data_8SSL # _model_server_result.job_id ogJXN7tlJ1GaqK9mqxn6xw _model_server_result.datetime_utc '2025-01-02 22:36:51' _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 8ssl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1101}' # _entry.id 8SSL # _exptl.entry_id 8SSL _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 8SSL _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SSL _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 ? _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 ? 2 D N N ? 2 F N N ? 2 G 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 A OD1 ASP 282 A ASP 262 1_555 E MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc2 D O2B GDP . A GDP 1101 1_555 E MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc3 D O3B GDP . A GDP 1101 1_555 E MG MG . A MG 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? # _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 8SSL _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 2 GDP A 1 1101 1102 GDP GDP . E 3 MG A 1 1102 1103 MG MG . F 2 GDP B 1 1101 1101 GDP GDP . G 2 GDP C 1 1101 1101 GDP GDP . # 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 . . . D 2 158.339 129.112 127.348 1 68.95 ? PB GDP 1101 A 1 HETATM 2 O O1B GDP . . . D 2 157.544 129.764 126.248 1 67.66 ? O1B GDP 1101 A 1 HETATM 3 O O2B GDP . . . D 2 157.756 127.759 127.669 1 71.26 ? O2B GDP 1101 A 1 HETATM 4 O O3B GDP . . . D 2 159.771 128.943 126.909 1 65.15 ? O3B GDP 1101 A 1 HETATM 5 O O3A GDP . . . D 2 158.267 130.031 128.657 1 76.64 ? O3A GDP 1101 A 1 HETATM 6 P PA GDP . . . D 2 156.867 130.079 129.435 1 76.12 ? PA GDP 1101 A 1 HETATM 7 O O1A GDP . . . D 2 155.731 129.857 128.472 1 72.26 ? O1A GDP 1101 A 1 HETATM 8 O O2A GDP . . . D 2 156.855 129.051 130.531 1 79.97 ? O2A GDP 1101 A 1 HETATM 9 O O5' GDP . . . D 2 156.782 131.541 130.082 1 53.46 ? O5' GDP 1101 A 1 HETATM 10 C C5' GDP . . . D 2 155.884 131.755 131.162 1 55.93 ? C5' GDP 1101 A 1 HETATM 11 C C4' GDP . . . D 2 156.184 133.118 131.754 1 54.41 ? C4' GDP 1101 A 1 HETATM 12 O O4' GDP . . . D 2 155.948 134.115 130.767 1 54.2 ? O4' GDP 1101 A 1 HETATM 13 C C3' GDP . . . D 2 155.277 133.436 132.925 1 55.26 ? C3' GDP 1101 A 1 HETATM 14 O O3' GDP . . . D 2 155.988 133.265 134.151 1 60.95 ? O3' GDP 1101 A 1 HETATM 15 C C2' GDP . . . D 2 154.894 134.888 132.744 1 51.57 ? C2' GDP 1101 A 1 HETATM 16 O O2' GDP . . . D 2 155.551 135.7 133.719 1 55.17 ? O2' GDP 1101 A 1 HETATM 17 C C1' GDP . . . D 2 155.371 135.274 131.36 1 52.55 ? C1' GDP 1101 A 1 HETATM 18 N N9 GDP . . . D 2 154.185 135.669 130.583 1 57.64 ? N9 GDP 1101 A 1 HETATM 19 C C8 GDP . . . D 2 153.389 134.83 129.907 1 62.17 ? C8 GDP 1101 A 1 HETATM 20 N N7 GDP . . . D 2 152.379 135.502 129.305 1 64.5 ? N7 GDP 1101 A 1 HETATM 21 C C5 GDP . . . D 2 152.532 136.801 129.602 1 63.5 ? C5 GDP 1101 A 1 HETATM 22 C C6 GDP . . . D 2 151.818 138.051 129.288 1 67.01 ? C6 GDP 1101 A 1 HETATM 23 O O6 GDP . . . D 2 150.793 138.036 128.576 1 72.68 ? O6 GDP 1101 A 1 HETATM 24 N N1 GDP . . . D 2 152.301 139.187 129.797 1 61.75 ? N1 GDP 1101 A 1 HETATM 25 C C2 GDP . . . D 2 153.401 139.216 130.568 1 55.88 ? C2 GDP 1101 A 1 HETATM 26 N N2 GDP . . . D 2 153.831 140.405 131.046 1 54.41 ? N2 GDP 1101 A 1 HETATM 27 N N3 GDP . . . D 2 154.106 138.111 130.895 1 57.01 ? N3 GDP 1101 A 1 HETATM 28 C C4 GDP . . . D 2 153.722 136.902 130.448 1 59.78 ? C4 GDP 1101 A 1 # _model_server_stats.io_time_ms 185 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #