data_6RPU # _model_server_result.job_id -gFG7tdPggLlrGAoI5yR-Q _model_server_result.datetime_utc '2025-07-10 05:48:56' _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 6rpu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 6RPU # _exptl.entry_id 6RPU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 932.366 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE" _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 6RPU _cell.length_a 148.538 _cell.length_b 148.538 _cell.length_c 103.828 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RPU _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_and_software_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 1,2,3,4,5,6,7,8 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 103.828 6 'crystal symmetry operation' 6_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 103.828 7 'crystal symmetry operation' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 103.828 8 'crystal symmetry operation' 8_556 -y,-x,-z+1 0 -1 0 -1 0 0 0 0 -1 0 0 103.828 # _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 'C20 H29 N10 O23 P5' _chem_comp.formula_weight 932.366 _chem_comp.id G5P _chem_comp.mon_nstd_flag . _chem_comp.name "P1-(5'-ADENOSYL)-P5-(5'-GUANOSYL) PENTAPHOSPHATE" _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 PE O1E G5P sing 89 n n PE O2E G5P doub 90 n n PE O3D G5P sing 91 n n PE O5F G5P sing 92 n n O1E H1E G5P sing 93 n n PD O1D G5P sing 94 n n PD O2D G5P doub 95 n n PD O3D G5P sing 96 n n PD O3G G5P sing 97 n n O1D H1D G5P sing 98 n n PG O1G G5P sing 99 n n PG O2G G5P doub 100 n n PG O3G G5P sing 101 n n PG O3B G5P sing 102 n n O1G H1G G5P sing 103 n n PB O1B G5P sing 104 n n PB O2B G5P doub 105 n n PB O3B G5P sing 106 n n PB O3A G5P sing 107 n n O1B H1B G5P sing 108 n n O3A PA G5P sing 109 n n PA O1A G5P sing 110 n n PA O2A G5P doub 111 n n PA O5' G5P sing 112 n n O1A H1A G5P sing 113 n n O5' C5' G5P sing 114 n n C5' C4' G5P sing 115 n n C5' "H5'1" G5P sing 116 n n C5' "H5'2" G5P sing 117 n n C4' O4' G5P sing 118 n n C4' C3' G5P sing 119 n n C4' H4' G5P sing 120 n n O4' C1' G5P sing 121 n n C3' O3' G5P sing 122 n n C3' C2' G5P sing 123 n n C3' H7 G5P sing 124 n n O3' H9 G5P sing 125 n n C2' O2' G5P sing 126 n n C2' C1' G5P sing 127 n n C2' H10 G5P sing 128 n n O2' H11 G5P sing 129 n n C1' N9 G5P sing 130 n n C1' H1' G5P sing 131 n n N9 C8 G5P sing 132 n y N9 C4 G5P sing 133 n y C8 N7 G5P doub 134 n y C8 H8 G5P sing 135 n n N7 C5 G5P sing 136 n y C5 C6 G5P sing 137 n y C5 C4 G5P doub 138 n y C6 O6 G5P doub 139 n n C6 N1 G5P sing 140 n y N1 C2 G5P sing 141 n y N1 HN1 G5P sing 142 n n C2 N2 G5P sing 143 n n C2 N3 G5P doub 144 n y N2 HN21 G5P sing 145 n n N2 HN22 G5P sing 146 n n N3 C4 G5P sing 147 n y O5F C5F G5P sing 148 n n C5F C4F G5P sing 149 n n C5F H11X G5P sing 150 n n C5F H12 G5P sing 151 n n C4F O4F G5P sing 152 n n C4F C3F G5P sing 153 n n C4F H1 G5P sing 154 n n O4F C1F G5P sing 155 n n C1F C2F G5P sing 156 n n C1F N9A G5P sing 157 n n C1F H2 G5P sing 158 n n C2F O2F G5P sing 159 n n C2F C3F G5P sing 160 n n C2F H2' G5P sing 161 n n O2F H3 G5P sing 162 n n C3F O3F G5P sing 163 n n C3F H3' G5P sing 164 n n O3F H4 G5P sing 165 n n N9A C4A G5P sing 166 n y N9A C8A G5P sing 167 n y C4A N3A G5P sing 168 n y C4A C5A G5P doub 169 n y N3A C2A G5P doub 170 n y C2A N1A G5P sing 171 n y C2A H6 G5P sing 172 n n N1A C6A G5P doub 173 n y C6A N6A G5P sing 174 n n C6A C5A G5P sing 175 n y N6A HN61 G5P sing 176 n n N6A HN62 G5P sing 177 n n C5A N7A G5P sing 178 n y N7A C8A G5P doub 179 n y C8A H5 G5P sing 180 n n # _atom_sites.entry_id 6RPU _atom_sites.fract_transf_matrix[1][1] 0.006732 _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] 0.006732 _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] 0.009631 _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 G5P A 1 601 601 G5P G5P . C 3 GDP A 1 602 602 GDP GDP . D 4 ACT A 1 603 701 ACT ACT . E 4 ACT A 1 604 702 ACT ACT . F 4 ACT A 1 605 801 ACT ACT . G 4 ACT A 1 606 901 ACT ACT . H 5 HOH A 1 701 31 HOH HOH . H 5 HOH A 2 702 20 HOH HOH . H 5 HOH A 3 703 4 HOH HOH . H 5 HOH A 4 704 10 HOH HOH . H 5 HOH A 5 705 17 HOH HOH . H 5 HOH A 6 706 5 HOH HOH . H 5 HOH A 7 707 1 HOH HOH . H 5 HOH A 8 708 54 HOH HOH . H 5 HOH A 9 709 21 HOH HOH . H 5 HOH A 10 710 24 HOH HOH . H 5 HOH A 11 711 8 HOH HOH . H 5 HOH A 12 712 15 HOH HOH . H 5 HOH A 13 713 18 HOH HOH . H 5 HOH A 14 714 13 HOH HOH . H 5 HOH A 15 715 27 HOH HOH . H 5 HOH A 16 716 2 HOH HOH . H 5 HOH A 17 717 3 HOH HOH . H 5 HOH A 18 718 9 HOH HOH . H 5 HOH A 19 719 11 HOH HOH . H 5 HOH A 20 720 19 HOH HOH . H 5 HOH A 21 721 50 HOH HOH . H 5 HOH A 22 722 29 HOH HOH . H 5 HOH A 23 723 44 HOH HOH . H 5 HOH A 24 724 16 HOH HOH . H 5 HOH A 25 725 49 HOH HOH . H 5 HOH A 26 726 34 HOH HOH . H 5 HOH A 27 727 43 HOH HOH . H 5 HOH A 28 728 22 HOH HOH . H 5 HOH A 29 729 42 HOH HOH . H 5 HOH A 30 730 52 HOH HOH . H 5 HOH A 31 731 26 HOH HOH . H 5 HOH A 32 732 47 HOH HOH . H 5 HOH A 33 733 30 HOH HOH . H 5 HOH A 34 734 38 HOH HOH . H 5 HOH A 35 735 39 HOH HOH . H 5 HOH A 36 736 36 HOH HOH . H 5 HOH A 37 737 33 HOH HOH . H 5 HOH A 38 738 45 HOH HOH . H 5 HOH A 39 739 55 HOH HOH . H 5 HOH A 40 740 40 HOH HOH . H 5 HOH A 41 741 53 HOH HOH . H 5 HOH A 42 742 41 HOH HOH . H 5 HOH A 43 743 51 HOH HOH . H 5 HOH A 44 744 46 HOH HOH . H 5 HOH A 45 745 56 HOH HOH . H 5 HOH A 46 746 14 HOH HOH . H 5 HOH A 47 747 35 HOH HOH . H 5 HOH A 48 748 6 HOH HOH . H 5 HOH A 49 749 7 HOH HOH . H 5 HOH A 50 750 48 HOH HOH . H 5 HOH A 51 751 37 HOH HOH . H 5 HOH A 52 752 12 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 PE G5P . . . B 2 4.456 -60.398 50.306 1 59.86 ? PE G5P 601 A 1 HETATM 2 O O1E G5P . . . B 2 3.267 -60.911 49.548 1 60.63 ? O1E G5P 601 A 1 HETATM 3 O O2E G5P . . . B 2 5.732 -60.075 49.581 1 60.09 ? O2E G5P 601 A 1 HETATM 4 P PD G5P . . . B 2 5.111 -58.125 51.789 1 66.82 ? PD G5P 601 A 1 HETATM 5 O O1D G5P . . . B 2 4.388 -57.132 52.651 1 67.53 ? O1D G5P 601 A 1 HETATM 6 O O2D G5P . . . B 2 6.155 -59.013 52.402 1 69.05 ? O2D G5P 601 A 1 HETATM 7 O O3D G5P . . . B 2 4.019 -59.068 51.086 1 61.62 ? O3D G5P 601 A 1 HETATM 8 P PG G5P . . . B 2 7.067 -56.394 50.928 1 69.5 ? PG G5P 601 A 1 HETATM 9 O O1G G5P . . . B 2 6.679 -55.483 52.054 1 69.29 ? O1G G5P 601 A 1 HETATM 10 O O2G G5P . . . B 2 8.275 -57.266 51.058 1 68.73 ? O2G G5P 601 A 1 HETATM 11 O O3G G5P . . . B 2 5.798 -57.313 50.594 1 68.05 ? O3G G5P 601 A 1 HETATM 12 P PB G5P . . . B 2 8.498 -54.554 49.347 1 70.98 ? PB G5P 601 A 1 HETATM 13 O O1B G5P . . . B 2 9.425 -55.179 48.342 1 72.54 ? O1B G5P 601 A 1 HETATM 14 O O2B G5P . . . B 2 9.054 -54.082 50.661 1 72.81 ? O2B G5P 601 A 1 HETATM 15 O O3B G5P . . . B 2 7.236 -55.516 49.603 1 70.6 ? O3B G5P 601 A 1 HETATM 16 O O3A G5P . . . B 2 7.726 -53.332 48.667 1 70.21 ? O3A G5P 601 A 1 HETATM 17 P PA G5P . . . B 2 7.051 -53.568 47.241 1 69.27 ? PA G5P 601 A 1 HETATM 18 O O1A G5P . . . B 2 7.463 -54.92 46.736 1 68.66 ? O1A G5P 601 A 1 HETATM 19 O O2A G5P . . . B 2 5.588 -53.235 47.35 1 67.33 ? O2A G5P 601 A 1 HETATM 20 O O5' G5P . . . B 2 7.778 -52.434 46.375 1 66.12 ? O5' G5P 601 A 1 HETATM 21 C C5' G5P . . . B 2 8.959 -52.745 45.646 1 63.77 ? C5' G5P 601 A 1 HETATM 22 C C4' G5P . . . B 2 9.098 -51.825 44.442 1 60.97 ? C4' G5P 601 A 1 HETATM 23 O O4' G5P . . . B 2 10.464 -51.456 44.259 1 59.9 ? O4' G5P 601 A 1 HETATM 24 C C3' G5P . . . B 2 8.654 -52.537 43.183 1 59.8 ? C3' G5P 601 A 1 HETATM 25 O O3' G5P . . . B 2 7.893 -51.657 42.353 1 59.64 ? O3' G5P 601 A 1 HETATM 26 C C2' G5P . . . B 2 9.946 -52.924 42.503 1 59.32 ? C2' G5P 601 A 1 HETATM 27 O O2' G5P . . . B 2 9.816 -52.938 41.081 1 58.41 ? O2' G5P 601 A 1 HETATM 28 C C1' G5P . . . B 2 10.934 -51.878 42.981 1 57.95 ? C1' G5P 601 A 1 HETATM 29 N N9 G5P . . . B 2 12.295 -52.432 43.129 1 59.48 ? N9 G5P 601 A 1 HETATM 30 C C8 G5P . . . B 2 13.371 -52.012 42.449 1 57.26 ? C8 G5P 601 A 1 HETATM 31 N N7 G5P . . . B 2 14.462 -52.73 42.798 1 57.6 ? N7 G5P 601 A 1 HETATM 32 C C5 G5P . . . B 2 14.084 -53.635 43.709 1 56.65 ? C5 G5P 601 A 1 HETATM 33 C C6 G5P . . . B 2 14.749 -54.702 44.484 1 56.48 ? C6 G5P 601 A 1 HETATM 34 O O6 G5P . . . B 2 15.967 -54.922 44.352 1 55.63 ? O6 G5P 601 A 1 HETATM 35 N N1 G5P . . . B 2 14.006 -55.423 45.328 1 57.11 ? N1 G5P 601 A 1 HETATM 36 C C2 G5P . . . B 2 12.689 -55.198 45.483 1 56.86 ? C2 G5P 601 A 1 HETATM 37 N N2 G5P . . . B 2 12.003 -55.968 46.357 1 56.42 ? N2 G5P 601 A 1 HETATM 38 N N3 G5P . . . B 2 12.016 -54.237 44.804 1 57.32 ? N3 G5P 601 A 1 HETATM 39 C C4 G5P . . . B 2 12.649 -53.445 43.914 1 58.8 ? C4 G5P 601 A 1 HETATM 40 O O5F G5P . . . B 2 4.768 -61.451 51.47 1 56.26 ? O5F G5P 601 A 1 HETATM 41 C C5F G5P . . . B 2 3.796 -62.417 51.852 1 54.92 ? C5F G5P 601 A 1 HETATM 42 C C4F G5P . . . B 2 4.46 -63.678 52.388 1 53.47 ? C4F G5P 601 A 1 HETATM 43 O O4F G5P . . . B 2 4.587 -64.624 51.332 1 52.74 ? O4F G5P 601 A 1 HETATM 44 C C1F G5P . . . B 2 5.942 -65.029 51.173 1 52.08 ? C1F G5P 601 A 1 HETATM 45 C C2F G5P . . . B 2 6.799 -64.045 51.94 1 49.83 ? C2F G5P 601 A 1 HETATM 46 O O2F G5P . . . B 2 7.903 -64.705 52.559 1 43.96 ? O2F G5P 601 A 1 HETATM 47 C C3F G5P . . . B 2 5.849 -63.435 52.948 1 52.84 ? C3F G5P 601 A 1 HETATM 48 O O3F G5P . . . B 2 5.964 -64.07 54.224 1 54.69 ? O3F G5P 601 A 1 HETATM 49 N N9A G5P . . . B 2 6.27 -65.005 49.736 1 59.33 ? N9A G5P 601 A 1 HETATM 50 C C4A G5P . . . B 2 6.513 -66.073 48.988 1 59.38 ? C4A G5P 601 A 1 HETATM 51 N N3A G5P . . . B 2 6.571 -67.401 49.214 1 58.49 ? N3A G5P 601 A 1 HETATM 52 C C2A G5P . . . B 2 6.859 -68.262 48.228 1 56.79 ? C2A G5P 601 A 1 HETATM 53 N N1A G5P . . . B 2 7.106 -67.872 46.969 1 56.69 ? N1A G5P 601 A 1 HETATM 54 C C6A G5P . . . B 2 7.079 -66.577 46.598 1 55.68 ? C6A G5P 601 A 1 HETATM 55 N N6A G5P . . . B 2 7.329 -66.214 45.321 1 58.69 ? N6A G5P 601 A 1 HETATM 56 C C5A G5P . . . B 2 6.77 -65.574 47.638 1 59.78 ? C5A G5P 601 A 1 HETATM 57 N N7A G5P . . . B 2 6.648 -64.24 47.697 1 56.02 ? N7A G5P 601 A 1 HETATM 58 C C8A G5P . . . B 2 6.338 -63.907 48.97 1 56.37 ? C8A G5P 601 A 1 HETATM 59 H "H5'1" G5P . . . B 2 8.92 -53.783 45.311 1 78.17 ? "H5'1" G5P 601 A 1 HETATM 60 H "H5'2" G5P . . . B 2 9.83 -52.632 46.295 1 78.17 ? "H5'2" G5P 601 A 1 HETATM 61 H H4' G5P . . . B 2 8.476 -50.932 44.593 1 74.82 ? H4' G5P 601 A 1 HETATM 62 H H7 G5P . . . B 2 8.081 -53.438 43.443 1 73.41 ? H7 G5P 601 A 1 HETATM 63 H H9 G5P . . . B 2 7.619 -52.127 41.553 1 73.22 ? H9 G5P 601 A 1 HETATM 64 H H10 G5P . . . B 2 10.262 -53.911 42.868 1 72.84 ? H10 G5P 601 A 1 HETATM 65 H H11 G5P . . . B 2 9.128 -53.568 40.826 1 71.74 ? H11 G5P 601 A 1 HETATM 66 H H1' G5P . . . B 2 10.938 -51.034 42.277 1 71.2 ? H1' G5P 601 A 1 HETATM 67 H H8 G5P . . . B 2 13.369 -51.204 41.728 1 70.37 ? H8 G5P 601 A 1 HETATM 68 H HN1 G5P . . . B 2 14.458 -56.178 45.882 1 70.18 ? HN1 G5P 601 A 1 HETATM 69 H HN21 G5P . . . B 2 12.481 -56.692 46.874 1 69.36 ? HN21 G5P 601 A 1 HETATM 70 H HN22 G5P . . . B 2 11.013 -55.821 46.49 1 69.36 ? HN22 G5P 601 A 1 HETATM 71 H H11X G5P . . . B 2 3.175 -62.67 50.99 1 67.55 ? H11X G5P 601 A 1 HETATM 72 H H12 G5P . . . B 2 3.146 -61.993 52.62 1 67.55 ? H12 G5P 601 A 1 HETATM 73 H H1 G5P . . . B 2 3.829 -64.094 53.185 1 65.82 ? H1 G5P 601 A 1 HETATM 74 H H2 G5P . . . B 2 6.09 -66.037 51.584 1 64.14 ? H2 G5P 601 A 1 HETATM 75 H H2' G5P . . . B 2 7.153 -63.262 51.255 1 61.44 ? H2' G5P 601 A 1 HETATM 76 H H3 G5P . . . B 2 8.464 -64.052 52.999 1 54.4 ? H3 G5P 601 A 1 HETATM 77 H H3' G5P . . . B 2 6.034 -62.355 53.027 1 65.06 ? H3' G5P 601 A 1 HETATM 78 H H4 G5P . . . B 2 6.875 -63.994 54.54 1 67.28 ? H4 G5P 601 A 1 HETATM 79 H H6 G5P . . . B 2 6.895 -69.32 48.459 1 69.8 ? H6 G5P 601 A 1 HETATM 80 H HN61 G5P . . . B 2 7.553 -66.289 44.339 1 72.08 ? HN61 G5P 601 A 1 HETATM 81 H HN62 G5P . . . B 2 7.431 -67.215 45.241 1 72.08 ? HN62 G5P 601 A 1 HETATM 82 H H5 G5P . . . B 2 6.18 -62.895 49.323 1 69.29 ? H5 G5P 601 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 37 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 603 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 82 #