data_6GFM # _model_server_result.job_id or_fMYsosGsBmGyl6tlU0g _model_server_result.datetime_utc '2025-08-12 05:05:45' _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 6gfm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6GFM # _exptl.entry_id 6GFM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 683.14 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen 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 6GFM _cell.length_a 176.92 _cell.length_b 176.92 _cell.length_c 94.48 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GFM _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall 'I 4bw 2bw' _symmetry.space_group_name_H-M 'I 41 2 2' # _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 'C10 H18 N5 O20 P5' _chem_comp.formula_weight 683.14 _chem_comp.id 0O2 _chem_comp.mon_nstd_flag . _chem_comp.name "guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)" _chem_comp.type non-polymer _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 O1G PG 0O2 doub 1 n n O2A PA 0O2 doub 2 n n PG O3B 0O2 sing 3 n n PG O2G 0O2 sing 4 n n PG O3G 0O2 sing 5 n n O3B PB 0O2 sing 6 n n O3A PA 0O2 sing 7 n n O3A PB 0O2 sing 8 n n O2B PB 0O2 doub 9 n n O1A PA 0O2 sing 10 n n PA O5' 0O2 sing 11 n n PB O1B 0O2 sing 12 n n O5' C5' 0O2 sing 13 n n C5' C4' 0O2 sing 14 n n C4' O4' 0O2 sing 15 n n C4' C3' 0O2 sing 16 n n O4' C1' 0O2 sing 17 n n O2C PC 0O2 doub 18 n n C8 N7 0O2 doub 19 n y C8 N9 0O2 sing 20 n y C3' C2' 0O2 sing 21 n n C3' O3' 0O2 sing 22 n n N7 C5 0O2 sing 23 n y C1' N9 0O2 sing 24 n n C1' C2' 0O2 sing 25 n n N9 C4 0O2 sing 26 n y C2' O2' 0O2 sing 27 n n O2D PD 0O2 doub 28 n n C5 C4 0O2 doub 29 n y C5 C6 0O2 sing 30 n n PC O3' 0O2 sing 31 n n PC O3C 0O2 sing 32 n n PC O1C 0O2 sing 33 n n C4 N3 0O2 sing 34 n n O6 C6 0O2 doub 35 n n C6 N1 0O2 sing 36 n n O1D PD 0O2 sing 37 n n O3C PD 0O2 sing 38 n n N3 C2 0O2 doub 39 n n PD O3D 0O2 sing 40 n n N1 C2 0O2 sing 41 n n C2 N2 0O2 sing 42 n n O1D H1 0O2 sing 43 n n O3D H2 0O2 sing 44 n n O2G H3 0O2 sing 45 n n O3G H4 0O2 sing 46 n n O1B H5 0O2 sing 47 n n O1A H6 0O2 sing 48 n n C5' H7 0O2 sing 49 n n C5' H8 0O2 sing 50 n n C4' H9 0O2 sing 51 n n C3' H10 0O2 sing 52 n n C2' H11 0O2 sing 53 n n O2' H12 0O2 sing 54 n n C1' H13 0O2 sing 55 n n C8 H14 0O2 sing 56 n n N2 H15 0O2 sing 57 n n N2 H16 0O2 sing 58 n n O1C H18 0O2 sing 59 n n N1 H19 0O2 sing 60 n n # _atom_sites.entry_id 6GFM _atom_sites.fract_transf_matrix[1][1] 0.005652 _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] 0.005652 _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] 0.010584 _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 0O2 A 1 501 461 0O2 PGP . C 3 HOH A 1 601 66 HOH HOH . C 3 HOH A 2 602 13 HOH HOH . C 3 HOH A 3 603 12 HOH HOH . C 3 HOH A 4 604 60 HOH HOH . C 3 HOH A 5 605 92 HOH HOH . C 3 HOH A 6 606 136 HOH HOH . C 3 HOH A 7 607 101 HOH HOH . C 3 HOH A 8 608 33 HOH HOH . C 3 HOH A 9 609 97 HOH HOH . C 3 HOH A 10 610 126 HOH HOH . C 3 HOH A 11 611 39 HOH HOH . C 3 HOH A 12 612 19 HOH HOH . C 3 HOH A 13 613 153 HOH HOH . C 3 HOH A 14 614 6 HOH HOH . C 3 HOH A 15 615 98 HOH HOH . C 3 HOH A 16 616 93 HOH HOH . C 3 HOH A 17 617 1 HOH HOH . C 3 HOH A 18 618 7 HOH HOH . C 3 HOH A 19 619 9 HOH HOH . C 3 HOH A 20 620 38 HOH HOH . C 3 HOH A 21 621 132 HOH HOH . C 3 HOH A 22 622 75 HOH HOH . C 3 HOH A 23 623 56 HOH HOH . C 3 HOH A 24 624 124 HOH HOH . C 3 HOH A 25 625 2 HOH HOH . C 3 HOH A 26 626 42 HOH HOH . C 3 HOH A 27 627 41 HOH HOH . C 3 HOH A 28 628 118 HOH HOH . C 3 HOH A 29 629 79 HOH HOH . C 3 HOH A 30 630 49 HOH HOH . C 3 HOH A 31 631 111 HOH HOH . C 3 HOH A 32 632 65 HOH HOH . C 3 HOH A 33 633 21 HOH HOH . C 3 HOH A 34 634 43 HOH HOH . C 3 HOH A 35 635 5 HOH HOH . C 3 HOH A 36 636 59 HOH HOH . C 3 HOH A 37 637 120 HOH HOH . C 3 HOH A 38 638 34 HOH HOH . C 3 HOH A 39 639 105 HOH HOH . C 3 HOH A 40 640 122 HOH HOH . C 3 HOH A 41 641 27 HOH HOH . C 3 HOH A 42 642 112 HOH HOH . C 3 HOH A 43 643 4 HOH HOH . C 3 HOH A 44 644 103 HOH HOH . C 3 HOH A 45 645 22 HOH HOH . C 3 HOH A 46 646 78 HOH HOH . C 3 HOH A 47 647 44 HOH HOH . C 3 HOH A 48 648 95 HOH HOH . C 3 HOH A 49 649 113 HOH HOH . C 3 HOH A 50 650 87 HOH HOH . C 3 HOH A 51 651 15 HOH HOH . C 3 HOH A 52 652 14 HOH HOH . C 3 HOH A 53 653 154 HOH HOH . C 3 HOH A 54 654 11 HOH HOH . C 3 HOH A 55 655 23 HOH HOH . C 3 HOH A 56 656 96 HOH HOH . C 3 HOH A 57 657 18 HOH HOH . C 3 HOH A 58 658 144 HOH HOH . C 3 HOH A 59 659 45 HOH HOH . C 3 HOH A 60 660 58 HOH HOH . C 3 HOH A 61 661 114 HOH HOH . C 3 HOH A 62 662 85 HOH HOH . C 3 HOH A 63 663 67 HOH HOH . C 3 HOH A 64 664 53 HOH HOH . C 3 HOH A 65 665 145 HOH HOH . C 3 HOH A 66 666 68 HOH HOH . C 3 HOH A 67 667 91 HOH HOH . C 3 HOH A 68 668 69 HOH HOH . C 3 HOH A 69 669 40 HOH HOH . C 3 HOH A 70 670 28 HOH HOH . C 3 HOH A 71 671 146 HOH HOH . C 3 HOH A 72 672 24 HOH HOH . C 3 HOH A 73 673 148 HOH HOH . C 3 HOH A 74 674 31 HOH HOH . C 3 HOH A 75 675 57 HOH HOH . C 3 HOH A 76 676 72 HOH HOH . C 3 HOH A 77 677 73 HOH HOH . C 3 HOH A 78 678 89 HOH HOH . C 3 HOH A 79 679 135 HOH HOH . C 3 HOH A 80 680 139 HOH HOH . C 3 HOH A 81 681 152 HOH HOH . C 3 HOH A 82 682 29 HOH HOH . C 3 HOH A 83 683 99 HOH HOH . C 3 HOH A 84 684 55 HOH HOH . C 3 HOH A 85 685 88 HOH HOH . C 3 HOH A 86 686 10 HOH HOH . C 3 HOH A 87 687 77 HOH HOH . C 3 HOH A 88 688 37 HOH HOH . C 3 HOH A 89 689 32 HOH HOH . C 3 HOH A 90 690 86 HOH HOH . C 3 HOH A 91 691 149 HOH HOH . C 3 HOH A 92 692 47 HOH HOH . C 3 HOH A 93 693 83 HOH HOH . C 3 HOH A 94 694 100 HOH HOH . C 3 HOH A 95 695 138 HOH HOH . C 3 HOH A 96 696 137 HOH HOH . C 3 HOH A 97 697 141 HOH HOH . C 3 HOH A 98 698 25 HOH HOH . C 3 HOH A 99 699 127 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 PD 0O2 . . . B 2 9.432 -19.484 -48.957 1 169.61 ? PD 0O2 501 A 1 HETATM 2 O O1D 0O2 . . . B 2 9.771 -18.08 -48.739 1 164.62 ? O1D 0O2 501 A 1 HETATM 3 O O2D 0O2 . . . B 2 10.588 -20.222 -48.455 1 165.01 -1 O2D 0O2 501 A 1 HETATM 4 O O3D 0O2 . . . B 2 8.39 -19.751 -47.97 1 175.5 -1 O3D 0O2 501 A 1 HETATM 5 P PG 0O2 . . . B 2 4.819 -29.799 -50.265 1 159.83 ? PG 0O2 501 A 1 HETATM 6 O O1G 0O2 . . . B 2 4.864 -30.596 -49.042 1 171.82 -1 O1G 0O2 501 A 1 HETATM 7 O O2G 0O2 . . . B 2 4.606 -30.78 -51.328 1 160.56 -1 O2G 0O2 501 A 1 HETATM 8 O O3G 0O2 . . . B 2 3.558 -29.068 -50.193 1 149.74 ? O3G 0O2 501 A 1 HETATM 9 P PB 0O2 . . . B 2 6.839 -28.607 -51.97 1 194.88 ? PB 0O2 501 A 1 HETATM 10 O O1B 0O2 . . . B 2 7.944 -29.54 -52.181 1 198.58 ? O1B 0O2 501 A 1 HETATM 11 O O2B 0O2 . . . B 2 5.928 -28.988 -53.048 1 199.09 -1 O2B 0O2 501 A 1 HETATM 12 O O3B 0O2 . . . B 2 6.139 -28.839 -50.495 1 181.14 ? O3B 0O2 501 A 1 HETATM 13 O O3A 0O2 . . . B 2 7.331 -27.042 -52.13 1 191.85 ? O3A 0O2 501 A 1 HETATM 14 P PA 0O2 . . . B 2 6.493 -25.895 -52.97 1 196.62 ? PA 0O2 501 A 1 HETATM 15 O O1A 0O2 . . . B 2 6.02 -26.406 -54.253 1 204.23 -1 O1A 0O2 501 A 1 HETATM 16 O O2A 0O2 . . . B 2 7.367 -24.81 -53.413 1 205.33 ? O2A 0O2 501 A 1 HETATM 17 O O5' 0O2 . . . B 2 5.248 -25.319 -52.058 1 170.46 ? O5' 0O2 501 A 1 HETATM 18 C C5' 0O2 . . . B 2 5.541 -24.851 -50.772 1 141.59 ? C5' 0O2 501 A 1 HETATM 19 C C4' 0O2 . . . B 2 5.402 -23.365 -50.75 1 119.59 ? C4' 0O2 501 A 1 HETATM 20 O O4' 0O2 . . . B 2 4.079 -22.987 -50.188 1 114.42 ? O4' 0O2 501 A 1 HETATM 21 C C3' 0O2 . . . B 2 6.432 -22.722 -49.88 1 115.85 ? C3' 0O2 501 A 1 HETATM 22 O O3' 0O2 . . . B 2 6.869 -21.487 -50.488 1 141.57 ? O3' 0O2 501 A 1 HETATM 23 C C2' 0O2 . . . B 2 5.727 -22.414 -48.637 1 100.67 ? C2' 0O2 501 A 1 HETATM 24 O O2' 0O2 . . . B 2 6.395 -21.366 -47.911 1 99.45 ? O2' 0O2 501 A 1 HETATM 25 C C1' 0O2 . . . B 2 4.399 -21.977 -49.149 1 98.19 ? C1' 0O2 501 A 1 HETATM 26 N N9 0O2 . . . B 2 3.382 -21.862 -48.158 1 81.89 ? N9 0O2 501 A 1 HETATM 27 C C8 0O2 . . . B 2 2.762 -20.793 -48.112 1 94.77 ? C8 0O2 501 A 1 HETATM 28 N N7 0O2 . . . B 2 1.838 -20.839 -47.132 1 90.78 ? N7 0O2 501 A 1 HETATM 29 C C5 0O2 . . . B 2 2.084 -22.278 -46.591 1 76.51 ? C5 0O2 501 A 1 HETATM 30 C C6 0O2 . . . B 2 1.458 -23.035 -45.525 1 66.68 ? C6 0O2 501 A 1 HETATM 31 O O6 0O2 . . . B 2 0.425 -22.47 -44.769 1 65.08 ? O6 0O2 501 A 1 HETATM 32 N N1 0O2 . . . B 2 1.921 -24.387 -45.257 1 81.7 ? N1 0O2 501 A 1 HETATM 33 C C2 0O2 . . . B 2 2.903 -24.925 -45.975 1 88.08 ? C2 0O2 501 A 1 HETATM 34 N N2 0O2 . . . B 2 3.346 -26.276 -45.688 1 103.64 ? N2 0O2 501 A 1 HETATM 35 N N3 0O2 . . . B 2 3.569 -24.135 -47.1 1 84.93 ? N3 0O2 501 A 1 HETATM 36 C C4 0O2 . . . B 2 3.108 -22.793 -47.365 1 78.72 ? C4 0O2 501 A 1 HETATM 37 P PC 0O2 . . . B 2 8.421 -21.304 -51.011 1 144.84 ? PC 0O2 501 A 1 HETATM 38 O O1C 0O2 . . . B 2 9.28 -22.401 -50.571 1 132.56 ? O1C 0O2 501 A 1 HETATM 39 O O2C 0O2 . . . B 2 8.489 -21.432 -52.467 1 130.56 -1 O2C 0O2 501 A 1 HETATM 40 O O3C 0O2 . . . B 2 9.017 -19.846 -50.512 1 163.41 ? O3C 0O2 501 A 1 HETATM 41 H H7 0O2 . . . B 2 4.949 -25.237 -50.153 1 170.41 ? H7 0O2 501 A 1 HETATM 42 H H8 0O2 . . . B 2 6.422 -25.085 -50.549 1 170.41 ? H8 0O2 501 A 1 HETATM 43 H H9 0O2 . . . B 2 5.477 -23.027 -51.623 1 144 ? H9 0O2 501 A 1 HETATM 44 H H10 0O2 . . . B 2 7.153 -23.303 -49.724 1 139.52 ? H10 0O2 501 A 1 HETATM 45 H H11 0O2 . . . B 2 5.638 -23.186 -48.11 1 121.31 ? H11 0O2 501 A 1 HETATM 46 H H12 0O2 . . . B 2 7.216 -21.502 -47.919 1 119.84 ? H12 0O2 501 A 1 HETATM 47 H H13 0O2 . . . B 2 4.505 -21.144 -49.569 1 118.33 ? H13 0O2 501 A 1 HETATM 48 H H14 0O2 . . . B 2 2.901 -20.122 -48.625 1 114.22 ? H14 0O2 501 A 1 HETATM 49 H H15 0O2 . . . B 2 3.238 -26.608 -44.893 1 124.86 ? H15 0O2 501 A 1 HETATM 50 H H16 0O2 . . . B 2 3.719 -26.752 -46.31 1 124.86 ? H16 0O2 501 A 1 HETATM 51 H H19 0O2 . . . B 2 4.21 -24.485 -47.569 1 102.42 ? H19 0O2 501 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 51 #