data_9KSV # _model_server_result.job_id fqjmUk7NSsXwd_DmbH-HQw _model_server_result.datetime_utc '2025-06-27 01:23:59' _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 9ksv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 9KSV # _exptl.entry_id 9KSV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _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 9KSV _cell.length_a 75.16 _cell.length_b 75.16 _cell.length_c 162.81 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9KSV _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 3 _struct_asym.id C _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 412 n n N1 C6 UDP sing 413 n n N1 C1' UDP sing 414 n n C2 N3 UDP sing 415 n n C2 O2 UDP doub 416 n n N3 C4 UDP sing 417 n n N3 HN3 UDP sing 418 n n C4 C5 UDP sing 419 n n C4 O4 UDP doub 420 n n C5 C6 UDP doub 421 n n C5 H5 UDP sing 422 n n C6 H6 UDP sing 423 n n C1' C2' UDP sing 424 n n C1' O4' UDP sing 425 n n C1' H1' UDP sing 426 n n C2' O2' UDP sing 427 n n C2' C3' UDP sing 428 n n C2' H2' UDP sing 429 n n O2' HO2' UDP sing 430 n n C3' C4' UDP sing 431 n n C3' O3' UDP sing 432 n n C3' H3' UDP sing 433 n n C4' O4' UDP sing 434 n n C4' C5' UDP sing 435 n n C4' H4' UDP sing 436 n n O3' HO3' UDP sing 437 n n C5' O5' UDP sing 438 n n C5' "H5'1" UDP sing 439 n n C5' "H5'2" UDP sing 440 n n O5' PA UDP sing 441 n n PA O1A UDP doub 442 n n PA O2A UDP sing 443 n n PA O3A UDP sing 444 n n O2A HOA2 UDP sing 445 n n O3A PB UDP sing 446 n n PB O1B UDP doub 447 n n PB O2B UDP sing 448 n n PB O3B UDP sing 449 n n O2B HOB2 UDP sing 450 n n O3B HOB3 UDP sing 451 n n # _atom_sites.entry_id 9KSV _atom_sites.fract_transf_matrix[1][1] 0.013305 _atom_sites.fract_transf_matrix[1][2] 0.007682 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015363 _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] 0.006142 _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 A1EGT A 1 501 501 A1EGT A7G . C 3 UDP A 1 502 502 UDP UDP . D 4 HOH A 1 601 33 HOH HOH . D 4 HOH A 2 602 37 HOH HOH . D 4 HOH A 3 603 41 HOH HOH . D 4 HOH A 4 604 5 HOH HOH . D 4 HOH A 5 605 64 HOH HOH . D 4 HOH A 6 606 38 HOH HOH . D 4 HOH A 7 607 55 HOH HOH . D 4 HOH A 8 608 60 HOH HOH . D 4 HOH A 9 609 4 HOH HOH . D 4 HOH A 10 610 11 HOH HOH . D 4 HOH A 11 611 14 HOH HOH . D 4 HOH A 12 612 7 HOH HOH . D 4 HOH A 13 613 3 HOH HOH . D 4 HOH A 14 614 47 HOH HOH . D 4 HOH A 15 615 17 HOH HOH . D 4 HOH A 16 616 12 HOH HOH . D 4 HOH A 17 617 57 HOH HOH . D 4 HOH A 18 618 1 HOH HOH . D 4 HOH A 19 619 6 HOH HOH . D 4 HOH A 20 620 71 HOH HOH . D 4 HOH A 21 621 52 HOH HOH . D 4 HOH A 22 622 27 HOH HOH . D 4 HOH A 23 623 10 HOH HOH . D 4 HOH A 24 624 72 HOH HOH . D 4 HOH A 25 625 42 HOH HOH . D 4 HOH A 26 626 44 HOH HOH . D 4 HOH A 27 627 13 HOH HOH . D 4 HOH A 28 628 70 HOH HOH . D 4 HOH A 29 629 58 HOH HOH . D 4 HOH A 30 630 75 HOH HOH . D 4 HOH A 31 631 22 HOH HOH . D 4 HOH A 32 632 15 HOH HOH . D 4 HOH A 33 633 43 HOH HOH . D 4 HOH A 34 634 40 HOH HOH . D 4 HOH A 35 635 34 HOH HOH . D 4 HOH A 36 636 68 HOH HOH . D 4 HOH A 37 637 50 HOH HOH . D 4 HOH A 38 638 16 HOH HOH . D 4 HOH A 39 639 19 HOH HOH . D 4 HOH A 40 640 24 HOH HOH . D 4 HOH A 41 641 74 HOH HOH . D 4 HOH A 42 642 48 HOH HOH . D 4 HOH A 43 643 23 HOH HOH . D 4 HOH A 44 644 28 HOH HOH . D 4 HOH A 45 645 35 HOH HOH . D 4 HOH A 46 646 29 HOH HOH . D 4 HOH A 47 647 32 HOH HOH . D 4 HOH A 48 648 54 HOH HOH . D 4 HOH A 49 649 76 HOH HOH . D 4 HOH A 50 650 31 HOH HOH . D 4 HOH A 51 651 67 HOH HOH . D 4 HOH A 52 652 62 HOH HOH . D 4 HOH A 53 653 69 HOH HOH . D 4 HOH A 54 654 26 HOH HOH . D 4 HOH A 55 655 9 HOH HOH . D 4 HOH A 56 656 56 HOH HOH . D 4 HOH A 57 657 66 HOH HOH . D 4 HOH A 58 658 20 HOH HOH . D 4 HOH A 59 659 46 HOH HOH . D 4 HOH A 60 660 63 HOH HOH . D 4 HOH A 61 661 30 HOH HOH . D 4 HOH A 62 662 73 HOH HOH . D 4 HOH A 63 663 39 HOH HOH . D 4 HOH A 64 664 25 HOH HOH . D 4 HOH A 65 665 53 HOH HOH . D 4 HOH A 66 666 45 HOH HOH . D 4 HOH A 67 667 65 HOH HOH . D 4 HOH A 68 668 49 HOH HOH . D 4 HOH A 69 669 2 HOH HOH . D 4 HOH A 70 670 59 HOH HOH . D 4 HOH A 71 671 51 HOH HOH . D 4 HOH A 72 672 18 HOH HOH . D 4 HOH A 73 673 21 HOH HOH . D 4 HOH A 74 674 36 HOH HOH . D 4 HOH A 75 675 8 HOH HOH . D 4 HOH A 76 676 61 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 3 -23.818 -4.69 12.159 1 42.17 ? N1 UDP 502 A 1 HETATM 2 C C2 UDP . . . C 3 -23.665 -3.335 11.94 1 38.8 ? C2 UDP 502 A 1 HETATM 3 N N3 UDP . . . C 3 -22.863 -3.011 10.878 1 43.01 ? N3 UDP 502 A 1 HETATM 4 C C4 UDP . . . C 3 -22.213 -3.887 10.031 1 43.84 ? C4 UDP 502 A 1 HETATM 5 C C5 UDP . . . C 3 -22.417 -5.277 10.323 1 41.4 ? C5 UDP 502 A 1 HETATM 6 C C6 UDP . . . C 3 -23.185 -5.621 11.368 1 41.39 ? C6 UDP 502 A 1 HETATM 7 O O2 UDP . . . C 3 -24.203 -2.488 12.633 1 43.14 ? O2 UDP 502 A 1 HETATM 8 O O4 UDP . . . C 3 -21.531 -3.435 9.111 1 49.27 ? O4 UDP 502 A 1 HETATM 9 C C1' UDP . . . C 3 -24.633 -5.104 13.317 1 42.78 ? C1' UDP 502 A 1 HETATM 10 C C2' UDP . . . C 3 -26.046 -5.564 12.954 1 39.6 ? C2' UDP 502 A 1 HETATM 11 O O2' UDP . . . C 3 -26.968 -4.491 12.937 1 37.11 ? O2' UDP 502 A 1 HETATM 12 C C3' UDP . . . C 3 -26.329 -6.579 14.068 1 37.73 ? C3' UDP 502 A 1 HETATM 13 C C4' UDP . . . C 3 -24.945 -7.199 14.328 1 40.22 ? C4' UDP 502 A 1 HETATM 14 O O4' UDP . . . C 3 -23.977 -6.206 13.905 1 41.69 ? O4' UDP 502 A 1 HETATM 15 O O3' UDP . . . C 3 -26.821 -5.943 15.241 1 36.15 ? O3' UDP 502 A 1 HETATM 16 C C5' UDP . . . C 3 -24.659 -8.509 13.642 1 34.58 ? C5' UDP 502 A 1 HETATM 17 O O5' UDP . . . C 3 -25.38 -9.547 14.35 1 36.74 ? O5' UDP 502 A 1 HETATM 18 P PA UDP . . . C 3 -26.166 -10.682 13.53 1 38.69 ? PA UDP 502 A 1 HETATM 19 O O1A UDP . . . C 3 -26.729 -11.692 14.468 1 39.41 -1 O1A UDP 502 A 1 HETATM 20 O O2A UDP . . . C 3 -27.152 -10.037 12.61 1 40.2 ? O2A UDP 502 A 1 HETATM 21 O O3A UDP . . . C 3 -24.953 -11.339 12.702 1 38.05 ? O3A UDP 502 A 1 HETATM 22 P PB UDP . . . C 3 -23.479 -11.899 13.113 1 44.97 ? PB UDP 502 A 1 HETATM 23 O O1B UDP . . . C 3 -22.531 -10.717 13.046 1 39.46 -1 O1B UDP 502 A 1 HETATM 24 O O2B UDP . . . C 3 -23.119 -12.968 12.092 1 50.5 ? O2B UDP 502 A 1 HETATM 25 O O3B UDP . . . C 3 -23.614 -12.462 14.521 1 48.24 -1 O3B UDP 502 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 353 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #