data_8H5D # _model_server_result.job_id CJonuScR0Tusyo1YAnL1XQ _model_server_result.datetime_utc '2025-09-17 01:10:24' _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 8h5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 8H5D # _exptl.entry_id 8H5D _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.1 _cell.angle_gamma 90 _cell.entry_id 8H5D _cell.length_a 46.753 _cell.length_b 79.979 _cell.length_c 99.244 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8H5D _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,F 1 1 B,E,G 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 343 n n N1 C6 UDP sing 344 n n N1 C1' UDP sing 345 n n C2 N3 UDP sing 346 n n C2 O2 UDP doub 347 n n N3 C4 UDP sing 348 n n N3 HN3 UDP sing 349 n n C4 C5 UDP sing 350 n n C4 O4 UDP doub 351 n n C5 C6 UDP doub 352 n n C5 H5 UDP sing 353 n n C6 H6 UDP sing 354 n n C1' C2' UDP sing 355 n n C1' O4' UDP sing 356 n n C1' H1' UDP sing 357 n n C2' O2' UDP sing 358 n n C2' C3' UDP sing 359 n n C2' H2' UDP sing 360 n n O2' HO2' UDP sing 361 n n C3' C4' UDP sing 362 n n C3' O3' UDP sing 363 n n C3' H3' UDP sing 364 n n C4' O4' UDP sing 365 n n C4' C5' UDP sing 366 n n C4' H4' UDP sing 367 n n O3' HO3' UDP sing 368 n n C5' O5' UDP sing 369 n n C5' "H5'1" UDP sing 370 n n C5' "H5'2" UDP sing 371 n n O5' PA UDP sing 372 n n PA O1A UDP doub 373 n n PA O2A UDP sing 374 n n PA O3A UDP sing 375 n n O2A HOA2 UDP sing 376 n n O3A PB UDP sing 377 n n PB O1B UDP doub 378 n n PB O2B UDP sing 379 n n PB O3B UDP sing 380 n n O2B HOB2 UDP sing 381 n n O3B HOB3 UDP sing 382 n n # _atom_sites.entry_id 8H5D _atom_sites.fract_transf_matrix[1][1] 0.021389 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000409 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012503 _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] 0.010078 _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 C 2 UDP A 1 501 1 UDP UDP . D 3 GOL A 1 502 1 GOL GOL . E 2 UDP B 1 501 2 UDP UDP . F 4 HOH A 1 601 178 HOH HOH . F 4 HOH A 2 602 167 HOH HOH . F 4 HOH A 3 603 37 HOH HOH . F 4 HOH A 4 604 54 HOH HOH . F 4 HOH A 5 605 87 HOH HOH . F 4 HOH A 6 606 162 HOH HOH . F 4 HOH A 7 607 59 HOH HOH . F 4 HOH A 8 608 224 HOH HOH . F 4 HOH A 9 609 248 HOH HOH . F 4 HOH A 10 610 81 HOH HOH . F 4 HOH A 11 611 3 HOH HOH . F 4 HOH A 12 612 31 HOH HOH . F 4 HOH A 13 613 76 HOH HOH . F 4 HOH A 14 614 43 HOH HOH . F 4 HOH A 15 615 56 HOH HOH . F 4 HOH A 16 616 176 HOH HOH . F 4 HOH A 17 617 82 HOH HOH . F 4 HOH A 18 618 141 HOH HOH . F 4 HOH A 19 619 173 HOH HOH . F 4 HOH A 20 620 154 HOH HOH . F 4 HOH A 21 621 78 HOH HOH . F 4 HOH A 22 622 66 HOH HOH . F 4 HOH A 23 623 22 HOH HOH . F 4 HOH A 24 624 17 HOH HOH . F 4 HOH A 25 625 36 HOH HOH . F 4 HOH A 26 626 39 HOH HOH . F 4 HOH A 27 627 36 HOH HOH . F 4 HOH A 28 628 10 HOH HOH . F 4 HOH A 29 629 5 HOH HOH . F 4 HOH A 30 630 34 HOH HOH . F 4 HOH A 31 631 30 HOH HOH . F 4 HOH A 32 632 85 HOH HOH . F 4 HOH A 33 633 71 HOH HOH . F 4 HOH A 34 634 159 HOH HOH . F 4 HOH A 35 635 102 HOH HOH . F 4 HOH A 36 636 32 HOH HOH . F 4 HOH A 37 637 144 HOH HOH . F 4 HOH A 38 638 94 HOH HOH . F 4 HOH A 39 639 214 HOH HOH . F 4 HOH A 40 640 149 HOH HOH . F 4 HOH A 41 641 57 HOH HOH . F 4 HOH A 42 642 79 HOH HOH . F 4 HOH A 43 643 62 HOH HOH . F 4 HOH A 44 644 161 HOH HOH . F 4 HOH A 45 645 49 HOH HOH . F 4 HOH A 46 646 89 HOH HOH . F 4 HOH A 47 647 227 HOH HOH . F 4 HOH A 48 648 31 HOH HOH . F 4 HOH A 49 649 117 HOH HOH . F 4 HOH A 50 650 160 HOH HOH . F 4 HOH A 51 651 139 HOH HOH . F 4 HOH A 52 652 4 HOH HOH . F 4 HOH A 53 653 21 HOH HOH . F 4 HOH A 54 654 45 HOH HOH . F 4 HOH A 55 655 145 HOH HOH . F 4 HOH A 56 656 110 HOH HOH . F 4 HOH A 57 657 150 HOH HOH . F 4 HOH A 58 658 112 HOH HOH . F 4 HOH A 59 659 26 HOH HOH . F 4 HOH A 60 660 15 HOH HOH . F 4 HOH A 61 661 137 HOH HOH . F 4 HOH A 62 662 116 HOH HOH . F 4 HOH A 63 663 143 HOH HOH . F 4 HOH A 64 664 42 HOH HOH . F 4 HOH A 65 665 92 HOH HOH . F 4 HOH A 66 666 238 HOH HOH . F 4 HOH A 67 667 232 HOH HOH . F 4 HOH A 68 668 220 HOH HOH . F 4 HOH A 69 669 90 HOH HOH . F 4 HOH A 70 670 29 HOH HOH . F 4 HOH A 71 671 169 HOH HOH . F 4 HOH A 72 672 131 HOH HOH . F 4 HOH A 73 673 70 HOH HOH . F 4 HOH A 74 674 61 HOH HOH . F 4 HOH A 75 675 129 HOH HOH . F 4 HOH A 76 676 122 HOH HOH . F 4 HOH A 77 677 36 HOH HOH . F 4 HOH A 78 678 157 HOH HOH . F 4 HOH A 79 679 68 HOH HOH . F 4 HOH A 80 680 23 HOH HOH . F 4 HOH A 81 681 12 HOH HOH . F 4 HOH A 82 682 204 HOH HOH . F 4 HOH A 83 683 41 HOH HOH . F 4 HOH A 84 684 66 HOH HOH . F 4 HOH A 85 685 43 HOH HOH . F 4 HOH A 86 686 46 HOH HOH . F 4 HOH A 87 687 122 HOH HOH . F 4 HOH A 88 688 240 HOH HOH . F 4 HOH A 89 689 25 HOH HOH . F 4 HOH A 90 690 51 HOH HOH . F 4 HOH A 91 691 165 HOH HOH . F 4 HOH A 92 692 71 HOH HOH . F 4 HOH A 93 693 312 HOH HOH . F 4 HOH A 94 694 101 HOH HOH . F 4 HOH A 95 695 237 HOH HOH . F 4 HOH A 96 696 9 HOH HOH . F 4 HOH A 97 697 58 HOH HOH . F 4 HOH A 98 698 107 HOH HOH . F 4 HOH A 99 699 172 HOH HOH . F 4 HOH A 100 700 239 HOH HOH . F 4 HOH A 101 701 5 HOH HOH . F 4 HOH A 102 702 133 HOH HOH . F 4 HOH A 103 703 43 HOH HOH . F 4 HOH A 104 704 37 HOH HOH . F 4 HOH A 105 705 120 HOH HOH . F 4 HOH A 106 706 196 HOH HOH . F 4 HOH A 107 707 78 HOH HOH . F 4 HOH A 108 708 19 HOH HOH . F 4 HOH A 109 709 34 HOH HOH . F 4 HOH A 110 710 105 HOH HOH . F 4 HOH A 111 711 81 HOH HOH . F 4 HOH A 112 712 218 HOH HOH . F 4 HOH A 113 713 11 HOH HOH . F 4 HOH A 114 714 219 HOH HOH . F 4 HOH A 115 715 190 HOH HOH . F 4 HOH A 116 716 40 HOH HOH . F 4 HOH A 117 717 70 HOH HOH . F 4 HOH A 118 718 22 HOH HOH . F 4 HOH A 119 719 208 HOH HOH . F 4 HOH A 120 720 182 HOH HOH . F 4 HOH A 121 721 326 HOH HOH . F 4 HOH A 122 722 184 HOH HOH . F 4 HOH A 123 723 167 HOH HOH . F 4 HOH A 124 724 322 HOH HOH . F 4 HOH A 125 725 320 HOH HOH . F 4 HOH A 126 726 189 HOH HOH . F 4 HOH A 127 727 192 HOH HOH . F 4 HOH A 128 728 125 HOH HOH . F 4 HOH A 129 729 325 HOH HOH . F 4 HOH A 130 730 24 HOH HOH . F 4 HOH A 131 731 235 HOH HOH . F 4 HOH A 132 732 324 HOH HOH . F 4 HOH A 133 733 175 HOH HOH . G 4 HOH B 1 601 186 HOH HOH . G 4 HOH B 2 602 109 HOH HOH . G 4 HOH B 3 603 2 HOH HOH . G 4 HOH B 4 604 14 HOH HOH . G 4 HOH B 5 605 114 HOH HOH . G 4 HOH B 6 606 33 HOH HOH . G 4 HOH B 7 607 230 HOH HOH . G 4 HOH B 8 608 19 HOH HOH . G 4 HOH B 9 609 73 HOH HOH . G 4 HOH B 10 610 142 HOH HOH . G 4 HOH B 11 611 83 HOH HOH . G 4 HOH B 12 612 72 HOH HOH . G 4 HOH B 13 613 200 HOH HOH . G 4 HOH B 14 614 11 HOH HOH . G 4 HOH B 15 615 93 HOH HOH . G 4 HOH B 16 616 206 HOH HOH . G 4 HOH B 17 617 152 HOH HOH . G 4 HOH B 18 618 20 HOH HOH . G 4 HOH B 19 619 35 HOH HOH . G 4 HOH B 20 620 128 HOH HOH . G 4 HOH B 21 621 53 HOH HOH . G 4 HOH B 22 622 233 HOH HOH . G 4 HOH B 23 623 197 HOH HOH . G 4 HOH B 24 624 104 HOH HOH . G 4 HOH B 25 625 216 HOH HOH . G 4 HOH B 26 626 42 HOH HOH . G 4 HOH B 27 627 47 HOH HOH . G 4 HOH B 28 628 199 HOH HOH . G 4 HOH B 29 629 44 HOH HOH . G 4 HOH B 30 630 55 HOH HOH . G 4 HOH B 31 631 13 HOH HOH . G 4 HOH B 32 632 25 HOH HOH . G 4 HOH B 33 633 6 HOH HOH . G 4 HOH B 34 634 171 HOH HOH . G 4 HOH B 35 635 158 HOH HOH . G 4 HOH B 36 636 212 HOH HOH . G 4 HOH B 37 637 201 HOH HOH . G 4 HOH B 38 638 115 HOH HOH . G 4 HOH B 39 639 80 HOH HOH . G 4 HOH B 40 640 249 HOH HOH . G 4 HOH B 41 641 221 HOH HOH . G 4 HOH B 42 642 119 HOH HOH . G 4 HOH B 43 643 58 HOH HOH . G 4 HOH B 44 644 19 HOH HOH . G 4 HOH B 45 645 99 HOH HOH . G 4 HOH B 46 646 84 HOH HOH . G 4 HOH B 47 647 24 HOH HOH . G 4 HOH B 48 648 111 HOH HOH . G 4 HOH B 49 649 28 HOH HOH . G 4 HOH B 50 650 1 HOH HOH . G 4 HOH B 51 651 241 HOH HOH . G 4 HOH B 52 652 211 HOH HOH . G 4 HOH B 53 653 8 HOH HOH . G 4 HOH B 54 654 164 HOH HOH . G 4 HOH B 55 655 183 HOH HOH . G 4 HOH B 56 656 144 HOH HOH . G 4 HOH B 57 657 64 HOH HOH . G 4 HOH B 58 658 135 HOH HOH . G 4 HOH B 59 659 108 HOH HOH . G 4 HOH B 60 660 53 HOH HOH . G 4 HOH B 61 661 168 HOH HOH . G 4 HOH B 62 662 40 HOH HOH . G 4 HOH B 63 663 65 HOH HOH . G 4 HOH B 64 664 60 HOH HOH . G 4 HOH B 65 665 91 HOH HOH . G 4 HOH B 66 666 225 HOH HOH . G 4 HOH B 67 667 170 HOH HOH . G 4 HOH B 68 668 103 HOH HOH . G 4 HOH B 69 669 86 HOH HOH . G 4 HOH B 70 670 236 HOH HOH . G 4 HOH B 71 671 45 HOH HOH . G 4 HOH B 72 672 172 HOH HOH . G 4 HOH B 73 673 174 HOH HOH . G 4 HOH B 74 674 27 HOH HOH . G 4 HOH B 75 675 50 HOH HOH . G 4 HOH B 76 676 137 HOH HOH . G 4 HOH B 77 677 106 HOH HOH . G 4 HOH B 78 678 69 HOH HOH . G 4 HOH B 79 679 148 HOH HOH . G 4 HOH B 80 680 74 HOH HOH . G 4 HOH B 81 681 101 HOH HOH . G 4 HOH B 82 682 96 HOH HOH . G 4 HOH B 83 683 32 HOH HOH . G 4 HOH B 84 684 57 HOH HOH . G 4 HOH B 85 685 49 HOH HOH . G 4 HOH B 86 686 134 HOH HOH . G 4 HOH B 87 687 156 HOH HOH . G 4 HOH B 88 688 63 HOH HOH . G 4 HOH B 89 689 77 HOH HOH . G 4 HOH B 90 690 127 HOH HOH . G 4 HOH B 91 691 146 HOH HOH . G 4 HOH B 92 692 105 HOH HOH . G 4 HOH B 93 693 59 HOH HOH . G 4 HOH B 94 694 169 HOH HOH . G 4 HOH B 95 695 52 HOH HOH . G 4 HOH B 96 696 3 HOH HOH . G 4 HOH B 97 697 64 HOH HOH . G 4 HOH B 98 698 130 HOH HOH . G 4 HOH B 99 699 33 HOH HOH . G 4 HOH B 100 700 27 HOH HOH . G 4 HOH B 101 701 60 HOH HOH . G 4 HOH B 102 702 67 HOH HOH . G 4 HOH B 103 703 217 HOH HOH . G 4 HOH B 104 704 49 HOH HOH . G 4 HOH B 105 705 250 HOH HOH . G 4 HOH B 106 706 14 HOH HOH . G 4 HOH B 107 707 24 HOH HOH . G 4 HOH B 108 708 244 HOH HOH . G 4 HOH B 109 709 234 HOH HOH . G 4 HOH B 110 710 67 HOH HOH . G 4 HOH B 111 711 181 HOH HOH . G 4 HOH B 112 712 166 HOH HOH . G 4 HOH B 113 713 327 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 . . . C 2 9.055 -7.421 5.514 1 16.44 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . C 2 9.761 -8.635 5.452 1 16.65 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . C 2 9.685 -9.415 4.384 1 20.07 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . C 2 8.932 -9.071 3.308 1 19.53 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . C 2 8.227 -7.887 3.352 1 17.03 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . C 2 8.311 -7.066 4.475 1 16.7 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . C 2 10.485 -9.031 6.346 1 15.63 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . C 2 8.872 -9.843 2.314 1 20.13 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . C 2 9.145 -6.55 6.693 1 15.98 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . C 2 10.163 -5.407 6.569 1 16.36 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . C 2 11.521 -5.826 6.856 1 16.13 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . C 2 9.599 -4.379 7.533 1 16.64 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . C 2 8.078 -4.622 7.522 1 16.48 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . C 2 7.9 -5.912 6.899 1 15.95 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . C 2 10.164 -4.563 8.854 1 16.99 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . C 2 7.295 -3.599 6.675 1 16.7 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . C 2 7.183 -2.32 7.281 1 16.97 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . C 2 7.045 -0.995 6.423 1 17.05 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . C 2 8.224 -0.999 5.46 1 18.12 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . C 2 7.086 0.049 7.454 1 16.31 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . C 2 5.713 -1.143 5.539 1 19.22 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . C 2 4.165 -1.577 5.834 1 20 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . C 2 3.462 -0.603 4.911 1 20.45 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . C 2 4.154 -3.004 5.393 1 22.39 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . C 2 3.911 -1.436 7.294 1 22.98 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #