data_8SGD # _model_server_result.job_id lkZYVfUqPmYi-WwHdYqJMA _model_server_result.datetime_utc '2025-08-01 23:41:41' _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 8sgd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 8SGD # _exptl.entry_id 8SGD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 8SGD _cell.length_a 58.277 _cell.length_b 154.271 _cell.length_c 156.264 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SGD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,K,L,M,X,Y 1 1 C,D,N,O,P,Q,R,S,T,U,V,W,Z,AA 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 N N 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 B OG1 THR 29 B THR 133 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc2 I O1G GTP . B GTP 501 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc3 I O2B GTP . B GTP 501 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc4 J MG MG . B MG 502 1_555 Y O HOH . B HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc5 J MG MG . B MG 502 1_555 Y O HOH . B HOH 637 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc6 C OE2 GLU 276 C GLU 285 1_555 Q NA NA . C NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc7 D OG1 THR 29 D THR 133 1_555 V MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc8 U O1G GTP . D GTP 501 1_555 V MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc9 U O2B GTP . D GTP 501 1_555 V MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? # _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 8SGD _atom_sites.fract_transf_matrix[1][1] 0.017159 _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] 0.006482 _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] 0.006399 _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 E 3 GDP A 1 401 401 GDP GDP . F 4 NA A 1 402 1 NA NA . G 4 NA A 1 403 2 NA NA . H 4 NA A 1 404 3 NA NA . I 5 GTP B 1 501 501 GTP GTP . J 6 MG B 1 502 502 MG MG . K 4 NA B 1 503 4 NA NA . L 4 NA B 1 504 5 NA NA . M 4 NA B 1 505 6 NA NA . N 3 GDP C 1 401 401 GDP GDP . O 4 NA C 1 402 7 NA NA . P 4 NA C 1 403 8 NA NA . Q 4 NA C 1 404 9 NA NA . R 4 NA C 1 405 10 NA NA . S 4 NA C 1 406 11 NA NA . T 4 NA C 1 407 13 NA NA . U 5 GTP D 1 501 501 GTP GTP . V 6 MG D 1 502 502 MG MG . W 4 NA D 1 503 12 NA NA . X 7 HOH A 1 501 21 HOH HOH . X 7 HOH A 2 502 107 HOH HOH . X 7 HOH A 3 503 119 HOH HOH . X 7 HOH A 4 504 89 HOH HOH . X 7 HOH A 5 505 16 HOH HOH . X 7 HOH A 6 506 74 HOH HOH . X 7 HOH A 7 507 52 HOH HOH . X 7 HOH A 8 508 7 HOH HOH . X 7 HOH A 9 509 17 HOH HOH . X 7 HOH A 10 510 55 HOH HOH . X 7 HOH A 11 511 69 HOH HOH . X 7 HOH A 12 512 151 HOH HOH . X 7 HOH A 13 513 12 HOH HOH . X 7 HOH A 14 514 32 HOH HOH . X 7 HOH A 15 515 8 HOH HOH . X 7 HOH A 16 516 77 HOH HOH . X 7 HOH A 17 517 62 HOH HOH . X 7 HOH A 18 518 92 HOH HOH . X 7 HOH A 19 519 116 HOH HOH . X 7 HOH A 20 520 102 HOH HOH . X 7 HOH A 21 521 86 HOH HOH . X 7 HOH A 22 522 105 HOH HOH . X 7 HOH A 23 523 49 HOH HOH . X 7 HOH A 24 524 127 HOH HOH . X 7 HOH A 25 525 75 HOH HOH . X 7 HOH A 26 526 123 HOH HOH . X 7 HOH A 27 527 108 HOH HOH . X 7 HOH A 28 528 143 HOH HOH . X 7 HOH A 29 529 2 HOH HOH . X 7 HOH A 30 530 65 HOH HOH . X 7 HOH A 31 531 79 HOH HOH . X 7 HOH A 32 532 132 HOH HOH . X 7 HOH A 33 533 71 HOH HOH . X 7 HOH A 34 534 130 HOH HOH . X 7 HOH A 35 535 38 HOH HOH . X 7 HOH A 36 536 22 HOH HOH . X 7 HOH A 37 537 96 HOH HOH . X 7 HOH A 38 538 152 HOH HOH . X 7 HOH A 39 539 88 HOH HOH . Y 7 HOH B 1 601 126 HOH HOH . Y 7 HOH B 2 602 33 HOH HOH . Y 7 HOH B 3 603 98 HOH HOH . Y 7 HOH B 4 604 148 HOH HOH . Y 7 HOH B 5 605 146 HOH HOH . Y 7 HOH B 6 606 14 HOH HOH . Y 7 HOH B 7 607 15 HOH HOH . Y 7 HOH B 8 608 106 HOH HOH . Y 7 HOH B 9 609 147 HOH HOH . Y 7 HOH B 10 610 48 HOH HOH . Y 7 HOH B 11 611 6 HOH HOH . Y 7 HOH B 12 612 99 HOH HOH . Y 7 HOH B 13 613 104 HOH HOH . Y 7 HOH B 14 614 27 HOH HOH . Y 7 HOH B 15 615 83 HOH HOH . Y 7 HOH B 16 616 120 HOH HOH . Y 7 HOH B 17 617 46 HOH HOH . Y 7 HOH B 18 618 26 HOH HOH . Y 7 HOH B 19 619 110 HOH HOH . Y 7 HOH B 20 620 109 HOH HOH . Y 7 HOH B 21 621 81 HOH HOH . Y 7 HOH B 22 622 24 HOH HOH . Y 7 HOH B 23 623 68 HOH HOH . Y 7 HOH B 24 624 70 HOH HOH . Y 7 HOH B 25 625 97 HOH HOH . Y 7 HOH B 26 626 13 HOH HOH . Y 7 HOH B 27 627 36 HOH HOH . Y 7 HOH B 28 628 111 HOH HOH . Y 7 HOH B 29 629 122 HOH HOH . Y 7 HOH B 30 630 125 HOH HOH . Y 7 HOH B 31 631 100 HOH HOH . Y 7 HOH B 32 632 142 HOH HOH . Y 7 HOH B 33 633 47 HOH HOH . Y 7 HOH B 34 634 153 HOH HOH . Y 7 HOH B 35 635 113 HOH HOH . Y 7 HOH B 36 636 34 HOH HOH . Y 7 HOH B 37 637 85 HOH HOH . Y 7 HOH B 38 638 63 HOH HOH . Y 7 HOH B 39 639 138 HOH HOH . Y 7 HOH B 40 640 43 HOH HOH . Y 7 HOH B 41 641 144 HOH HOH . Y 7 HOH B 42 642 3 HOH HOH . Y 7 HOH B 43 643 80 HOH HOH . Y 7 HOH B 44 644 66 HOH HOH . Y 7 HOH B 45 645 121 HOH HOH . Y 7 HOH B 46 646 129 HOH HOH . Y 7 HOH B 47 647 154 HOH HOH . Y 7 HOH B 48 648 76 HOH HOH . Y 7 HOH B 49 649 124 HOH HOH . Z 7 HOH C 1 501 10 HOH HOH . Z 7 HOH C 2 502 117 HOH HOH . Z 7 HOH C 3 503 87 HOH HOH . Z 7 HOH C 4 504 78 HOH HOH . Z 7 HOH C 5 505 54 HOH HOH . Z 7 HOH C 6 506 41 HOH HOH . Z 7 HOH C 7 507 60 HOH HOH . Z 7 HOH C 8 508 4 HOH HOH . Z 7 HOH C 9 509 23 HOH HOH . Z 7 HOH C 10 510 61 HOH HOH . Z 7 HOH C 11 511 57 HOH HOH . Z 7 HOH C 12 512 118 HOH HOH . Z 7 HOH C 13 513 28 HOH HOH . Z 7 HOH C 14 514 50 HOH HOH . Z 7 HOH C 15 515 53 HOH HOH . Z 7 HOH C 16 516 37 HOH HOH . Z 7 HOH C 17 517 114 HOH HOH . Z 7 HOH C 18 518 128 HOH HOH . Z 7 HOH C 19 519 115 HOH HOH . Z 7 HOH C 20 520 72 HOH HOH . Z 7 HOH C 21 521 25 HOH HOH . Z 7 HOH C 22 522 101 HOH HOH . Z 7 HOH C 23 523 112 HOH HOH . Z 7 HOH C 24 524 145 HOH HOH . Z 7 HOH C 25 525 31 HOH HOH . Z 7 HOH C 26 526 149 HOH HOH . Z 7 HOH C 27 527 103 HOH HOH . Z 7 HOH C 28 528 51 HOH HOH . Z 7 HOH C 29 529 58 HOH HOH . Z 7 HOH C 30 530 135 HOH HOH . Z 7 HOH C 31 531 134 HOH HOH . Z 7 HOH C 32 532 35 HOH HOH . Z 7 HOH C 33 533 137 HOH HOH . Z 7 HOH C 34 534 139 HOH HOH . Z 7 HOH C 35 535 136 HOH HOH . Z 7 HOH C 36 536 30 HOH HOH . Z 7 HOH C 37 537 91 HOH HOH . Z 7 HOH C 38 538 82 HOH HOH . Z 7 HOH C 39 539 84 HOH HOH . AA 7 HOH D 1 601 29 HOH HOH . AA 7 HOH D 2 602 95 HOH HOH . AA 7 HOH D 3 603 56 HOH HOH . AA 7 HOH D 4 604 19 HOH HOH . AA 7 HOH D 5 605 156 HOH HOH . AA 7 HOH D 6 606 9 HOH HOH . AA 7 HOH D 7 607 42 HOH HOH . AA 7 HOH D 8 608 1 HOH HOH . AA 7 HOH D 9 609 140 HOH HOH . AA 7 HOH D 10 610 44 HOH HOH . AA 7 HOH D 11 611 150 HOH HOH . AA 7 HOH D 12 612 18 HOH HOH . AA 7 HOH D 13 613 11 HOH HOH . AA 7 HOH D 14 614 20 HOH HOH . AA 7 HOH D 15 615 59 HOH HOH . AA 7 HOH D 16 616 39 HOH HOH . AA 7 HOH D 17 617 93 HOH HOH . AA 7 HOH D 18 618 90 HOH HOH . AA 7 HOH D 19 619 94 HOH HOH . AA 7 HOH D 20 620 64 HOH HOH . AA 7 HOH D 21 621 73 HOH HOH . AA 7 HOH D 22 622 40 HOH HOH . AA 7 HOH D 23 623 45 HOH HOH . AA 7 HOH D 24 624 157 HOH HOH . AA 7 HOH D 25 625 5 HOH HOH . AA 7 HOH D 26 626 131 HOH HOH . AA 7 HOH D 27 627 133 HOH HOH . AA 7 HOH D 28 628 155 HOH HOH . AA 7 HOH D 29 629 67 HOH HOH . AA 7 HOH D 30 630 141 HOH HOH . AA 7 HOH D 31 631 158 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 . . . N 3 -19.927 -11.092 30.448 1 44.26 ? PB GDP 401 C 1 HETATM 2 O O1B GDP . . . N 3 -18.529 -10.533 30.328 1 51.26 ? O1B GDP 401 C 1 HETATM 3 O O2B GDP . . . N 3 -19.831 -12.539 30.87 1 48.04 ? O2B GDP 401 C 1 HETATM 4 O O3B GDP . . . N 3 -20.703 -10.315 31.481 1 46.57 ? O3B GDP 401 C 1 HETATM 5 O O3A GDP . . . N 3 -20.668 -10.999 29.021 1 46.95 ? O3A GDP 401 C 1 HETATM 6 P PA GDP . . . N 3 -22.234 -10.635 28.88 1 46 ? PA GDP 401 C 1 HETATM 7 O O1A GDP . . . N 3 -22.453 -9.15 28.706 1 43.31 ? O1A GDP 401 C 1 HETATM 8 O O2A GDP . . . N 3 -23.025 -11.152 30.056 1 43.24 ? O2A GDP 401 C 1 HETATM 9 O O5' GDP . . . N 3 -22.634 -11.4 27.524 1 52.35 ? O5' GDP 401 C 1 HETATM 10 C C5' GDP . . . N 3 -21.953 -11.062 26.319 1 38.05 ? C5' GDP 401 C 1 HETATM 11 C C4' GDP . . . N 3 -22.837 -11.404 25.136 1 46.44 ? C4' GDP 401 C 1 HETATM 12 O O4' GDP . . . N 3 -23.246 -12.764 25.246 1 39.34 ? O4' GDP 401 C 1 HETATM 13 C C3' GDP . . . N 3 -24.091 -10.555 25.167 1 40.22 ? C3' GDP 401 C 1 HETATM 14 O O3' GDP . . . N 3 -24.223 -9.882 23.913 1 54.7 ? O3' GDP 401 C 1 HETATM 15 C C2' GDP . . . N 3 -25.24 -11.522 25.378 1 42 ? C2' GDP 401 C 1 HETATM 16 O O2' GDP . . . N 3 -26.332 -11.203 24.513 1 58.38 ? O2' GDP 401 C 1 HETATM 17 C C1' GDP . . . N 3 -24.654 -12.885 25.047 1 44.4 ? C1' GDP 401 C 1 HETATM 18 N N9 GDP . . . N 3 -25.188 -13.953 25.928 1 46.69 ? N9 GDP 401 C 1 HETATM 19 C C8 GDP . . . N 3 -25.407 -13.887 27.255 1 47.77 ? C8 GDP 401 C 1 HETATM 20 N N7 GDP . . . N 3 -25.889 -15.069 27.728 1 42.72 ? N7 GDP 401 C 1 HETATM 21 C C5 GDP . . . N 3 -25.97 -15.92 26.687 1 46.26 ? C5 GDP 401 C 1 HETATM 22 C C6 GDP . . . N 3 -26.39 -17.325 26.467 1 48.39 ? C6 GDP 401 C 1 HETATM 23 O O6 GDP . . . N 3 -26.801 -18.031 27.41 1 47.56 ? O6 GDP 401 C 1 HETATM 24 N N1 GDP . . . N 3 -26.316 -17.823 25.227 1 47.96 ? N1 GDP 401 C 1 HETATM 25 C C2 GDP . . . N 3 -25.878 -17.091 24.187 1 45.45 ? C2 GDP 401 C 1 HETATM 26 N N2 GDP . . . N 3 -25.833 -17.661 22.96 1 57.77 ? N2 GDP 401 C 1 HETATM 27 N N3 GDP . . . N 3 -25.478 -15.802 24.313 1 45.93 ? N3 GDP 401 C 1 HETATM 28 C C4 GDP . . . N 3 -25.501 -15.178 25.511 1 46.72 ? C4 GDP 401 C 1 # _model_server_stats.io_time_ms 90 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 30 _model_server_stats.element_count 28 #