data_2RJ1 # _model_server_result.job_id PX32suD5vqfLSlMXONmMDw _model_server_result.datetime_utc '2024-11-26 04:27:51' _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 2rj1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":453}' # _entry.id 2RJ1 # _exptl.entry_id 2RJ1 _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 2RJ1 _cell.length_a 52.45 _cell.length_b 149.12 _cell.length_c 79.64 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RJ1 _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,F 1 1 A,B,C,D,E,F 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 -39.82 # _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 B MN MN . A MN 1 1_555 A OD2 ASP 150 A ASP 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc2 B MN MN . A MN 1 1_555 A OD1 ASP 152 A ASP 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc3 B MN MN . A MN 1 1_555 A OD2 ASP 152 A ASP 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc4 B MN MN . A MN 1 1_555 D O3B UDP . A UDP 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc5 B MN MN . A MN 1 1_555 D O1A UDP . A UDP 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc6 B MN MN . A MN 1 1_555 F O HOH . A HOH 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? # _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 440 n n N1 C6 UDP sing 441 n n N1 C1' UDP sing 442 n n C2 N3 UDP sing 443 n n C2 O2 UDP doub 444 n n N3 C4 UDP sing 445 n n N3 HN3 UDP sing 446 n n C4 C5 UDP sing 447 n n C4 O4 UDP doub 448 n n C5 C6 UDP doub 449 n n C5 H5 UDP sing 450 n n C6 H6 UDP sing 451 n n C1' C2' UDP sing 452 n n C1' O4' UDP sing 453 n n C1' H1' UDP sing 454 n n C2' O2' UDP sing 455 n n C2' C3' UDP sing 456 n n C2' H2' UDP sing 457 n n O2' HO2' UDP sing 458 n n C3' C4' UDP sing 459 n n C3' O3' UDP sing 460 n n C3' H3' UDP sing 461 n n C4' O4' UDP sing 462 n n C4' C5' UDP sing 463 n n C4' H4' UDP sing 464 n n O3' HO3' UDP sing 465 n n C5' O5' UDP sing 466 n n C5' "H5'1" UDP sing 467 n n C5' "H5'2" UDP sing 468 n n O5' PA UDP sing 469 n n PA O1A UDP doub 470 n n PA O2A UDP sing 471 n n PA O3A UDP sing 472 n n O2A HOA2 UDP sing 473 n n O3A PB UDP sing 474 n n PB O1B UDP doub 475 n n PB O2B UDP sing 476 n n PB O3B UDP sing 477 n n O2B HOB2 UDP sing 478 n n O3B HOB3 UDP sing 479 n n # _atom_sites.entry_id 2RJ1 _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] 0.006706 _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] 0.012557 _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 1 1 MN MN . C 3 BHE A 1 452 452 BHE BHE . D 4 UDP A 1 453 1 UDP UDP . E 5 GOL A 1 454 355 GOL GOL . F 6 HOH A 1 455 2 HOH HOH . F 6 HOH A 2 456 3 HOH HOH . F 6 HOH A 3 457 4 HOH HOH . F 6 HOH A 4 458 5 HOH HOH . F 6 HOH A 5 459 6 HOH HOH . F 6 HOH A 6 460 7 HOH HOH . F 6 HOH A 7 461 8 HOH HOH . F 6 HOH A 8 462 9 HOH HOH . F 6 HOH A 9 463 10 HOH HOH . F 6 HOH A 10 464 11 HOH HOH . F 6 HOH A 11 465 12 HOH HOH . F 6 HOH A 12 466 13 HOH HOH . F 6 HOH A 13 467 14 HOH HOH . F 6 HOH A 14 468 15 HOH HOH . F 6 HOH A 15 469 16 HOH HOH . F 6 HOH A 16 470 17 HOH HOH . F 6 HOH A 17 471 18 HOH HOH . F 6 HOH A 18 472 19 HOH HOH . F 6 HOH A 19 473 20 HOH HOH . F 6 HOH A 20 474 21 HOH HOH . F 6 HOH A 21 475 22 HOH HOH . F 6 HOH A 22 476 23 HOH HOH . F 6 HOH A 23 477 24 HOH HOH . F 6 HOH A 24 478 25 HOH HOH . F 6 HOH A 25 479 26 HOH HOH . F 6 HOH A 26 480 27 HOH HOH . F 6 HOH A 27 481 28 HOH HOH . F 6 HOH A 28 482 29 HOH HOH . F 6 HOH A 29 483 30 HOH HOH . F 6 HOH A 30 484 31 HOH HOH . F 6 HOH A 31 485 32 HOH HOH . F 6 HOH A 32 486 33 HOH HOH . F 6 HOH A 33 487 34 HOH HOH . F 6 HOH A 34 488 35 HOH HOH . F 6 HOH A 35 489 36 HOH HOH . F 6 HOH A 36 490 37 HOH HOH . F 6 HOH A 37 491 38 HOH HOH . F 6 HOH A 38 492 39 HOH HOH . F 6 HOH A 39 493 40 HOH HOH . F 6 HOH A 40 494 41 HOH HOH . F 6 HOH A 41 495 42 HOH HOH . F 6 HOH A 42 496 43 HOH HOH . F 6 HOH A 43 497 44 HOH HOH . F 6 HOH A 44 498 45 HOH HOH . F 6 HOH A 45 499 46 HOH HOH . F 6 HOH A 46 500 47 HOH HOH . F 6 HOH A 47 501 48 HOH HOH . F 6 HOH A 48 502 49 HOH HOH . F 6 HOH A 49 503 50 HOH HOH . F 6 HOH A 50 504 51 HOH HOH . F 6 HOH A 51 505 52 HOH HOH . F 6 HOH A 52 506 53 HOH HOH . F 6 HOH A 53 507 54 HOH HOH . F 6 HOH A 54 508 55 HOH HOH . F 6 HOH A 55 509 56 HOH HOH . F 6 HOH A 56 510 57 HOH HOH . F 6 HOH A 57 511 58 HOH HOH . F 6 HOH A 58 512 59 HOH HOH . F 6 HOH A 59 513 60 HOH HOH . F 6 HOH A 60 514 61 HOH HOH . F 6 HOH A 61 515 62 HOH HOH . F 6 HOH A 62 516 63 HOH HOH . F 6 HOH A 63 517 64 HOH HOH . F 6 HOH A 64 518 65 HOH HOH . F 6 HOH A 65 519 66 HOH HOH . F 6 HOH A 66 520 67 HOH HOH . F 6 HOH A 67 521 68 HOH HOH . F 6 HOH A 68 522 69 HOH HOH . F 6 HOH A 69 523 70 HOH HOH . F 6 HOH A 70 524 71 HOH HOH . F 6 HOH A 71 525 72 HOH HOH . F 6 HOH A 72 526 73 HOH HOH . F 6 HOH A 73 527 74 HOH HOH . F 6 HOH A 74 528 75 HOH HOH . F 6 HOH A 75 529 76 HOH HOH . F 6 HOH A 76 530 77 HOH HOH . F 6 HOH A 77 531 78 HOH HOH . F 6 HOH A 78 532 79 HOH HOH . F 6 HOH A 79 533 80 HOH HOH . F 6 HOH A 80 534 81 HOH HOH . F 6 HOH A 81 535 82 HOH HOH . F 6 HOH A 82 536 83 HOH HOH . F 6 HOH A 83 537 84 HOH HOH . F 6 HOH A 84 538 85 HOH HOH . F 6 HOH A 85 539 86 HOH HOH . F 6 HOH A 86 540 87 HOH HOH . F 6 HOH A 87 541 89 HOH HOH . F 6 HOH A 88 542 90 HOH HOH . F 6 HOH A 89 543 91 HOH HOH . F 6 HOH A 90 544 92 HOH HOH . F 6 HOH A 91 545 93 HOH HOH . F 6 HOH A 92 546 94 HOH HOH . F 6 HOH A 93 547 95 HOH HOH . F 6 HOH A 94 548 96 HOH HOH . F 6 HOH A 95 549 97 HOH HOH . F 6 HOH A 96 550 98 HOH HOH . F 6 HOH A 97 551 99 HOH HOH . F 6 HOH A 98 552 100 HOH HOH . F 6 HOH A 99 553 101 HOH HOH . F 6 HOH A 100 554 102 HOH HOH . F 6 HOH A 101 555 103 HOH HOH . F 6 HOH A 102 556 104 HOH HOH . F 6 HOH A 103 557 105 HOH HOH . F 6 HOH A 104 558 106 HOH HOH . F 6 HOH A 105 559 107 HOH HOH . F 6 HOH A 106 560 108 HOH HOH . F 6 HOH A 107 561 109 HOH HOH . F 6 HOH A 108 562 110 HOH HOH . F 6 HOH A 109 563 111 HOH HOH . F 6 HOH A 110 564 112 HOH HOH . F 6 HOH A 111 565 113 HOH HOH . F 6 HOH A 112 566 114 HOH HOH . F 6 HOH A 113 567 115 HOH HOH . F 6 HOH A 114 568 116 HOH HOH . F 6 HOH A 115 569 117 HOH HOH . F 6 HOH A 116 570 118 HOH HOH . F 6 HOH A 117 571 119 HOH HOH . F 6 HOH A 118 572 120 HOH HOH . F 6 HOH A 119 573 121 HOH HOH . F 6 HOH A 120 574 122 HOH HOH . F 6 HOH A 121 575 123 HOH HOH . F 6 HOH A 122 576 124 HOH HOH . F 6 HOH A 123 577 125 HOH HOH . F 6 HOH A 124 578 126 HOH HOH . F 6 HOH A 125 579 127 HOH HOH . F 6 HOH A 126 580 128 HOH HOH . F 6 HOH A 127 581 129 HOH HOH . F 6 HOH A 128 582 130 HOH HOH . F 6 HOH A 129 583 131 HOH HOH . F 6 HOH A 130 584 132 HOH HOH . F 6 HOH A 131 585 133 HOH HOH . F 6 HOH A 132 586 134 HOH HOH . F 6 HOH A 133 587 135 HOH HOH . F 6 HOH A 134 588 136 HOH HOH . F 6 HOH A 135 589 137 HOH HOH . F 6 HOH A 136 590 138 HOH HOH . F 6 HOH A 137 591 139 HOH HOH . F 6 HOH A 138 592 141 HOH HOH . F 6 HOH A 139 593 142 HOH HOH . F 6 HOH A 140 594 143 HOH HOH . F 6 HOH A 141 595 145 HOH HOH . F 6 HOH A 142 596 146 HOH HOH . F 6 HOH A 143 597 147 HOH HOH . F 6 HOH A 144 598 148 HOH HOH . F 6 HOH A 145 599 149 HOH HOH . F 6 HOH A 146 600 150 HOH HOH . F 6 HOH A 147 601 151 HOH HOH . F 6 HOH A 148 602 152 HOH HOH . F 6 HOH A 149 603 153 HOH HOH . F 6 HOH A 150 604 154 HOH HOH . F 6 HOH A 151 605 155 HOH HOH . F 6 HOH A 152 606 156 HOH HOH . F 6 HOH A 153 607 157 HOH HOH . F 6 HOH A 154 608 158 HOH HOH . F 6 HOH A 155 609 159 HOH HOH . F 6 HOH A 156 610 160 HOH HOH . F 6 HOH A 157 611 161 HOH HOH . F 6 HOH A 158 612 162 HOH HOH . F 6 HOH A 159 613 163 HOH HOH . F 6 HOH A 160 614 164 HOH HOH . F 6 HOH A 161 615 165 HOH HOH . F 6 HOH A 162 616 166 HOH HOH . F 6 HOH A 163 617 167 HOH HOH . F 6 HOH A 164 618 168 HOH HOH . F 6 HOH A 165 619 169 HOH HOH . F 6 HOH A 166 620 170 HOH HOH . F 6 HOH A 167 621 171 HOH HOH . F 6 HOH A 168 622 172 HOH HOH . F 6 HOH A 169 623 173 HOH HOH . F 6 HOH A 170 624 174 HOH HOH . F 6 HOH A 171 625 175 HOH HOH . F 6 HOH A 172 626 176 HOH HOH . F 6 HOH A 173 627 177 HOH HOH . F 6 HOH A 174 628 178 HOH HOH . F 6 HOH A 175 629 179 HOH HOH . F 6 HOH A 176 630 180 HOH HOH . F 6 HOH A 177 631 181 HOH HOH . F 6 HOH A 178 632 182 HOH HOH . F 6 HOH A 179 633 183 HOH HOH . F 6 HOH A 180 634 184 HOH HOH . F 6 HOH A 181 635 185 HOH HOH . F 6 HOH A 182 636 186 HOH HOH . F 6 HOH A 183 637 187 HOH HOH . F 6 HOH A 184 638 188 HOH HOH . F 6 HOH A 185 639 189 HOH HOH . F 6 HOH A 186 640 190 HOH HOH . F 6 HOH A 187 641 191 HOH HOH . F 6 HOH A 188 642 192 HOH HOH . F 6 HOH A 189 643 193 HOH HOH . F 6 HOH A 190 644 194 HOH HOH . F 6 HOH A 191 645 195 HOH HOH . F 6 HOH A 192 646 196 HOH HOH . F 6 HOH A 193 647 197 HOH HOH . F 6 HOH A 194 648 198 HOH HOH . F 6 HOH A 195 649 199 HOH HOH . F 6 HOH A 196 650 200 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 16.44 23.236 7.619 1 14.24 ? N1 UDP 453 A 1 HETATM 2 C C2 UDP . . . D 4 17.627 23.939 7.886 1 15.62 ? C2 UDP 453 A 1 HETATM 3 N N3 UDP . . . D 4 18.153 23.903 9.181 1 16.29 ? N3 UDP 453 A 1 HETATM 4 C C4 UDP . . . D 4 17.532 23.191 10.194 1 17.67 ? C4 UDP 453 A 1 HETATM 5 C C5 UDP . . . D 4 16.342 22.489 9.925 1 15.81 ? C5 UDP 453 A 1 HETATM 6 C C6 UDP . . . D 4 15.794 22.521 8.638 1 15.97 ? C6 UDP 453 A 1 HETATM 7 O O2 UDP . . . D 4 18.184 24.569 6.988 1 15.57 ? O2 UDP 453 A 1 HETATM 8 O O4 UDP . . . D 4 18.054 23.205 11.313 1 16.86 ? O4 UDP 453 A 1 HETATM 9 C C1' UDP . . . D 4 15.908 23.325 6.243 1 14.68 ? C1' UDP 453 A 1 HETATM 10 C C2' UDP . . . D 4 16.79 22.555 5.259 1 13.56 ? C2' UDP 453 A 1 HETATM 11 O O2' UDP . . . D 4 16.665 23.143 3.958 1 12.78 ? O2' UDP 453 A 1 HETATM 12 C C3' UDP . . . D 4 16.094 21.209 5.253 1 12.06 ? C3' UDP 453 A 1 HETATM 13 C C4' UDP . . . D 4 14.599 21.608 5.301 1 12.65 ? C4' UDP 453 A 1 HETATM 14 O O4' UDP . . . D 4 14.575 22.746 6.2 1 13.93 ? O4' UDP 453 A 1 HETATM 15 O O3' UDP . . . D 4 16.391 20.45 4.067 1 11.94 ? O3' UDP 453 A 1 HETATM 16 C C5' UDP . . . D 4 13.655 20.502 5.811 1 12.72 ? C5' UDP 453 A 1 HETATM 17 O O5' UDP . . . D 4 14.142 19.969 7.019 1 13.02 ? O5' UDP 453 A 1 HETATM 18 P PA UDP . . . D 4 14.668 18.461 7.025 1 14.85 ? PA UDP 453 A 1 HETATM 19 O O1A UDP . . . D 4 15.449 18.23 5.79 1 13.74 ? O1A UDP 453 A 1 HETATM 20 O O2A UDP . . . D 4 15.301 18.233 8.342 1 14.86 ? O2A UDP 453 A 1 HETATM 21 O O3A UDP . . . D 4 13.276 17.631 6.993 1 14.27 ? O3A UDP 453 A 1 HETATM 22 P PB UDP . . . D 4 13.082 16.087 6.587 1 15.86 ? PB UDP 453 A 1 HETATM 23 O O1B UDP . . . D 4 14.02 15.191 7.545 1 16.47 ? O1B UDP 453 A 1 HETATM 24 O O2B UDP . . . D 4 11.621 15.817 6.808 1 15.42 ? O2B UDP 453 A 1 HETATM 25 O O3B UDP . . . D 4 13.435 15.899 5.054 1 13.95 ? O3B UDP 453 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #