data_7AC5 # _model_server_result.job_id tsw6RO7hwCnWJRoyr-m0Ww _model_server_result.datetime_utc '2025-06-27 10:36:31' _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 7ac5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 7AC5 # _exptl.entry_id 7AC5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 96.78 _cell.angle_gamma 90 _cell.entry_id 7AC5 _cell.length_a 73.32 _cell.length_b 92.03 _cell.length_c 83.54 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7AC5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,I,J _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 6 _struct_asym.id F _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 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc2 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc3 E MG MG . A MG 502 1_555 H O HOH . A HOH 620 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc4 E MG MG . A MG 502 1_555 H O HOH . A HOH 628 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc5 E MG MG . A MG 502 1_555 H O HOH . A HOH 631 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc6 E MG MG . A MG 502 1_555 H O HOH . A HOH 646 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? # _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 7AC5 _atom_sites.fract_transf_matrix[1][1] 0.013639 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001623 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010866 _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] 0.012055 _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 D 4 GTP A 1 501 501 GTP GTP . E 5 MG A 1 502 502 MG MG . F 6 GDP B 1 501 491 GDP GDP . G 7 PG0 B 1 502 501 PG0 1PE . H 8 HOH A 1 601 147 HOH HOH . H 8 HOH A 2 602 30 HOH HOH . H 8 HOH A 3 603 149 HOH HOH . H 8 HOH A 4 604 21 HOH HOH . H 8 HOH A 5 605 22 HOH HOH . H 8 HOH A 6 606 61 HOH HOH . H 8 HOH A 7 607 7 HOH HOH . H 8 HOH A 8 608 66 HOH HOH . H 8 HOH A 9 609 144 HOH HOH . H 8 HOH A 10 610 121 HOH HOH . H 8 HOH A 11 611 78 HOH HOH . H 8 HOH A 12 612 88 HOH HOH . H 8 HOH A 13 613 13 HOH HOH . H 8 HOH A 14 614 126 HOH HOH . H 8 HOH A 15 615 93 HOH HOH . H 8 HOH A 16 616 133 HOH HOH . H 8 HOH A 17 617 11 HOH HOH . H 8 HOH A 18 618 111 HOH HOH . H 8 HOH A 19 619 41 HOH HOH . H 8 HOH A 20 620 108 HOH HOH . H 8 HOH A 21 621 129 HOH HOH . H 8 HOH A 22 622 119 HOH HOH . H 8 HOH A 23 623 15 HOH HOH . H 8 HOH A 24 624 68 HOH HOH . H 8 HOH A 25 625 100 HOH HOH . H 8 HOH A 26 626 62 HOH HOH . H 8 HOH A 27 627 4 HOH HOH . H 8 HOH A 28 628 110 HOH HOH . H 8 HOH A 29 629 40 HOH HOH . H 8 HOH A 30 630 53 HOH HOH . H 8 HOH A 31 631 1 HOH HOH . H 8 HOH A 32 632 45 HOH HOH . H 8 HOH A 33 633 135 HOH HOH . H 8 HOH A 34 634 34 HOH HOH . H 8 HOH A 35 635 31 HOH HOH . H 8 HOH A 36 636 124 HOH HOH . H 8 HOH A 37 637 20 HOH HOH . H 8 HOH A 38 638 113 HOH HOH . H 8 HOH A 39 639 81 HOH HOH . H 8 HOH A 40 640 55 HOH HOH . H 8 HOH A 41 641 58 HOH HOH . H 8 HOH A 42 642 115 HOH HOH . H 8 HOH A 43 643 122 HOH HOH . H 8 HOH A 44 644 123 HOH HOH . H 8 HOH A 45 645 83 HOH HOH . H 8 HOH A 46 646 2 HOH HOH . H 8 HOH A 47 647 116 HOH HOH . H 8 HOH A 48 648 70 HOH HOH . H 8 HOH A 49 649 118 HOH HOH . H 8 HOH A 50 650 82 HOH HOH . H 8 HOH A 51 651 17 HOH HOH . H 8 HOH A 52 652 142 HOH HOH . H 8 HOH A 53 653 137 HOH HOH . H 8 HOH A 54 654 134 HOH HOH . H 8 HOH A 55 655 89 HOH HOH . H 8 HOH A 56 656 107 HOH HOH . H 8 HOH A 57 657 44 HOH HOH . H 8 HOH A 58 658 74 HOH HOH . H 8 HOH A 59 659 95 HOH HOH . H 8 HOH A 60 660 80 HOH HOH . H 8 HOH A 61 661 67 HOH HOH . H 8 HOH A 62 662 109 HOH HOH . H 8 HOH A 63 663 72 HOH HOH . I 8 HOH B 1 601 50 HOH HOH . I 8 HOH B 2 602 28 HOH HOH . I 8 HOH B 3 603 9 HOH HOH . I 8 HOH B 4 604 71 HOH HOH . I 8 HOH B 5 605 141 HOH HOH . I 8 HOH B 6 606 148 HOH HOH . I 8 HOH B 7 607 52 HOH HOH . I 8 HOH B 8 608 130 HOH HOH . I 8 HOH B 9 609 117 HOH HOH . I 8 HOH B 10 610 59 HOH HOH . I 8 HOH B 11 611 128 HOH HOH . I 8 HOH B 12 612 12 HOH HOH . I 8 HOH B 13 613 125 HOH HOH . I 8 HOH B 14 614 103 HOH HOH . I 8 HOH B 15 615 76 HOH HOH . I 8 HOH B 16 616 140 HOH HOH . I 8 HOH B 17 617 75 HOH HOH . I 8 HOH B 18 618 27 HOH HOH . I 8 HOH B 19 619 57 HOH HOH . I 8 HOH B 20 620 104 HOH HOH . I 8 HOH B 21 621 91 HOH HOH . I 8 HOH B 22 622 96 HOH HOH . I 8 HOH B 23 623 105 HOH HOH . I 8 HOH B 24 624 98 HOH HOH . I 8 HOH B 25 625 14 HOH HOH . I 8 HOH B 26 626 10 HOH HOH . I 8 HOH B 27 627 139 HOH HOH . I 8 HOH B 28 628 86 HOH HOH . I 8 HOH B 29 629 77 HOH HOH . I 8 HOH B 30 630 63 HOH HOH . I 8 HOH B 31 631 97 HOH HOH . I 8 HOH B 32 632 32 HOH HOH . I 8 HOH B 33 633 47 HOH HOH . I 8 HOH B 34 634 143 HOH HOH . I 8 HOH B 35 635 106 HOH HOH . I 8 HOH B 36 636 90 HOH HOH . I 8 HOH B 37 637 79 HOH HOH . I 8 HOH B 38 638 60 HOH HOH . I 8 HOH B 39 639 132 HOH HOH . J 8 HOH F 1 201 18 HOH HOH . J 8 HOH F 2 202 85 HOH HOH . J 8 HOH F 3 203 5 HOH HOH . J 8 HOH F 4 204 112 HOH HOH . J 8 HOH F 5 205 16 HOH HOH . J 8 HOH F 6 206 131 HOH HOH . J 8 HOH F 7 207 127 HOH HOH . J 8 HOH F 8 208 3 HOH HOH . J 8 HOH F 9 209 19 HOH HOH . J 8 HOH F 10 210 56 HOH HOH . J 8 HOH F 11 211 65 HOH HOH . J 8 HOH F 12 212 120 HOH HOH . J 8 HOH F 13 213 92 HOH HOH . J 8 HOH F 14 214 150 HOH HOH . J 8 HOH F 15 215 42 HOH HOH . J 8 HOH F 16 216 43 HOH HOH . J 8 HOH F 17 217 23 HOH HOH . J 8 HOH F 18 218 6 HOH HOH . J 8 HOH F 19 219 35 HOH HOH . J 8 HOH F 20 220 51 HOH HOH . J 8 HOH F 21 221 49 HOH HOH . J 8 HOH F 22 222 24 HOH HOH . J 8 HOH F 23 223 114 HOH HOH . J 8 HOH F 24 224 39 HOH HOH . J 8 HOH F 25 225 33 HOH HOH . J 8 HOH F 26 226 38 HOH HOH . J 8 HOH F 27 227 37 HOH HOH . J 8 HOH F 28 228 99 HOH HOH . J 8 HOH F 29 229 87 HOH HOH . J 8 HOH F 30 230 25 HOH HOH . J 8 HOH F 31 231 54 HOH HOH . J 8 HOH F 32 232 69 HOH HOH . J 8 HOH F 33 233 146 HOH HOH . J 8 HOH F 34 234 73 HOH HOH . J 8 HOH F 35 235 145 HOH HOH . J 8 HOH F 36 236 102 HOH HOH . J 8 HOH F 37 237 26 HOH HOH . J 8 HOH F 38 238 8 HOH HOH . J 8 HOH F 39 239 64 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 . . . F 6 77.858 11.536 51.52 1 45.79 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . F 6 78.652 12.079 50.359 1 42.96 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . F 6 78.526 10.32 52.101 1 45.56 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . F 6 77.751 12.586 52.596 1 46.09 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . F 6 76.375 11.154 51.038 1 47.56 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . F 6 76.086 10.342 49.679 1 45.55 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . F 6 77.342 10.139 48.867 1 49.26 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . F 6 75.453 9.006 49.991 1 48.57 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . F 6 75.048 11.306 48.913 1 45.47 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . F 6 73.743 10.836 48.558 1 50.11 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . F 6 73.487 11.214 47.106 1 48.95 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . F 6 74.53 10.579 46.34 1 47.32 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . F 6 72.181 10.771 46.451 1 49.32 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . F 6 71.923 11.743 45.429 1 46.77 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . F 6 72.456 9.412 45.841 1 51.73 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . F 6 71.708 9.163 44.649 1 54.29 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . F 6 73.96 9.516 45.54 1 52.09 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . F 6 74.684 8.235 45.704 1 54 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . F 6 75.037 7.627 46.846 1 54.31 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . F 6 75.694 6.472 46.564 1 55.69 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . F 6 75.773 6.349 45.219 1 54.4 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . F 6 76.332 5.38 44.238 1 52.83 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . F 6 76.916 4.348 44.622 1 48.83 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . F 6 76.194 5.634 42.929 1 57.21 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . F 6 75.561 6.743 42.492 1 54.49 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . F 6 75.453 6.946 41.16 1 53.89 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . F 6 75.025 7.675 43.322 1 51.77 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . F 6 75.104 7.525 44.664 1 53.77 ? C4 GDP 501 B 1 HETATM 29 H H4' GDP . . . F 6 73.45 12.313 47.109 1 58.78 ? H4' GDP 501 B 1 HETATM 30 H H3' GDP . . . F 6 71.323 10.702 47.135 1 59.23 ? H3' GDP 501 B 1 HETATM 31 H HO3' GDP . . . F 6 71.755 11.292 44.59 1 56.16 ? HO3' GDP 501 B 1 HETATM 32 H H2' GDP . . . F 6 72.166 8.579 46.496 1 62.12 ? H2' GDP 501 B 1 HETATM 33 H HO2' GDP . . . F 6 71.397 8.247 44.649 1 65.19 ? HO2' GDP 501 B 1 HETATM 34 H H1' GDP . . . F 6 74.06 9.761 44.473 1 62.55 ? H1' GDP 501 B 1 HETATM 35 H H8 GDP . . . F 6 74.829 7.999 47.842 1 65.21 ? H8 GDP 501 B 1 HETATM 36 H HN1 GDP . . . F 6 76.583 4.963 42.236 1 68.69 ? HN1 GDP 501 B 1 HETATM 37 H HN21 GDP . . . F 6 75.839 6.274 40.517 1 64.71 ? HN21 GDP 501 B 1 HETATM 38 H HN22 GDP . . . F 6 74.989 7.77 40.811 1 64.71 ? HN22 GDP 501 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #