data_7YZ5 # _model_server_result.job_id 3Lj7UbjtwC5O-gv1umva3g _model_server_result.datetime_utc '2024-11-16 19:45:47' _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 7yz5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 7YZ5 # _exptl.entry_id 7YZ5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _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 96.82 _cell.angle_gamma 90 _cell.entry_id 7YZ5 _cell.length_a 74.28 _cell.length_b 91.87 _cell.length_c 83.69 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YZ5 _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 7 _struct_asym.id G _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 OD1 ASP 39 A ASP 39 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.03 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc5 A OE1 GLU 55 A GLU 55 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc7 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc8 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc9 E MG MG . A MG 502 1_555 H O HOH . A HOH 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc10 E MG MG . A MG 502 1_555 H O HOH . A HOH 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc11 E MG MG . A MG 502 1_555 H O HOH . A HOH 635 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc12 E MG MG . A MG 502 1_555 H O HOH . A HOH 641 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc13 F CA CA . A CA 503 1_555 H O HOH . A HOH 637 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? # _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 7YZ5 _atom_sites.fract_transf_matrix[1][1] 0.013463 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00161 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010885 _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] 0.012034 _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 CA A 1 503 1 CA CA . G 7 GDP B 1 501 501 GDP GDP . H 8 HOH A 1 601 124 HOH HOH . H 8 HOH A 2 602 26 HOH HOH . H 8 HOH A 3 603 14 HOH HOH . H 8 HOH A 4 604 153 HOH HOH . H 8 HOH A 5 605 123 HOH HOH . H 8 HOH A 6 606 34 HOH HOH . H 8 HOH A 7 607 150 HOH HOH . H 8 HOH A 8 608 27 HOH HOH . H 8 HOH A 9 609 87 HOH HOH . H 8 HOH A 10 610 136 HOH HOH . H 8 HOH A 11 611 78 HOH HOH . H 8 HOH A 12 612 24 HOH HOH . H 8 HOH A 13 613 12 HOH HOH . H 8 HOH A 14 614 104 HOH HOH . H 8 HOH A 15 615 17 HOH HOH . H 8 HOH A 16 616 65 HOH HOH . H 8 HOH A 17 617 19 HOH HOH . H 8 HOH A 18 618 33 HOH HOH . H 8 HOH A 19 619 118 HOH HOH . H 8 HOH A 20 620 66 HOH HOH . H 8 HOH A 21 621 2 HOH HOH . H 8 HOH A 22 622 5 HOH HOH . H 8 HOH A 23 623 43 HOH HOH . H 8 HOH A 24 624 133 HOH HOH . H 8 HOH A 25 625 72 HOH HOH . H 8 HOH A 26 626 121 HOH HOH . H 8 HOH A 27 627 7 HOH HOH . H 8 HOH A 28 628 47 HOH HOH . H 8 HOH A 29 629 13 HOH HOH . H 8 HOH A 30 630 1 HOH HOH . H 8 HOH A 31 631 70 HOH HOH . H 8 HOH A 32 632 35 HOH HOH . H 8 HOH A 33 633 61 HOH HOH . H 8 HOH A 34 634 101 HOH HOH . H 8 HOH A 35 635 3 HOH HOH . H 8 HOH A 36 636 157 HOH HOH . H 8 HOH A 37 637 15 HOH HOH . H 8 HOH A 38 638 132 HOH HOH . H 8 HOH A 39 639 91 HOH HOH . H 8 HOH A 40 640 96 HOH HOH . H 8 HOH A 41 641 4 HOH HOH . H 8 HOH A 42 642 90 HOH HOH . H 8 HOH A 43 643 81 HOH HOH . H 8 HOH A 44 644 50 HOH HOH . H 8 HOH A 45 645 114 HOH HOH . H 8 HOH A 46 646 117 HOH HOH . H 8 HOH A 47 647 159 HOH HOH . H 8 HOH A 48 648 20 HOH HOH . H 8 HOH A 49 649 38 HOH HOH . H 8 HOH A 50 650 31 HOH HOH . H 8 HOH A 51 651 16 HOH HOH . H 8 HOH A 52 652 93 HOH HOH . H 8 HOH A 53 653 88 HOH HOH . H 8 HOH A 54 654 40 HOH HOH . H 8 HOH A 55 655 149 HOH HOH . H 8 HOH A 56 656 97 HOH HOH . H 8 HOH A 57 657 145 HOH HOH . H 8 HOH A 58 658 53 HOH HOH . H 8 HOH A 59 659 119 HOH HOH . H 8 HOH A 60 660 37 HOH HOH . H 8 HOH A 61 661 144 HOH HOH . H 8 HOH A 62 662 95 HOH HOH . H 8 HOH A 63 663 60 HOH HOH . H 8 HOH A 64 664 107 HOH HOH . H 8 HOH A 65 665 67 HOH HOH . H 8 HOH A 66 666 151 HOH HOH . H 8 HOH A 67 667 51 HOH HOH . H 8 HOH A 68 668 100 HOH HOH . H 8 HOH A 69 669 127 HOH HOH . H 8 HOH A 70 670 57 HOH HOH . H 8 HOH A 71 671 147 HOH HOH . H 8 HOH A 72 672 62 HOH HOH . H 8 HOH A 73 673 141 HOH HOH . H 8 HOH A 74 674 74 HOH HOH . H 8 HOH A 75 675 126 HOH HOH . H 8 HOH A 76 676 109 HOH HOH . I 8 HOH B 1 601 120 HOH HOH . I 8 HOH B 2 602 155 HOH HOH . I 8 HOH B 3 603 130 HOH HOH . I 8 HOH B 4 604 92 HOH HOH . I 8 HOH B 5 605 139 HOH HOH . I 8 HOH B 6 606 85 HOH HOH . I 8 HOH B 7 607 69 HOH HOH . I 8 HOH B 8 608 75 HOH HOH . I 8 HOH B 9 609 21 HOH HOH . I 8 HOH B 10 610 148 HOH HOH . I 8 HOH B 11 611 10 HOH HOH . I 8 HOH B 12 612 22 HOH HOH . I 8 HOH B 13 613 138 HOH HOH . I 8 HOH B 14 614 112 HOH HOH . I 8 HOH B 15 615 154 HOH HOH . I 8 HOH B 16 616 49 HOH HOH . I 8 HOH B 17 617 8 HOH HOH . I 8 HOH B 18 618 102 HOH HOH . I 8 HOH B 19 619 113 HOH HOH . I 8 HOH B 20 620 48 HOH HOH . I 8 HOH B 21 621 83 HOH HOH . I 8 HOH B 22 622 9 HOH HOH . I 8 HOH B 23 623 86 HOH HOH . I 8 HOH B 24 624 39 HOH HOH . I 8 HOH B 25 625 89 HOH HOH . I 8 HOH B 26 626 105 HOH HOH . I 8 HOH B 27 627 68 HOH HOH . I 8 HOH B 28 628 142 HOH HOH . I 8 HOH B 29 629 84 HOH HOH . I 8 HOH B 30 630 98 HOH HOH . I 8 HOH B 31 631 11 HOH HOH . I 8 HOH B 32 632 110 HOH HOH . I 8 HOH B 33 633 18 HOH HOH . I 8 HOH B 34 634 71 HOH HOH . I 8 HOH B 35 635 46 HOH HOH . I 8 HOH B 36 636 36 HOH HOH . I 8 HOH B 37 637 122 HOH HOH . I 8 HOH B 38 638 99 HOH HOH . I 8 HOH B 39 639 106 HOH HOH . I 8 HOH B 40 640 108 HOH HOH . I 8 HOH B 41 641 63 HOH HOH . J 8 HOH F 1 201 28 HOH HOH . J 8 HOH F 2 202 77 HOH HOH . J 8 HOH F 3 203 79 HOH HOH . J 8 HOH F 4 204 41 HOH HOH . J 8 HOH F 5 205 55 HOH HOH . J 8 HOH F 6 206 103 HOH HOH . J 8 HOH F 7 207 58 HOH HOH . J 8 HOH F 8 208 125 HOH HOH . J 8 HOH F 9 209 56 HOH HOH . J 8 HOH F 10 210 32 HOH HOH . J 8 HOH F 11 211 23 HOH HOH . J 8 HOH F 12 212 6 HOH HOH . J 8 HOH F 13 213 29 HOH HOH . J 8 HOH F 14 214 82 HOH HOH . J 8 HOH F 15 215 52 HOH HOH . J 8 HOH F 16 216 44 HOH HOH . J 8 HOH F 17 217 94 HOH HOH . J 8 HOH F 18 218 73 HOH HOH . J 8 HOH F 19 219 129 HOH HOH . J 8 HOH F 20 220 45 HOH HOH . J 8 HOH F 21 221 59 HOH HOH . J 8 HOH F 22 222 30 HOH HOH . J 8 HOH F 23 223 25 HOH HOH . J 8 HOH F 24 224 54 HOH HOH . J 8 HOH F 25 225 111 HOH HOH . J 8 HOH F 26 226 64 HOH HOH . J 8 HOH F 27 227 143 HOH HOH . J 8 HOH F 28 228 128 HOH HOH . J 8 HOH F 29 229 42 HOH HOH . J 8 HOH F 30 230 116 HOH HOH . J 8 HOH F 31 231 140 HOH HOH . J 8 HOH F 32 232 152 HOH HOH . J 8 HOH F 33 233 146 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 . . . G 7 27.882 -23.38 -10.012 1 35.39 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . G 7 28.108 -22.277 -11.019 1 36.62 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . G 7 27.235 -24.551 -10.714 1 43.16 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . G 7 26.99 -22.86 -8.91 1 33.19 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . G 7 29.314 -23.825 -9.427 1 34.37 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . G 7 29.484 -24.574 -8.011 1 34.37 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . G 7 30.1 -25.939 -8.206 1 30.75 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . G 7 28.165 -24.695 -7.285 1 34.34 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . G 7 30.501 -23.617 -7.208 1 49.3 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . G 7 31.8 -24.084 -6.854 1 39.32 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . G 7 32.08 -23.77 -5.394 1 26.88 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . G 7 31.064 -24.398 -4.613 1 32.55 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . G 7 33.41 -24.358 -4.965 1 32.72 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . G 7 34.138 -23.399 -4.193 1 40.26 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . G 7 33.07 -25.553 -4.1 1 27.85 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . G 7 33.923 -25.585 -2.953 1 43.57 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . G 7 31.622 -25.339 -3.692 1 30.53 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . G 7 30.845 -26.6 -3.768 1 31.63 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . G 7 30.458 -27.219 -4.899 1 40.8 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . G 7 29.751 -28.346 -4.624 1 37.59 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . G 7 29.673 -28.456 -3.285 1 34.14 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . G 7 29.069 -29.408 -2.324 1 32.07 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . G 7 28.441 -30.414 -2.719 1 32.13 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . G 7 29.216 -29.159 -1.017 1 37.6 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . G 7 29.886 -28.085 -0.558 1 36.75 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . G 7 29.989 -27.905 0.782 1 35.37 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . G 7 30.463 -27.173 -1.381 1 33.43 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . G 7 30.391 -27.302 -2.727 1 35.06 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #