data_3JT1 # _model_server_result.job_id AaCw93jXKfxDAtrgp9jK9w _model_server_result.datetime_utc '2024-11-12 20:37:48' _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 3jt1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":526}' # _entry.id 3JT1 # _exptl.entry_id 3JT1 _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 3JT1 _cell.length_a 122.571 _cell.length_b 122.571 _cell.length_c 103.982 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JT1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _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 3JT1 _atom_sites.fract_transf_matrix[1][1] 0.008159 _atom_sites.fract_transf_matrix[1][2] 0.00471 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009421 _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] 0.009617 _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 1 526 1 UDP UDP . C 3 HOH A 1 527 2 HOH HOH . C 3 HOH A 2 528 3 HOH HOH . C 3 HOH A 3 529 4 HOH HOH . C 3 HOH A 4 530 5 HOH HOH . C 3 HOH A 5 531 7 HOH HOH . C 3 HOH A 6 532 8 HOH HOH . C 3 HOH A 7 533 9 HOH HOH . C 3 HOH A 8 534 10 HOH HOH . C 3 HOH A 9 535 11 HOH HOH . C 3 HOH A 10 536 12 HOH HOH . C 3 HOH A 11 537 13 HOH HOH . C 3 HOH A 12 538 14 HOH HOH . C 3 HOH A 13 539 15 HOH HOH . C 3 HOH A 14 540 16 HOH HOH . C 3 HOH A 15 541 17 HOH HOH . C 3 HOH A 16 542 18 HOH HOH . C 3 HOH A 17 543 19 HOH HOH . C 3 HOH A 18 544 20 HOH HOH . C 3 HOH A 19 545 21 HOH HOH . C 3 HOH A 20 546 22 HOH HOH . C 3 HOH A 21 547 24 HOH HOH . C 3 HOH A 22 548 25 HOH HOH . C 3 HOH A 23 549 26 HOH HOH . C 3 HOH A 24 550 27 HOH HOH . C 3 HOH A 25 551 28 HOH HOH . C 3 HOH A 26 552 29 HOH HOH . C 3 HOH A 27 553 30 HOH HOH . C 3 HOH A 28 554 31 HOH HOH . C 3 HOH A 29 555 32 HOH HOH . C 3 HOH A 30 556 33 HOH HOH . C 3 HOH A 31 557 36 HOH HOH . C 3 HOH A 32 558 37 HOH HOH . C 3 HOH A 33 559 39 HOH HOH . C 3 HOH A 34 560 40 HOH HOH . C 3 HOH A 35 561 41 HOH HOH . C 3 HOH A 36 562 42 HOH HOH . C 3 HOH A 37 563 43 HOH HOH . C 3 HOH A 38 564 44 HOH HOH . C 3 HOH A 39 565 45 HOH HOH . C 3 HOH A 40 566 46 HOH HOH . C 3 HOH A 41 567 47 HOH HOH . C 3 HOH A 42 568 49 HOH HOH . C 3 HOH A 43 569 50 HOH HOH . C 3 HOH A 44 570 51 HOH HOH . C 3 HOH A 45 571 52 HOH HOH . C 3 HOH A 46 572 53 HOH HOH . C 3 HOH A 47 573 55 HOH HOH . C 3 HOH A 48 574 56 HOH HOH . C 3 HOH A 49 575 57 HOH HOH . C 3 HOH A 50 576 58 HOH HOH . C 3 HOH A 51 577 59 HOH HOH . C 3 HOH A 52 578 60 HOH HOH . C 3 HOH A 53 579 63 HOH HOH . C 3 HOH A 54 580 64 HOH HOH . C 3 HOH A 55 581 65 HOH HOH . C 3 HOH A 56 582 66 HOH HOH . C 3 HOH A 57 583 67 HOH HOH . C 3 HOH A 58 584 68 HOH HOH . C 3 HOH A 59 585 72 HOH HOH . C 3 HOH A 60 586 73 HOH HOH . C 3 HOH A 61 587 74 HOH HOH . C 3 HOH A 62 588 77 HOH HOH . C 3 HOH A 63 589 81 HOH HOH . C 3 HOH A 64 590 82 HOH HOH . C 3 HOH A 65 591 84 HOH HOH . C 3 HOH A 66 592 85 HOH HOH . C 3 HOH A 67 593 86 HOH HOH . C 3 HOH A 68 594 87 HOH HOH . C 3 HOH A 69 595 88 HOH HOH . C 3 HOH A 70 596 89 HOH HOH . C 3 HOH A 71 597 90 HOH HOH . C 3 HOH A 72 598 91 HOH HOH . C 3 HOH A 73 599 92 HOH HOH . C 3 HOH A 74 600 93 HOH HOH . C 3 HOH A 75 601 94 HOH HOH . C 3 HOH A 76 602 95 HOH HOH . C 3 HOH A 77 603 96 HOH HOH . C 3 HOH A 78 604 97 HOH HOH . C 3 HOH A 79 605 98 HOH HOH . C 3 HOH A 80 606 99 HOH HOH . C 3 HOH A 81 607 100 HOH HOH . C 3 HOH A 82 608 101 HOH HOH . C 3 HOH A 83 609 102 HOH HOH . C 3 HOH A 84 610 103 HOH HOH . C 3 HOH A 85 611 104 HOH HOH . C 3 HOH A 86 612 105 HOH HOH . C 3 HOH A 87 613 106 HOH HOH . C 3 HOH A 88 614 107 HOH HOH . C 3 HOH A 89 615 108 HOH HOH . C 3 HOH A 90 616 109 HOH HOH . C 3 HOH A 91 617 110 HOH HOH . C 3 HOH A 92 618 111 HOH HOH . C 3 HOH A 93 619 114 HOH HOH . C 3 HOH A 94 620 115 HOH HOH . C 3 HOH A 95 621 116 HOH HOH . C 3 HOH A 96 622 117 HOH HOH . C 3 HOH A 97 623 119 HOH HOH . C 3 HOH A 98 624 120 HOH HOH . C 3 HOH A 99 625 121 HOH HOH . C 3 HOH A 100 626 122 HOH HOH . C 3 HOH A 101 627 123 HOH HOH . C 3 HOH A 102 628 124 HOH HOH . C 3 HOH A 103 629 125 HOH HOH . C 3 HOH A 104 630 126 HOH HOH . C 3 HOH A 105 631 127 HOH HOH . C 3 HOH A 106 632 129 HOH HOH . C 3 HOH A 107 633 130 HOH HOH . C 3 HOH A 108 634 131 HOH HOH . C 3 HOH A 109 635 132 HOH HOH . C 3 HOH A 110 636 133 HOH HOH . C 3 HOH A 111 637 136 HOH HOH . C 3 HOH A 112 638 137 HOH HOH . C 3 HOH A 113 639 138 HOH HOH . C 3 HOH A 114 640 139 HOH HOH . C 3 HOH A 115 641 141 HOH HOH . C 3 HOH A 116 642 142 HOH HOH . C 3 HOH A 117 643 143 HOH HOH . C 3 HOH A 118 644 144 HOH HOH . C 3 HOH A 119 645 145 HOH HOH . C 3 HOH A 120 646 146 HOH HOH . C 3 HOH A 121 647 147 HOH HOH . C 3 HOH A 122 648 148 HOH HOH . C 3 HOH A 123 649 149 HOH HOH . C 3 HOH A 124 650 150 HOH HOH . C 3 HOH A 125 651 151 HOH HOH . C 3 HOH A 126 652 152 HOH HOH . C 3 HOH A 127 653 153 HOH HOH . C 3 HOH A 128 654 154 HOH HOH . C 3 HOH A 129 655 156 HOH HOH . C 3 HOH A 130 656 157 HOH HOH . C 3 HOH A 131 657 158 HOH HOH . C 3 HOH A 132 658 159 HOH HOH . C 3 HOH A 133 659 160 HOH HOH . C 3 HOH A 134 660 162 HOH HOH . C 3 HOH A 135 661 163 HOH HOH . C 3 HOH A 136 662 164 HOH HOH . C 3 HOH A 137 663 165 HOH HOH . C 3 HOH A 138 664 166 HOH HOH . C 3 HOH A 139 665 167 HOH HOH . C 3 HOH A 140 666 168 HOH HOH . C 3 HOH A 141 667 169 HOH HOH . C 3 HOH A 142 668 174 HOH HOH . C 3 HOH A 143 669 175 HOH HOH . C 3 HOH A 144 670 176 HOH HOH . C 3 HOH A 145 671 177 HOH HOH . C 3 HOH A 146 672 180 HOH HOH . C 3 HOH A 147 673 181 HOH HOH . C 3 HOH A 148 674 182 HOH HOH . C 3 HOH A 149 675 183 HOH HOH . C 3 HOH A 150 676 184 HOH HOH . C 3 HOH A 151 677 185 HOH HOH . C 3 HOH A 152 678 186 HOH HOH . C 3 HOH A 153 679 187 HOH HOH . C 3 HOH A 154 680 188 HOH HOH . C 3 HOH A 155 681 189 HOH HOH . C 3 HOH A 156 682 190 HOH HOH . C 3 HOH A 157 683 191 HOH HOH . C 3 HOH A 158 684 192 HOH HOH . C 3 HOH A 159 685 193 HOH HOH . C 3 HOH A 160 686 194 HOH HOH . C 3 HOH A 161 687 195 HOH HOH . C 3 HOH A 162 688 196 HOH HOH . C 3 HOH A 163 689 197 HOH HOH . C 3 HOH A 164 690 198 HOH HOH . C 3 HOH A 165 691 199 HOH HOH . C 3 HOH A 166 692 200 HOH HOH . C 3 HOH A 167 693 201 HOH HOH . C 3 HOH A 168 694 202 HOH HOH . C 3 HOH A 169 695 203 HOH HOH . C 3 HOH A 170 696 204 HOH HOH . C 3 HOH A 171 697 205 HOH HOH . C 3 HOH A 172 698 206 HOH HOH . C 3 HOH A 173 699 207 HOH HOH . C 3 HOH A 174 700 208 HOH HOH . C 3 HOH A 175 701 209 HOH HOH . C 3 HOH A 176 702 210 HOH HOH . C 3 HOH A 177 703 211 HOH HOH . C 3 HOH A 178 704 212 HOH HOH . C 3 HOH A 179 705 213 HOH HOH . C 3 HOH A 180 706 214 HOH HOH . C 3 HOH A 181 707 215 HOH HOH . C 3 HOH A 182 708 216 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 45.264 -8.826 38.668 1 67.3 ? N1 UDP 526 A 1 HETATM 2 C C2 UDP . . . B 2 46.186 -8.789 39.673 1 64.84 ? C2 UDP 526 A 1 HETATM 3 N N3 UDP . . . B 2 47.358 -9.466 39.578 1 65.68 ? N3 UDP 526 A 1 HETATM 4 C C4 UDP . . . B 2 47.616 -10.188 38.459 1 68.22 ? C4 UDP 526 A 1 HETATM 5 C C5 UDP . . . B 2 46.693 -10.217 37.43 1 67.39 ? C5 UDP 526 A 1 HETATM 6 C C6 UDP . . . B 2 45.608 -9.368 37.476 1 66.41 ? C6 UDP 526 A 1 HETATM 7 O O2 UDP . . . B 2 45.965 -8.148 40.672 1 61.78 ? O2 UDP 526 A 1 HETATM 8 O O4 UDP . . . B 2 48.664 -10.793 38.38 1 66.18 ? O4 UDP 526 A 1 HETATM 9 C C1' UDP . . . B 2 44.009 -8.069 38.827 1 69.65 ? C1' UDP 526 A 1 HETATM 10 C C2' UDP . . . B 2 44.266 -6.611 38.533 1 69.37 ? C2' UDP 526 A 1 HETATM 11 O O2' UDP . . . B 2 43.463 -5.85 39.391 1 57.99 ? O2' UDP 526 A 1 HETATM 12 C C3' UDP . . . B 2 43.892 -6.482 37.07 1 70.61 ? C3' UDP 526 A 1 HETATM 13 C C4' UDP . . . B 2 42.887 -7.589 36.83 1 75.78 ? C4' UDP 526 A 1 HETATM 14 O O4' UDP . . . B 2 43.028 -8.481 37.906 1 72.23 ? O4' UDP 526 A 1 HETATM 15 O O3' UDP . . . B 2 43.383 -5.222 36.753 1 68.83 ? O3' UDP 526 A 1 HETATM 16 C C5' UDP . . . B 2 43.197 -8.393 35.582 1 81.91 ? C5' UDP 526 A 1 HETATM 17 O O5' UDP . . . B 2 42.372 -8.068 34.495 1 89.97 ? O5' UDP 526 A 1 HETATM 18 P PA UDP . . . B 2 43.131 -7.897 33.1 1 96.18 ? PA UDP 526 A 1 HETATM 19 O O1A UDP . . . B 2 43.913 -6.655 33.159 1 95.96 ? O1A UDP 526 A 1 HETATM 20 O O2A UDP . . . B 2 43.976 -9.073 32.887 1 94.7 ? O2A UDP 526 A 1 HETATM 21 O O3A UDP . . . B 2 42.092 -7.708 31.888 1 97.84 ? O3A UDP 526 A 1 HETATM 22 P PB UDP . . . B 2 42.563 -6.829 30.609 1 99.63 ? PB UDP 526 A 1 HETATM 23 O O1B UDP . . . B 2 43.378 -7.687 29.738 1 99.51 ? O1B UDP 526 A 1 HETATM 24 O O2B UDP . . . B 2 43.353 -5.678 31.054 1 97.98 ? O2B UDP 526 A 1 HETATM 25 O O3B UDP . . . B 2 41.417 -6.365 29.84 1 98.12 ? O3B UDP 526 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 208 _model_server_stats.encode_time_ms 27 _model_server_stats.element_count 25 #