data_8CQB # _model_server_result.job_id SmE0tojzzzElOyHwZVZ8_g _model_server_result.datetime_utc '2024-10-12 17:19:36' _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 8cqb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 8CQB # _exptl.entry_id 8CQB _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 C N N ? 2 F 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 covale ? covale1 B NH2 ARG 48 B ARG 48 1_555 F O1A GDP . B GDP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? metalc ? metalc1 A OG SER 52 A SER 52 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc2 A OG1 THR 75 A THR 75 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc3 B OG SER 52 B SER 52 1_555 H MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc4 B OG1 THR 75 B THR 75 1_555 H MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc5 B OD2 ASP 97 B ASP 97 1_555 H MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc6 F O2B GDP . B GDP 601 1_555 H MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? # _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 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 8CQB _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 C 2 GDP A 1 601 1 GDP GDP . D 3 AF3 A 1 602 2 AF3 AF3 . E 4 MG A 1 603 3 MG MG . F 2 GDP B 1 601 1 GDP GDP . G 3 AF3 B 1 602 2 AF3 AF3 . H 4 MG B 1 603 3 MG MG . # 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 2 132.98 148.908 175.146 1 28.46 ? PB GDP 601 B 1 HETATM 2 O O1B GDP . . . F 2 133.95 148.305 174.159 1 28.46 ? O1B GDP 601 B 1 HETATM 3 O O2B GDP . . . F 2 133.152 150.408 175.139 1 28.46 ? O2B GDP 601 B 1 HETATM 4 O O3B GDP . . . F 2 131.577 148.547 174.719 1 28.46 ? O3B GDP 601 B 1 HETATM 5 O O3A GDP . . . F 2 133.301 148.336 176.617 1 28.46 ? O3A GDP 601 B 1 HETATM 6 P PA GDP . . . F 2 132.211 148.46 177.795 1 28.46 ? PA GDP 601 B 1 HETATM 7 O O1A GDP . . . F 2 130.802 148.335 177.269 1 28.46 ? O1A GDP 601 B 1 HETATM 8 O O2A GDP . . . F 2 132.393 149.771 178.521 1 28.46 ? O2A GDP 601 B 1 HETATM 9 O O5' GDP . . . F 2 132.52 147.23 178.783 1 28.46 ? O5' GDP 601 B 1 HETATM 10 C C5' GDP . . . F 2 131.407 146.438 179.185 1 28.46 ? C5' GDP 601 B 1 HETATM 11 C C4' GDP . . . F 2 131.63 145.768 180.533 1 28.46 ? C4' GDP 601 B 1 HETATM 12 O O4' GDP . . . F 2 132.854 145.035 180.563 1 28.46 ? O4' GDP 601 B 1 HETATM 13 C C3' GDP . . . F 2 131.712 146.765 181.678 1 28.46 ? C3' GDP 601 B 1 HETATM 14 O O3' GDP . . . F 2 130.457 146.831 182.359 1 28.46 ? O3' GDP 601 B 1 HETATM 15 C C2' GDP . . . F 2 132.778 146.208 182.6 1 28.46 ? C2' GDP 601 B 1 HETATM 16 O O2' GDP . . . F 2 132.22 145.935 183.887 1 28.46 ? O2' GDP 601 B 1 HETATM 17 C C1' GDP . . . F 2 133.231 144.916 181.935 1 28.46 ? C1' GDP 601 B 1 HETATM 18 N N9 GDP . . . F 2 134.691 144.713 182.099 1 28.46 ? N9 GDP 601 B 1 HETATM 19 C C8 GDP . . . F 2 135.549 145.554 182.705 1 28.46 ? C8 GDP 601 B 1 HETATM 20 N N7 GDP . . . F 2 136.814 145.061 182.682 1 28.46 ? N7 GDP 601 B 1 HETATM 21 C C5 GDP . . . F 2 136.775 143.88 182.038 1 28.46 ? C5 GDP 601 B 1 HETATM 22 C C6 GDP . . . F 2 137.755 142.835 181.658 1 28.46 ? C6 GDP 601 B 1 HETATM 23 O O6 GDP . . . F 2 138.965 142.953 181.948 1 28.46 ? O6 GDP 601 B 1 HETATM 24 N N1 GDP . . . F 2 137.304 141.763 180.995 1 28.46 ? N1 GDP 601 B 1 HETATM 25 C C2 GDP . . . F 2 136.006 141.61 180.669 1 28.46 ? C2 GDP 601 B 1 HETATM 26 N N2 GDP . . . F 2 135.632 140.494 179.997 1 28.46 ? N2 GDP 601 B 1 HETATM 27 N N3 GDP . . . F 2 135.055 142.526 180.985 1 28.46 ? N3 GDP 601 B 1 HETATM 28 C C4 GDP . . . F 2 135.374 143.657 181.655 1 28.46 ? C4 GDP 601 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #