data_2RJ8 # _model_server_result.job_id 9owMNT_LHvbZJATlbb9JDQ _model_server_result.datetime_utc '2024-11-07 13:06:59' _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 2rj8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 2RJ8 # _exptl.entry_id 2RJ8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _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 90 _cell.entry_id 2RJ8 _cell.length_a 52.45 _cell.length_b 149.6 _cell.length_c 78.74 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RJ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA,PQS dimeric 2 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,B,C,D,E 1 1 A,B,C,D,E 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -39.37 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 D O3B UDP . A UDP 1 1_555 B MN MN . A MN 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc2 D O1A UDP . A UDP 1 1_555 B MN MN . A MN 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc3 A OD2 ASP 150 A ASP 211 1_555 B MN MN . A MN 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc4 A OD1 ASP 152 A ASP 213 1_555 B MN MN . A MN 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? # _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 427 n n N1 C6 UDP sing 428 n n N1 C1' UDP sing 429 n n C2 N3 UDP sing 430 n n C2 O2 UDP doub 431 n n N3 C4 UDP sing 432 n n N3 HN3 UDP sing 433 n n C4 C5 UDP sing 434 n n C4 O4 UDP doub 435 n n C5 C6 UDP doub 436 n n C5 H5 UDP sing 437 n n C6 H6 UDP sing 438 n n C1' C2' UDP sing 439 n n C1' O4' UDP sing 440 n n C1' H1' UDP sing 441 n n C2' O2' UDP sing 442 n n C2' C3' UDP sing 443 n n C2' H2' UDP sing 444 n n O2' HO2' UDP sing 445 n n C3' C4' UDP sing 446 n n C3' O3' UDP sing 447 n n C3' H3' UDP sing 448 n n C4' O4' UDP sing 449 n n C4' C5' UDP sing 450 n n C4' H4' UDP sing 451 n n O3' HO3' UDP sing 452 n n C5' O5' UDP sing 453 n n C5' "H5'1" UDP sing 454 n n C5' "H5'2" UDP sing 455 n n O5' PA UDP sing 456 n n PA O1A UDP doub 457 n n PA O2A UDP sing 458 n n PA O3A UDP sing 459 n n O2A HOA2 UDP sing 460 n n O3A PB UDP sing 461 n n PB O1B UDP doub 462 n n PB O2B UDP sing 463 n n PB O3B UDP sing 464 n n O2B HOB2 UDP sing 465 n n O3B HOB3 UDP sing 466 n n # _atom_sites.entry_id 2RJ8 _atom_sites.fract_transf_matrix[1][1] 0.019066 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006684 _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] 0.0127 _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 MN A 1 356 169 MN MN . C 3 BHE A 1 452 452 BHE BHE . D 4 UDP A 1 1 1 UDP UDP . E 5 HOH A 1 453 1 HOH HOH . E 5 HOH A 2 454 2 HOH HOH . E 5 HOH A 3 455 3 HOH HOH . E 5 HOH A 4 456 4 HOH HOH . E 5 HOH A 5 457 5 HOH HOH . E 5 HOH A 6 458 6 HOH HOH . E 5 HOH A 7 459 7 HOH HOH . E 5 HOH A 8 460 8 HOH HOH . E 5 HOH A 9 461 9 HOH HOH . E 5 HOH A 10 462 10 HOH HOH . E 5 HOH A 11 463 11 HOH HOH . E 5 HOH A 12 464 12 HOH HOH . E 5 HOH A 13 465 13 HOH HOH . E 5 HOH A 14 466 14 HOH HOH . E 5 HOH A 15 467 15 HOH HOH . E 5 HOH A 16 468 16 HOH HOH . E 5 HOH A 17 469 17 HOH HOH . E 5 HOH A 18 470 18 HOH HOH . E 5 HOH A 19 471 19 HOH HOH . E 5 HOH A 20 472 20 HOH HOH . E 5 HOH A 21 473 21 HOH HOH . E 5 HOH A 22 474 22 HOH HOH . E 5 HOH A 23 475 23 HOH HOH . E 5 HOH A 24 476 24 HOH HOH . E 5 HOH A 25 477 25 HOH HOH . E 5 HOH A 26 478 26 HOH HOH . E 5 HOH A 27 479 27 HOH HOH . E 5 HOH A 28 480 28 HOH HOH . E 5 HOH A 29 481 29 HOH HOH . E 5 HOH A 30 482 30 HOH HOH . E 5 HOH A 31 483 31 HOH HOH . E 5 HOH A 32 484 32 HOH HOH . E 5 HOH A 33 485 33 HOH HOH . E 5 HOH A 34 486 34 HOH HOH . E 5 HOH A 35 487 35 HOH HOH . E 5 HOH A 36 488 36 HOH HOH . E 5 HOH A 37 489 37 HOH HOH . E 5 HOH A 38 490 38 HOH HOH . E 5 HOH A 39 491 39 HOH HOH . E 5 HOH A 40 492 40 HOH HOH . E 5 HOH A 41 493 41 HOH HOH . E 5 HOH A 42 494 42 HOH HOH . E 5 HOH A 43 495 43 HOH HOH . E 5 HOH A 44 496 44 HOH HOH . E 5 HOH A 45 497 45 HOH HOH . E 5 HOH A 46 498 46 HOH HOH . E 5 HOH A 47 499 47 HOH HOH . E 5 HOH A 48 500 48 HOH HOH . E 5 HOH A 49 501 49 HOH HOH . E 5 HOH A 50 502 50 HOH HOH . E 5 HOH A 51 503 51 HOH HOH . E 5 HOH A 52 504 52 HOH HOH . E 5 HOH A 53 505 53 HOH HOH . E 5 HOH A 54 506 54 HOH HOH . E 5 HOH A 55 507 55 HOH HOH . E 5 HOH A 56 508 56 HOH HOH . E 5 HOH A 57 509 57 HOH HOH . E 5 HOH A 58 510 58 HOH HOH . E 5 HOH A 59 511 59 HOH HOH . E 5 HOH A 60 512 60 HOH HOH . E 5 HOH A 61 513 61 HOH HOH . E 5 HOH A 62 514 62 HOH HOH . E 5 HOH A 63 515 63 HOH HOH . E 5 HOH A 64 516 64 HOH HOH . E 5 HOH A 65 517 65 HOH HOH . E 5 HOH A 66 518 66 HOH HOH . E 5 HOH A 67 519 67 HOH HOH . E 5 HOH A 68 520 68 HOH HOH . E 5 HOH A 69 521 69 HOH HOH . E 5 HOH A 70 522 70 HOH HOH . E 5 HOH A 71 523 71 HOH HOH . E 5 HOH A 72 524 72 HOH HOH . E 5 HOH A 73 525 73 HOH HOH . E 5 HOH A 74 526 74 HOH HOH . E 5 HOH A 75 527 75 HOH HOH . E 5 HOH A 76 528 76 HOH HOH . E 5 HOH A 77 529 77 HOH HOH . E 5 HOH A 78 530 78 HOH HOH . E 5 HOH A 79 531 79 HOH HOH . E 5 HOH A 80 532 80 HOH HOH . E 5 HOH A 81 533 81 HOH HOH . E 5 HOH A 82 534 82 HOH HOH . E 5 HOH A 83 535 83 HOH HOH . E 5 HOH A 84 536 84 HOH HOH . E 5 HOH A 85 537 85 HOH HOH . E 5 HOH A 86 538 86 HOH HOH . E 5 HOH A 87 539 87 HOH HOH . E 5 HOH A 88 540 88 HOH HOH . E 5 HOH A 89 541 89 HOH HOH . E 5 HOH A 90 542 90 HOH HOH . E 5 HOH A 91 543 91 HOH HOH . E 5 HOH A 92 544 92 HOH HOH . E 5 HOH A 93 545 93 HOH HOH . E 5 HOH A 94 546 94 HOH HOH . E 5 HOH A 95 547 95 HOH HOH . E 5 HOH A 96 548 96 HOH HOH . E 5 HOH A 97 549 97 HOH HOH . E 5 HOH A 98 550 98 HOH HOH . E 5 HOH A 99 551 99 HOH HOH . E 5 HOH A 100 552 100 HOH HOH . E 5 HOH A 101 553 101 HOH HOH . E 5 HOH A 102 554 102 HOH HOH . E 5 HOH A 103 555 103 HOH HOH . E 5 HOH A 104 556 104 HOH HOH . E 5 HOH A 105 557 105 HOH HOH . E 5 HOH A 106 558 106 HOH HOH . E 5 HOH A 107 559 107 HOH HOH . E 5 HOH A 108 560 108 HOH HOH . E 5 HOH A 109 561 109 HOH HOH . E 5 HOH A 110 562 110 HOH HOH . E 5 HOH A 111 563 111 HOH HOH . E 5 HOH A 112 564 113 HOH HOH . E 5 HOH A 113 565 114 HOH HOH . E 5 HOH A 114 566 115 HOH HOH . E 5 HOH A 115 567 116 HOH HOH . E 5 HOH A 116 568 117 HOH HOH . E 5 HOH A 117 569 118 HOH HOH . E 5 HOH A 118 570 119 HOH HOH . E 5 HOH A 119 571 120 HOH HOH . E 5 HOH A 120 572 121 HOH HOH . E 5 HOH A 121 573 122 HOH HOH . E 5 HOH A 122 574 123 HOH HOH . E 5 HOH A 123 575 124 HOH HOH . E 5 HOH A 124 576 125 HOH HOH . E 5 HOH A 125 577 126 HOH HOH . E 5 HOH A 126 578 127 HOH HOH . E 5 HOH A 127 579 128 HOH HOH . E 5 HOH A 128 580 129 HOH HOH . E 5 HOH A 129 581 130 HOH HOH . E 5 HOH A 130 582 131 HOH HOH . E 5 HOH A 131 583 132 HOH HOH . E 5 HOH A 132 584 133 HOH HOH . E 5 HOH A 133 585 134 HOH HOH . E 5 HOH A 134 586 135 HOH HOH . E 5 HOH A 135 587 136 HOH HOH . E 5 HOH A 136 588 137 HOH HOH . E 5 HOH A 137 589 138 HOH HOH . E 5 HOH A 138 590 139 HOH HOH . E 5 HOH A 139 591 140 HOH HOH . E 5 HOH A 140 592 141 HOH HOH . E 5 HOH A 141 593 142 HOH HOH . E 5 HOH A 142 594 143 HOH HOH . E 5 HOH A 143 595 144 HOH HOH . E 5 HOH A 144 596 145 HOH HOH . E 5 HOH A 145 597 146 HOH HOH . E 5 HOH A 146 598 147 HOH HOH . E 5 HOH A 147 599 148 HOH HOH . E 5 HOH A 148 600 149 HOH HOH . E 5 HOH A 149 601 150 HOH HOH . E 5 HOH A 150 602 151 HOH HOH . E 5 HOH A 151 603 152 HOH HOH . E 5 HOH A 152 604 153 HOH HOH . E 5 HOH A 153 605 154 HOH HOH . E 5 HOH A 154 606 155 HOH HOH . E 5 HOH A 155 607 156 HOH HOH . E 5 HOH A 156 608 157 HOH HOH . E 5 HOH A 157 609 158 HOH HOH . E 5 HOH A 158 610 159 HOH HOH . E 5 HOH A 159 611 161 HOH HOH . E 5 HOH A 160 612 162 HOH HOH . E 5 HOH A 161 613 163 HOH HOH . E 5 HOH A 162 614 164 HOH HOH . E 5 HOH A 163 615 165 HOH HOH . E 5 HOH A 164 616 166 HOH HOH . E 5 HOH A 165 617 168 HOH HOH . E 5 HOH A 166 618 170 HOH HOH . E 5 HOH A 167 619 171 HOH HOH . E 5 HOH A 168 620 172 HOH HOH . E 5 HOH A 169 621 173 HOH HOH . E 5 HOH A 170 622 174 HOH HOH . E 5 HOH A 171 623 175 HOH HOH . E 5 HOH A 172 624 176 HOH HOH . E 5 HOH A 173 625 177 HOH HOH . E 5 HOH A 174 626 178 HOH HOH . E 5 HOH A 175 627 179 HOH HOH . E 5 HOH A 176 628 180 HOH HOH . E 5 HOH A 177 629 181 HOH HOH . E 5 HOH A 178 630 182 HOH HOH . E 5 HOH A 179 631 183 HOH HOH . E 5 HOH A 180 632 184 HOH HOH . E 5 HOH A 181 633 185 HOH HOH . E 5 HOH A 182 634 186 HOH HOH . E 5 HOH A 183 635 187 HOH HOH . E 5 HOH A 184 636 188 HOH HOH . E 5 HOH A 185 637 189 HOH HOH . E 5 HOH A 186 638 190 HOH HOH . E 5 HOH A 187 639 191 HOH HOH . E 5 HOH A 188 640 192 HOH HOH . E 5 HOH A 189 641 193 HOH HOH . E 5 HOH A 190 642 194 HOH HOH . E 5 HOH A 191 643 195 HOH HOH . E 5 HOH A 192 644 196 HOH HOH . E 5 HOH A 193 645 197 HOH HOH . E 5 HOH A 194 646 198 HOH HOH . E 5 HOH A 195 647 199 HOH HOH . E 5 HOH A 196 648 200 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 . . . D 4 -16.458 -23.205 7.873 1 21.04 ? N1 UDP 1 A 1 HETATM 2 C C2 UDP . . . D 4 -17.644 -23.931 8.133 1 21.78 ? C2 UDP 1 A 1 HETATM 3 N N3 UDP . . . D 4 -18.213 -23.875 9.415 1 22.4 ? N3 UDP 1 A 1 HETATM 4 C C4 UDP . . . D 4 -17.607 -23.113 10.439 1 24.48 ? C4 UDP 1 A 1 HETATM 5 C C5 UDP . . . D 4 -16.436 -22.385 10.176 1 23.04 ? C5 UDP 1 A 1 HETATM 6 C C6 UDP . . . D 4 -15.858 -22.429 8.901 1 23.6 ? C6 UDP 1 A 1 HETATM 7 O O2 UDP . . . D 4 -18.175 -24.601 7.24 1 20.57 ? O2 UDP 1 A 1 HETATM 8 O O4 UDP . . . D 4 -18.13 -23.095 11.558 1 22.55 ? O4 UDP 1 A 1 HETATM 9 C C1' UDP . . . D 4 -15.9 -23.291 6.501 1 20.16 ? C1' UDP 1 A 1 HETATM 10 C C2' UDP . . . D 4 -16.801 -22.507 5.527 1 19.3 ? C2' UDP 1 A 1 HETATM 11 O O2' UDP . . . D 4 -16.675 -23.077 4.213 1 18.12 ? O2' UDP 1 A 1 HETATM 12 C C3' UDP . . . D 4 -16.102 -21.164 5.552 1 16.61 ? C3' UDP 1 A 1 HETATM 13 C C4' UDP . . . D 4 -14.627 -21.605 5.535 1 17.32 ? C4' UDP 1 A 1 HETATM 14 O O4' UDP . . . D 4 -14.562 -22.739 6.443 1 18.51 ? O4' UDP 1 A 1 HETATM 15 O O3' UDP . . . D 4 -16.38 -20.46 4.336 1 16.66 ? O3' UDP 1 A 1 HETATM 16 C C5' UDP . . . D 4 -13.675 -20.526 6.006 1 16.99 ? C5' UDP 1 A 1 HETATM 17 O O5' UDP . . . D 4 -14.116 -19.966 7.254 1 18.29 ? O5' UDP 1 A 1 HETATM 18 P PA UDP . . . D 4 -14.702 -18.431 7.315 1 20.26 ? PA UDP 1 A 1 HETATM 19 O O1A UDP . . . D 4 -15.429 -18.163 6.042 1 17.86 ? O1A UDP 1 A 1 HETATM 20 O O2A UDP . . . D 4 -15.426 -18.234 8.592 1 19.86 ? O2A UDP 1 A 1 HETATM 21 O O3A UDP . . . D 4 -13.312 -17.628 7.359 1 18.95 ? O3A UDP 1 A 1 HETATM 22 P PB UDP . . . D 4 -13.148 -16.095 6.82 1 19.83 ? PB UDP 1 A 1 HETATM 23 O O1B UDP . . . D 4 -14.074 -15.213 7.763 1 21.46 ? O1B UDP 1 A 1 HETATM 24 O O2B UDP . . . D 4 -11.622 -15.784 7.133 1 20.4 ? O2B UDP 1 A 1 HETATM 25 O O3B UDP . . . D 4 -13.492 -15.907 5.375 1 21.79 ? O3B UDP 1 A 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #