data_8UQO # _model_server_result.job_id X84gbOrKNO4ewrsC9JPrkg _model_server_result.datetime_utc '2024-11-14 18:57:46' _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 8uqo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 8UQO # _exptl.entry_id 8UQO _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 90 _cell.angle_gamma 90 _cell.entry_id 8UQO _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8UQO _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,H,I,J,K _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 # _struct_asym.details ? _struct_asym.entity_id 5 _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 E OG SER 49 A SER 53 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc2 E OG1 THR 182 A THR 186 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc3 G O2B GDP . A GDP 401 1_555 I MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc4 F OD1 ASN 333 Q ASN 333 1_555 J CA CA . Q CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3 ? metalc ? metalc5 F OE1 GLU 362 Q GLU 362 1_555 J CA CA . Q CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc6 F OD2 ASP 364 Q ASP 364 1_555 J CA CA . Q CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc7 F OE1 GLU 413 Q GLU 413 1_555 J CA CA . Q CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc8 F OE2 GLU 413 Q GLU 413 1_555 J CA CA . Q CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 8UQO _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 G 5 GDP A 1 401 401 GDP GDP . H 6 ALF A 1 402 402 ALF ALF . I 7 MG A 1 403 403 MG MG . J 8 CA Q 1 1301 1301 CA CA . K 9 HOH A 1 501 404 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 5 162.902 138.354 178.988 1 43.24 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . G 5 163.073 139.129 177.717 1 43.24 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . G 5 162.086 137.122 178.707 1 43.24 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . G 5 162.109 139.243 179.906 1 43.24 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . G 5 164.326 137.991 179.648 1 43.24 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . G 5 165.546 137.448 178.758 1 43.24 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . G 5 165.638 138.061 177.395 1 43.24 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . G 5 165.459 135.96 178.634 1 43.24 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . G 5 166.883 137.845 179.529 1 43.24 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . G 5 167.699 138.782 178.84 1 43.24 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . G 5 169.164 138.435 178.939 1 43.24 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . G 5 169.654 138.711 180.242 1 43.24 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . G 5 169.307 136.953 178.731 1 43.24 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . G 5 170.112 136.709 177.582 1 43.24 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . G 5 170.025 136.482 179.962 1 43.24 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . G 5 171.069 135.578 179.644 1 43.24 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . G 5 170.621 137.726 180.538 1 43.24 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . G 5 170.716 137.441 181.962 1 43.24 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . G 5 169.695 137.11 182.749 1 43.24 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . G 5 170.116 136.892 184.012 1 43.24 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . G 5 171.437 137.082 184.022 1 43.24 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . G 5 172.5 137.013 185.029 1 43.24 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . G 5 172.224 136.712 186.204 1 43.24 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . G 5 173.749 137.275 184.653 1 43.24 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . G 5 174.051 137.596 183.393 1 43.24 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . G 5 175.341 137.845 183.096 1 43.24 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . G 5 173.127 137.68 182.412 1 43.24 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . G 5 171.829 137.438 182.668 1 43.24 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #