data_4GBP # _model_server_result.job_id gDIVb8TqOe8URNCB7JrFPw _model_server_result.datetime_utc '2024-11-07 09:53:59' _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 4gbp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 4GBP # _exptl.entry_id 4GBP _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 4GBP _cell.length_a 52.189 _cell.length_b 150.769 _cell.length_c 79.397 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GBP _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 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_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 52.189 0 39.6985 # _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 A OD2 ASP 149 A ASP 211 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc2 A OD1 ASP 151 A ASP 213 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc3 A OD2 ASP 151 A ASP 213 1_555 C MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc4 C MN MN . A MN 402 1_555 D O1A UDP . A UDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc5 C MN MN . A MN 402 1_555 D O3B UDP . A UDP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? # _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 382 n n N1 C6 UDP sing 383 n n N1 C1' UDP sing 384 n n C2 N3 UDP sing 385 n n C2 O2 UDP doub 386 n n N3 C4 UDP sing 387 n n N3 HN3 UDP sing 388 n n C4 C5 UDP sing 389 n n C4 O4 UDP doub 390 n n C5 C6 UDP doub 391 n n C5 H5 UDP sing 392 n n C6 H6 UDP sing 393 n n C1' C2' UDP sing 394 n n C1' O4' UDP sing 395 n n C1' H1' UDP sing 396 n n C2' O2' UDP sing 397 n n C2' C3' UDP sing 398 n n C2' H2' UDP sing 399 n n O2' HO2' UDP sing 400 n n C3' C4' UDP sing 401 n n C3' O3' UDP sing 402 n n C3' H3' UDP sing 403 n n C4' O4' UDP sing 404 n n C4' C5' UDP sing 405 n n C4' H4' UDP sing 406 n n O3' HO3' UDP sing 407 n n C5' O5' UDP sing 408 n n C5' "H5'1" UDP sing 409 n n C5' "H5'2" UDP sing 410 n n O5' PA UDP sing 411 n n PA O1A UDP doub 412 n n PA O2A UDP sing 413 n n PA O3A UDP sing 414 n n O2A HOA2 UDP sing 415 n n O3A PB UDP sing 416 n n PB O1B UDP doub 417 n n PB O2B UDP sing 418 n n PB O3B UDP sing 419 n n O2B HOB2 UDP sing 420 n n O3B HOB3 UDP sing 421 n n # _atom_sites.entry_id 4GBP _atom_sites.fract_transf_matrix[1][1] 0.019161 _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] 0.006633 _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] 0.012595 _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 GAL A 1 401 2 GAL GAL . C 3 MN A 1 402 1 MN MN . D 4 UDP A 1 403 1 UDP UDP . E 2 GAL A 1 404 2 GAL GAL . F 5 HOH A 1 501 1 HOH HOH . F 5 HOH A 2 502 2 HOH HOH . F 5 HOH A 3 503 3 HOH HOH . F 5 HOH A 4 504 4 HOH HOH . F 5 HOH A 5 505 5 HOH HOH . F 5 HOH A 6 506 6 HOH HOH . F 5 HOH A 7 507 7 HOH HOH . F 5 HOH A 8 508 8 HOH HOH . F 5 HOH A 9 509 9 HOH HOH . F 5 HOH A 10 510 10 HOH HOH . F 5 HOH A 11 511 11 HOH HOH . F 5 HOH A 12 512 12 HOH HOH . F 5 HOH A 13 513 13 HOH HOH . F 5 HOH A 14 514 14 HOH HOH . F 5 HOH A 15 515 15 HOH HOH . F 5 HOH A 16 516 16 HOH HOH . F 5 HOH A 17 517 17 HOH HOH . F 5 HOH A 18 518 18 HOH HOH . F 5 HOH A 19 519 19 HOH HOH . F 5 HOH A 20 520 20 HOH HOH . F 5 HOH A 21 521 21 HOH HOH . F 5 HOH A 22 522 22 HOH HOH . F 5 HOH A 23 523 23 HOH HOH . F 5 HOH A 24 524 24 HOH HOH . F 5 HOH A 25 525 25 HOH HOH . F 5 HOH A 26 526 26 HOH HOH . F 5 HOH A 27 527 27 HOH HOH . F 5 HOH A 28 528 28 HOH HOH . F 5 HOH A 29 529 29 HOH HOH . F 5 HOH A 30 530 30 HOH HOH . F 5 HOH A 31 531 31 HOH HOH . F 5 HOH A 32 532 32 HOH HOH . F 5 HOH A 33 533 33 HOH HOH . F 5 HOH A 34 534 34 HOH HOH . F 5 HOH A 35 535 35 HOH HOH . F 5 HOH A 36 536 36 HOH HOH . F 5 HOH A 37 537 37 HOH HOH . F 5 HOH A 38 538 38 HOH HOH . F 5 HOH A 39 539 39 HOH HOH . F 5 HOH A 40 540 40 HOH HOH . F 5 HOH A 41 541 41 HOH HOH . F 5 HOH A 42 542 42 HOH HOH . F 5 HOH A 43 543 43 HOH HOH . F 5 HOH A 44 544 44 HOH HOH . F 5 HOH A 45 545 45 HOH HOH . F 5 HOH A 46 546 46 HOH HOH . F 5 HOH A 47 547 47 HOH HOH . F 5 HOH A 48 548 48 HOH HOH . F 5 HOH A 49 549 49 HOH HOH . F 5 HOH A 50 550 50 HOH HOH . F 5 HOH A 51 551 51 HOH HOH . F 5 HOH A 52 552 52 HOH HOH . F 5 HOH A 53 553 53 HOH HOH . F 5 HOH A 54 554 54 HOH HOH . F 5 HOH A 55 555 55 HOH HOH . F 5 HOH A 56 556 56 HOH HOH . F 5 HOH A 57 557 57 HOH HOH . F 5 HOH A 58 558 58 HOH HOH . F 5 HOH A 59 559 59 HOH HOH . F 5 HOH A 60 560 60 HOH HOH . F 5 HOH A 61 561 61 HOH HOH . F 5 HOH A 62 562 62 HOH HOH . F 5 HOH A 63 563 63 HOH HOH . F 5 HOH A 64 564 64 HOH HOH . F 5 HOH A 65 565 65 HOH HOH . F 5 HOH A 66 566 66 HOH HOH . F 5 HOH A 67 567 67 HOH HOH . F 5 HOH A 68 568 68 HOH HOH . F 5 HOH A 69 569 69 HOH HOH . F 5 HOH A 70 570 70 HOH HOH . F 5 HOH A 71 571 71 HOH HOH . F 5 HOH A 72 572 72 HOH HOH . F 5 HOH A 73 573 73 HOH HOH . F 5 HOH A 74 574 74 HOH HOH . F 5 HOH A 75 575 75 HOH HOH . F 5 HOH A 76 576 76 HOH HOH . F 5 HOH A 77 577 77 HOH HOH . F 5 HOH A 78 578 78 HOH HOH . F 5 HOH A 79 579 79 HOH HOH . F 5 HOH A 80 580 80 HOH HOH . F 5 HOH A 81 581 81 HOH HOH . F 5 HOH A 82 582 82 HOH HOH . F 5 HOH A 83 583 83 HOH HOH . F 5 HOH A 84 584 84 HOH HOH . F 5 HOH A 85 585 85 HOH HOH . F 5 HOH A 86 586 86 HOH HOH . F 5 HOH A 87 587 87 HOH HOH . F 5 HOH A 88 588 88 HOH HOH . F 5 HOH A 89 589 89 HOH HOH . F 5 HOH A 90 590 90 HOH HOH . F 5 HOH A 91 591 91 HOH HOH . F 5 HOH A 92 592 94 HOH HOH . F 5 HOH A 93 593 95 HOH HOH . F 5 HOH A 94 594 97 HOH HOH . F 5 HOH A 95 595 99 HOH HOH . F 5 HOH A 96 596 100 HOH HOH . F 5 HOH A 97 597 101 HOH HOH . F 5 HOH A 98 598 102 HOH HOH . F 5 HOH A 99 599 103 HOH HOH . F 5 HOH A 100 600 104 HOH HOH . F 5 HOH A 101 601 105 HOH HOH . F 5 HOH A 102 602 107 HOH HOH . F 5 HOH A 103 603 108 HOH HOH . F 5 HOH A 104 604 110 HOH HOH . F 5 HOH A 105 605 111 HOH HOH . F 5 HOH A 106 606 112 HOH HOH . F 5 HOH A 107 607 114 HOH HOH . F 5 HOH A 108 608 115 HOH HOH . F 5 HOH A 109 609 116 HOH HOH . F 5 HOH A 110 610 117 HOH HOH . F 5 HOH A 111 611 118 HOH HOH . F 5 HOH A 112 612 119 HOH HOH . F 5 HOH A 113 613 120 HOH HOH . F 5 HOH A 114 614 121 HOH HOH . F 5 HOH A 115 615 122 HOH HOH . F 5 HOH A 116 616 124 HOH HOH . F 5 HOH A 117 617 125 HOH HOH . F 5 HOH A 118 618 126 HOH HOH . F 5 HOH A 119 619 128 HOH HOH . F 5 HOH A 120 620 129 HOH HOH . F 5 HOH A 121 621 131 HOH HOH . F 5 HOH A 122 622 133 HOH HOH . F 5 HOH A 123 623 134 HOH HOH . F 5 HOH A 124 624 135 HOH HOH . F 5 HOH A 125 625 136 HOH HOH . F 5 HOH A 126 626 137 HOH HOH . F 5 HOH A 127 627 138 HOH HOH . F 5 HOH A 128 628 140 HOH HOH . F 5 HOH A 129 629 141 HOH HOH . F 5 HOH A 130 630 142 HOH HOH . F 5 HOH A 131 631 143 HOH HOH . F 5 HOH A 132 632 144 HOH HOH . F 5 HOH A 133 633 145 HOH HOH . F 5 HOH A 134 634 147 HOH HOH . F 5 HOH A 135 635 148 HOH HOH . F 5 HOH A 136 636 149 HOH HOH . F 5 HOH A 137 637 150 HOH HOH . F 5 HOH A 138 638 151 HOH HOH . F 5 HOH A 139 639 152 HOH HOH . F 5 HOH A 140 640 153 HOH HOH . F 5 HOH A 141 641 154 HOH HOH . F 5 HOH A 142 642 155 HOH HOH . F 5 HOH A 143 643 156 HOH HOH . F 5 HOH A 144 644 157 HOH HOH . F 5 HOH A 145 645 158 HOH HOH . F 5 HOH A 146 646 159 HOH HOH . F 5 HOH A 147 647 160 HOH HOH . F 5 HOH A 148 648 161 HOH HOH . F 5 HOH A 149 649 162 HOH HOH . F 5 HOH A 150 650 163 HOH HOH . F 5 HOH A 151 651 164 HOH HOH . F 5 HOH A 152 652 165 HOH HOH . F 5 HOH A 153 653 166 HOH HOH . F 5 HOH A 154 654 167 HOH HOH . F 5 HOH A 155 655 168 HOH HOH . F 5 HOH A 156 656 169 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 10.117 23.695 -7.741 1 28.45 ? N1 UDP 403 A 1 HETATM 2 C C2 UDP . . . D 4 8.901 24.384 -7.976 1 29 ? C2 UDP 403 A 1 HETATM 3 N N3 UDP . . . D 4 8.424 24.374 -9.28 1 29.7 ? N3 UDP 403 A 1 HETATM 4 C C4 UDP . . . D 4 9.152 23.749 -10.326 1 33.1 ? C4 UDP 403 A 1 HETATM 5 C C5 UDP . . . D 4 10.348 23.06 -10.083 1 32 ? C5 UDP 403 A 1 HETATM 6 C C6 UDP . . . D 4 10.84 23.043 -8.786 1 30.33 ? C6 UDP 403 A 1 HETATM 7 O O2 UDP . . . D 4 8.257 24.951 -7.067 1 23.95 ? O2 UDP 403 A 1 HETATM 8 O O4 UDP . . . D 4 8.681 23.795 -11.466 1 29.77 ? O4 UDP 403 A 1 HETATM 9 C C1' UDP . . . D 4 10.644 23.696 -6.361 1 24.42 ? C1' UDP 403 A 1 HETATM 10 C C2' UDP . . . D 4 9.754 22.834 -5.472 1 20.81 ? C2' UDP 403 A 1 HETATM 11 O O2' UDP . . . D 4 9.85 23.438 -4.197 1 19.11 ? O2' UDP 403 A 1 HETATM 12 C C3' UDP . . . D 4 10.476 21.519 -5.516 1 20.03 ? C3' UDP 403 A 1 HETATM 13 C C4' UDP . . . D 4 11.93 21.965 -5.499 1 21.71 ? C4' UDP 403 A 1 HETATM 14 O O4' UDP . . . D 4 12.007 23.21 -6.289 1 24.26 ? O4' UDP 403 A 1 HETATM 15 O O3' UDP . . . D 4 10.147 20.78 -4.335 1 18 ? O3' UDP 403 A 1 HETATM 16 C C5' UDP . . . D 4 12.951 20.995 -6.154 1 24.29 ? C5' UDP 403 A 1 HETATM 17 O O5' UDP . . . D 4 12.556 20.423 -7.394 0.8 22.88 ? O5' UDP 403 A 1 HETATM 18 P PA UDP . . . D 4 12.041 18.95 -7.312 0.8 24.23 ? PA UDP 403 A 1 HETATM 19 O O1A UDP . . . D 4 11.361 18.639 -6.024 0.8 22.74 ? O1A UDP 403 A 1 HETATM 20 O O2A UDP . . . D 4 11.369 18.848 -8.616 0.8 22.82 ? O2A UDP 403 A 1 HETATM 21 O O3A UDP . . . D 4 13.401 18.075 -7.455 0.8 22.9 ? O3A UDP 403 A 1 HETATM 22 P PB UDP . . . D 4 13.431 16.597 -6.946 0.8 22.69 ? PB UDP 403 A 1 HETATM 23 O O1B UDP . . . D 4 12.329 15.787 -7.584 0.8 22.48 ? O1B UDP 403 A 1 HETATM 24 O O2B UDP . . . D 4 14.8 16.073 -7.422 0.8 20.78 ? O2B UDP 403 A 1 HETATM 25 O O3B UDP . . . D 4 13.294 16.577 -5.435 0.8 22.95 ? O3B UDP 403 A 1 HETATM 26 H HN3 UDP . . . D 4 7.577 24.851 -9.496 1 29.94 ? HN3 UDP 403 A 1 HETATM 27 H H5 UDP . . . D 4 10.978 23.109 -10.858 1 32.08 ? H5 UDP 403 A 1 HETATM 28 H H6 UDP . . . D 4 11.791 23.294 -8.967 1 29.64 ? H6 UDP 403 A 1 HETATM 29 H H1' UDP . . . D 4 10.635 24.661 -6.096 1 24.32 ? H1' UDP 403 A 1 HETATM 30 H H2' UDP . . . D 4 8.77 22.682 -5.564 1 20.81 ? H2' UDP 403 A 1 HETATM 31 H HO2' UDP . . . D 4 10.462 24.233 -4.282 0 18.77 ? HO2' UDP 403 A 1 HETATM 32 H H3' UDP . . . D 4 10.226 21.22 -6.436 1 21.09 ? H3' UDP 403 A 1 HETATM 33 H H4' UDP . . . D 4 12.184 22.12 -4.544 1 22.28 ? H4' UDP 403 A 1 HETATM 34 H HO3' UDP . . . D 4 9.528 21.347 -3.78 0 18.3 ? HO3' UDP 403 A 1 HETATM 35 H "H5'1" UDP . . . D 4 13.808 21.497 -6.276 1 23.84 ? "H5'1" UDP 403 A 1 HETATM 36 H "H5'2" UDP . . . D 4 13.63 20.411 -5.711 1 23.77 ? "H5'2" UDP 403 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #