data_5UZH # _model_server_result.job_id ZqbIyF5RKJ8ADJIcYz8Yfw _model_server_result.datetime_utc '2024-11-02 17:23:00' _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 5uzh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5UZH # _exptl.entry_id 5UZH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 5UZH _cell.length_a 92.73 _cell.length_b 92.73 _cell.length_c 94.66 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5UZH _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _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,E,F,G,H _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 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 5UZH _atom_sites.fract_transf_matrix[1][1] 0.010784 _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] 0.010784 _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] 0.010564 _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 GDP A 1 401 401 GDP GDP . C 3 NAP A 1 402 411 NAP NAP . D 4 MPD A 1 403 501 MPD MPD . E 4 MPD A 1 404 502 MPD MPD . F 4 MPD A 1 405 503 MPD MPD . G 5 CL A 1 406 601 CL CL . H 6 HOH A 1 501 59 HOH HOH . H 6 HOH A 2 502 31 HOH HOH . H 6 HOH A 3 503 80 HOH HOH . H 6 HOH A 4 504 85 HOH HOH . H 6 HOH A 5 505 60 HOH HOH . H 6 HOH A 6 506 149 HOH HOH . H 6 HOH A 7 507 58 HOH HOH . H 6 HOH A 8 508 14 HOH HOH . H 6 HOH A 9 509 92 HOH HOH . H 6 HOH A 10 510 129 HOH HOH . H 6 HOH A 11 511 36 HOH HOH . H 6 HOH A 12 512 162 HOH HOH . H 6 HOH A 13 513 42 HOH HOH . H 6 HOH A 14 514 43 HOH HOH . H 6 HOH A 15 515 2 HOH HOH . H 6 HOH A 16 516 133 HOH HOH . H 6 HOH A 17 517 52 HOH HOH . H 6 HOH A 18 518 123 HOH HOH . H 6 HOH A 19 519 67 HOH HOH . H 6 HOH A 20 520 29 HOH HOH . H 6 HOH A 21 521 56 HOH HOH . H 6 HOH A 22 522 27 HOH HOH . H 6 HOH A 23 523 120 HOH HOH . H 6 HOH A 24 524 21 HOH HOH . H 6 HOH A 25 525 95 HOH HOH . H 6 HOH A 26 526 76 HOH HOH . H 6 HOH A 27 527 12 HOH HOH . H 6 HOH A 28 528 81 HOH HOH . H 6 HOH A 29 529 22 HOH HOH . H 6 HOH A 30 530 23 HOH HOH . H 6 HOH A 31 531 35 HOH HOH . H 6 HOH A 32 532 46 HOH HOH . H 6 HOH A 33 533 94 HOH HOH . H 6 HOH A 34 534 9 HOH HOH . H 6 HOH A 35 535 99 HOH HOH . H 6 HOH A 36 536 16 HOH HOH . H 6 HOH A 37 537 17 HOH HOH . H 6 HOH A 38 538 10 HOH HOH . H 6 HOH A 39 539 104 HOH HOH . H 6 HOH A 40 540 51 HOH HOH . H 6 HOH A 41 541 45 HOH HOH . H 6 HOH A 42 542 3 HOH HOH . H 6 HOH A 43 543 114 HOH HOH . H 6 HOH A 44 544 50 HOH HOH . H 6 HOH A 45 545 78 HOH HOH . H 6 HOH A 46 546 44 HOH HOH . H 6 HOH A 47 547 39 HOH HOH . H 6 HOH A 48 548 161 HOH HOH . H 6 HOH A 49 549 54 HOH HOH . H 6 HOH A 50 550 102 HOH HOH . H 6 HOH A 51 551 28 HOH HOH . H 6 HOH A 52 552 97 HOH HOH . H 6 HOH A 53 553 63 HOH HOH . H 6 HOH A 54 554 40 HOH HOH . H 6 HOH A 55 555 19 HOH HOH . H 6 HOH A 56 556 163 HOH HOH . H 6 HOH A 57 557 96 HOH HOH . H 6 HOH A 58 558 5 HOH HOH . H 6 HOH A 59 559 61 HOH HOH . H 6 HOH A 60 560 106 HOH HOH . H 6 HOH A 61 561 53 HOH HOH . H 6 HOH A 62 562 137 HOH HOH . H 6 HOH A 63 563 11 HOH HOH . H 6 HOH A 64 564 8 HOH HOH . H 6 HOH A 65 565 127 HOH HOH . H 6 HOH A 66 566 69 HOH HOH . H 6 HOH A 67 567 15 HOH HOH . H 6 HOH A 68 568 37 HOH HOH . H 6 HOH A 69 569 26 HOH HOH . H 6 HOH A 70 570 25 HOH HOH . H 6 HOH A 71 571 110 HOH HOH . H 6 HOH A 72 572 30 HOH HOH . H 6 HOH A 73 573 65 HOH HOH . H 6 HOH A 74 574 93 HOH HOH . H 6 HOH A 75 575 6 HOH HOH . H 6 HOH A 76 576 48 HOH HOH . H 6 HOH A 77 577 70 HOH HOH . H 6 HOH A 78 578 66 HOH HOH . H 6 HOH A 79 579 136 HOH HOH . H 6 HOH A 80 580 98 HOH HOH . H 6 HOH A 81 581 91 HOH HOH . H 6 HOH A 82 582 82 HOH HOH . H 6 HOH A 83 583 33 HOH HOH . H 6 HOH A 84 584 89 HOH HOH . H 6 HOH A 85 585 4 HOH HOH . H 6 HOH A 86 586 38 HOH HOH . H 6 HOH A 87 587 77 HOH HOH . H 6 HOH A 88 588 24 HOH HOH . H 6 HOH A 89 589 68 HOH HOH . H 6 HOH A 90 590 86 HOH HOH . H 6 HOH A 91 591 105 HOH HOH . H 6 HOH A 92 592 142 HOH HOH . H 6 HOH A 93 593 108 HOH HOH . H 6 HOH A 94 594 55 HOH HOH . H 6 HOH A 95 595 20 HOH HOH . H 6 HOH A 96 596 109 HOH HOH . H 6 HOH A 97 597 101 HOH HOH . H 6 HOH A 98 598 117 HOH HOH . H 6 HOH A 99 599 150 HOH HOH . H 6 HOH A 100 600 128 HOH HOH . H 6 HOH A 101 601 100 HOH HOH . H 6 HOH A 102 602 74 HOH HOH . H 6 HOH A 103 603 143 HOH HOH . H 6 HOH A 104 604 49 HOH HOH . H 6 HOH A 105 605 122 HOH HOH . H 6 HOH A 106 606 139 HOH HOH . H 6 HOH A 107 607 125 HOH HOH . H 6 HOH A 108 608 87 HOH HOH . H 6 HOH A 109 609 57 HOH HOH . H 6 HOH A 110 610 7 HOH HOH . H 6 HOH A 111 611 119 HOH HOH . H 6 HOH A 112 612 13 HOH HOH . H 6 HOH A 113 613 34 HOH HOH . H 6 HOH A 114 614 138 HOH HOH . H 6 HOH A 115 615 124 HOH HOH . H 6 HOH A 116 616 1 HOH HOH . H 6 HOH A 117 617 64 HOH HOH . H 6 HOH A 118 618 71 HOH HOH . H 6 HOH A 119 619 47 HOH HOH . H 6 HOH A 120 620 41 HOH HOH . H 6 HOH A 121 621 146 HOH HOH . H 6 HOH A 122 622 131 HOH HOH . H 6 HOH A 123 623 145 HOH HOH . H 6 HOH A 124 624 152 HOH HOH . H 6 HOH A 125 625 116 HOH HOH . H 6 HOH A 126 626 115 HOH HOH . H 6 HOH A 127 627 159 HOH HOH . H 6 HOH A 128 628 79 HOH HOH . H 6 HOH A 129 629 113 HOH HOH . H 6 HOH A 130 630 72 HOH HOH . H 6 HOH A 131 631 134 HOH HOH . H 6 HOH A 132 632 147 HOH HOH . H 6 HOH A 133 633 165 HOH HOH . H 6 HOH A 134 634 90 HOH HOH . H 6 HOH A 135 635 73 HOH HOH . H 6 HOH A 136 636 75 HOH HOH . H 6 HOH A 137 637 151 HOH HOH . H 6 HOH A 138 638 88 HOH HOH . H 6 HOH A 139 639 140 HOH HOH . H 6 HOH A 140 640 166 HOH HOH . H 6 HOH A 141 641 83 HOH HOH . H 6 HOH A 142 642 157 HOH HOH . H 6 HOH A 143 643 144 HOH HOH . H 6 HOH A 144 644 158 HOH HOH . H 6 HOH A 145 645 156 HOH HOH . H 6 HOH A 146 646 132 HOH HOH . H 6 HOH A 147 647 130 HOH HOH . H 6 HOH A 148 648 164 HOH HOH . H 6 HOH A 149 649 155 HOH HOH . H 6 HOH A 150 650 153 HOH HOH . H 6 HOH A 151 651 62 HOH HOH . H 6 HOH A 152 652 135 HOH HOH . H 6 HOH A 153 653 32 HOH HOH . H 6 HOH A 154 654 167 HOH HOH . H 6 HOH A 155 655 118 HOH HOH . H 6 HOH A 156 656 18 HOH HOH . H 6 HOH A 157 657 84 HOH HOH . H 6 HOH A 158 658 121 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 P PB GDP . . . B 2 -25.965 1.03 5.226 1 43.56 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . B 2 -24.928 0.935 4.143 1 42.52 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . B 2 -26.934 2.166 4.881 1 48.53 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . B 2 -25.286 1.258 6.559 1 36.97 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . B 2 -26.729 -0.381 5.234 1 43.13 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . B 2 -27.119 -1.196 6.564 1 31.13 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . B 2 -28.193 -2.156 6.157 1 30.62 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . B 2 -25.918 -1.882 7.169 1 31.87 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . B 2 -27.652 -0.114 7.637 1 27.78 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . B 2 -28.915 0.523 7.457 1 28.94 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . B 2 -29.348 1.177 8.77 1 26.77 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . B 2 -29.859 0.147 9.614 1 28.42 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . B 2 -28.202 1.818 9.538 1 29.63 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . B 2 -28.623 3.077 10.074 1 25.75 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . B 2 -27.962 0.894 10.712 1 28.91 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . B 2 -27.47 1.601 11.854 1 24.59 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . B 2 -29.365 0.363 10.929 1 26.71 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . B 2 -29.318 -0.895 11.701 1 32.51 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . B 2 -30.038 -1.155 12.814 1 30.24 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . B 2 -29.77 -2.395 13.284 1 31.23 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . B 2 -28.856 -2.939 12.456 1 33.96 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . B 2 -28.136 -4.218 12.379 1 34.22 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . B 2 -28.364 -5.078 13.262 1 31.51 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . B 2 -27.269 -4.416 11.357 1 29.22 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . B 2 -27.034 -3.477 10.422 1 32.43 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . B 2 -26.143 -3.733 9.419 1 22.22 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . B 2 -27.675 -2.275 10.436 1 27.94 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . B 2 -28.561 -1.952 11.409 1 35.01 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #