data_9KSZ # _model_server_result.job_id 6cy9HTvX0u94jSNh3o4sdg _model_server_result.datetime_utc '2025-07-16 01:38:24' _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 9ksz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 9KSZ # _exptl.entry_id 9KSZ _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 120 _cell.entry_id 9KSZ _cell.length_a 75.779 _cell.length_b 75.779 _cell.length_c 164.505 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9KSZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 9KSZ _atom_sites.fract_transf_matrix[1][1] 0.013196 _atom_sites.fract_transf_matrix[1][2] 0.007619 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015238 _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] 0.006079 _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 HOH A 1 601 85 HOH HOH . C 3 HOH A 2 602 58 HOH HOH . C 3 HOH A 3 603 76 HOH HOH . C 3 HOH A 4 604 117 HOH HOH . C 3 HOH A 5 605 9 HOH HOH . C 3 HOH A 6 606 131 HOH HOH . C 3 HOH A 7 607 28 HOH HOH . C 3 HOH A 8 608 31 HOH HOH . C 3 HOH A 9 609 69 HOH HOH . C 3 HOH A 10 610 35 HOH HOH . C 3 HOH A 11 611 15 HOH HOH . C 3 HOH A 12 612 11 HOH HOH . C 3 HOH A 13 613 8 HOH HOH . C 3 HOH A 14 614 23 HOH HOH . C 3 HOH A 15 615 66 HOH HOH . C 3 HOH A 16 616 140 HOH HOH . C 3 HOH A 17 617 51 HOH HOH . C 3 HOH A 18 618 34 HOH HOH . C 3 HOH A 19 619 78 HOH HOH . C 3 HOH A 20 620 19 HOH HOH . C 3 HOH A 21 621 87 HOH HOH . C 3 HOH A 22 622 137 HOH HOH . C 3 HOH A 23 623 102 HOH HOH . C 3 HOH A 24 624 109 HOH HOH . C 3 HOH A 25 625 16 HOH HOH . C 3 HOH A 26 626 30 HOH HOH . C 3 HOH A 27 627 13 HOH HOH . C 3 HOH A 28 628 71 HOH HOH . C 3 HOH A 29 629 110 HOH HOH . C 3 HOH A 30 630 20 HOH HOH . C 3 HOH A 31 631 90 HOH HOH . C 3 HOH A 32 632 22 HOH HOH . C 3 HOH A 33 633 5 HOH HOH . C 3 HOH A 34 634 42 HOH HOH . C 3 HOH A 35 635 127 HOH HOH . C 3 HOH A 36 636 46 HOH HOH . C 3 HOH A 37 637 37 HOH HOH . C 3 HOH A 38 638 83 HOH HOH . C 3 HOH A 39 639 67 HOH HOH . C 3 HOH A 40 640 55 HOH HOH . C 3 HOH A 41 641 18 HOH HOH . C 3 HOH A 42 642 38 HOH HOH . C 3 HOH A 43 643 121 HOH HOH . C 3 HOH A 44 644 79 HOH HOH . C 3 HOH A 45 645 91 HOH HOH . C 3 HOH A 46 646 114 HOH HOH . C 3 HOH A 47 647 32 HOH HOH . C 3 HOH A 48 648 86 HOH HOH . C 3 HOH A 49 649 134 HOH HOH . C 3 HOH A 50 650 14 HOH HOH . C 3 HOH A 51 651 7 HOH HOH . C 3 HOH A 52 652 4 HOH HOH . C 3 HOH A 53 653 57 HOH HOH . C 3 HOH A 54 654 133 HOH HOH . C 3 HOH A 55 655 47 HOH HOH . C 3 HOH A 56 656 56 HOH HOH . C 3 HOH A 57 657 26 HOH HOH . C 3 HOH A 58 658 49 HOH HOH . C 3 HOH A 59 659 77 HOH HOH . C 3 HOH A 60 660 36 HOH HOH . C 3 HOH A 61 661 107 HOH HOH . C 3 HOH A 62 662 21 HOH HOH . C 3 HOH A 63 663 65 HOH HOH . C 3 HOH A 64 664 84 HOH HOH . C 3 HOH A 65 665 45 HOH HOH . C 3 HOH A 66 666 123 HOH HOH . C 3 HOH A 67 667 139 HOH HOH . C 3 HOH A 68 668 52 HOH HOH . C 3 HOH A 69 669 112 HOH HOH . C 3 HOH A 70 670 73 HOH HOH . C 3 HOH A 71 671 80 HOH HOH . C 3 HOH A 72 672 25 HOH HOH . C 3 HOH A 73 673 64 HOH HOH . C 3 HOH A 74 674 29 HOH HOH . C 3 HOH A 75 675 105 HOH HOH . C 3 HOH A 76 676 41 HOH HOH . C 3 HOH A 77 677 68 HOH HOH . C 3 HOH A 78 678 108 HOH HOH . C 3 HOH A 79 679 33 HOH HOH . C 3 HOH A 80 680 81 HOH HOH . C 3 HOH A 81 681 122 HOH HOH . C 3 HOH A 82 682 61 HOH HOH . C 3 HOH A 83 683 106 HOH HOH . C 3 HOH A 84 684 70 HOH HOH . C 3 HOH A 85 685 82 HOH HOH . C 3 HOH A 86 686 124 HOH HOH . C 3 HOH A 87 687 135 HOH HOH . C 3 HOH A 88 688 126 HOH HOH . C 3 HOH A 89 689 104 HOH HOH . C 3 HOH A 90 690 130 HOH HOH . C 3 HOH A 91 691 89 HOH HOH . C 3 HOH A 92 692 50 HOH HOH . C 3 HOH A 93 693 24 HOH HOH . C 3 HOH A 94 694 94 HOH HOH . C 3 HOH A 95 695 72 HOH HOH . C 3 HOH A 96 696 118 HOH HOH . C 3 HOH A 97 697 92 HOH HOH . C 3 HOH A 98 698 74 HOH HOH . C 3 HOH A 99 699 101 HOH HOH . C 3 HOH A 100 700 48 HOH HOH . C 3 HOH A 101 701 62 HOH HOH . C 3 HOH A 102 702 44 HOH HOH . C 3 HOH A 103 703 115 HOH HOH . C 3 HOH A 104 704 95 HOH HOH . C 3 HOH A 105 705 40 HOH HOH . C 3 HOH A 106 706 128 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 24.001 4.299 12.3 1 45.35 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 23.95 2.958 11.972 1 45.94 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 23.099 2.646 10.946 1 45.05 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 22.306 3.517 10.231 1 47.57 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 22.409 4.889 10.634 1 46.37 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 23.234 5.224 11.636 1 44.89 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 24.61 2.109 12.548 1 50.28 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 21.59 3.08 9.333 1 50.55 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 24.884 4.689 13.414 1 42.78 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 26.276 5.125 12.966 1 39.55 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 27.128 4.002 12.955 1 35.95 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 26.645 6.108 14.078 1 42.09 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 25.305 6.79 14.378 1 43.13 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 24.299 5.791 14.073 1 43.87 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 27.128 5.428 15.227 1 46.57 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 25.018 8.051 13.602 1 42.9 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 25.448 9.194 14.379 1 43.52 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 26.257 10.364 13.648 1 46.54 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 26.825 11.285 14.668 1 40.65 -1 O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 27.189 9.772 12.653 1 42.93 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 25.085 11.109 12.854 1 42.4 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 23.603 11.611 13.219 1 45.99 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 22.695 10.443 13.02 1 45.91 -1 O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 23.311 12.732 12.272 1 51.1 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 23.658 12.065 14.639 1 41.07 -1 O3B UDP 501 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #