH WAT . C 3 HOH A 123 723 140 HOH WAT . C 3 HOH A 124 724 121 HOH WAT . C 3 HOH A 125 725 71 HOH WAT . C 3 HOH A 126 726 35 HOH WAT . C 3 HOH A 127 727 111 HOH WAT . C 3 HOH A 128 728 183 HOH WAT . C 3 HOH A 129 729 33 HOH WAT . C 3 HOH A 130 730 133 HOH WAT . C 3 HOH A 131 731 142 HOH WAT . C 3 HOH A 132 732 48 HOH WAT . C 3 HOH A 133 733 158 HOH WAT . C 3 HOH A 134 734 182 HOH WAT . C 3 HOH A 135 735 151 HOH WAT . C 3 HOH A 136 736 141 HOH WAT . C 3 HOH A 137 737 187 HOH WAT . C 3 HOH A 138 738 115 HOH WAT . C 3 HOH A 139 739 132 HOH WAT . C 3 HOH A 140 740 154 HOH WAT . C 3 HOH A 141 741 99 HOH WAT . # 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 3.403 4.035 28.431 1 18.75 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 2.264 3.929 29.21 1 20.21 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 2.25 3.268 30.314 1 20.59 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 3.321 2.685 30.76 1 22.24 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 4.497 2.759 30.025 1 22.8 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 4.504 3.452 28.831 1 21.81 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 1.258 4.475 28.865 1 23.58 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 3.294 2.106 31.815 1 22.47 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 3.304 4.754 27.177 1 22.32 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 3.74 6.217 27.1 1 20.53 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 2.796 7.146 27.476 1 18.69 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 4.197 6.339 25.672 1 20.71 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 4.699 4.953 25.374 1 22.76 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 4.005 4.074 26.196 1 21.48 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 3.184 6.644 24.744 1 18.74 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 6.194 4.75 25.462 1 18.73 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 6.846 5.112 24.275 1 19.38 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 8.209 5.833 24.236 1 19.2 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 8.525 6.321 22.984 1 20.61 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 8.344 6.801 25.213 1 21.62 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 9.267 4.827 24.681 1 22.73 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 9.427 3.265 24.493 1 21.96 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 9.337 3.083 22.994 1 27.28 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 10.701 2.899 24.965 1 25.26 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 8.402 2.542 25.144 1 25.07 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 25 #