data_8FC9 # _model_server_result.job_id r5d6oEcZqFfBtV631GNZCg _model_server_result.datetime_utc '2024-10-11 06:16:59' _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 8fc9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":302}' # _entry.id 8FC9 # _exptl.entry_id 8FC9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 8FC9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8FC9 _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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,L,M,N,O,P _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 ? 4 J N N ? 4 L N N ? 4 N N N ? 4 P 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 19 E THR 19 1_555 I MG MG . E MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc2 B O THR 37 E THR 37 1_555 I MG MG . E MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc3 I MG MG . E MG 301 1_555 J O1B GDP . E GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc4 C OG1 THR 19 F THR 19 1_555 K MG MG . F MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc5 C O THR 37 F THR 37 1_555 K MG MG . F MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc6 K MG MG . F MG 301 1_555 L O1B GDP . F GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc7 D OG1 THR 19 G THR 19 1_555 M MG MG . G MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc8 D O THR 37 G THR 37 1_555 M MG MG . G MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc9 M MG MG . G MG 301 1_555 N O1B GDP . G GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc10 E OG1 THR 19 H THR 19 1_555 O MG MG . H MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc11 E O THR 37 H THR 37 1_555 O MG MG . H MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc12 O MG MG . H MG 301 1_555 P O1B GDP . H GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? # _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 8FC9 _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 I 3 MG E 1 301 301 MG MG . J 4 GDP E 1 302 302 GDP GDP . K 3 MG F 1 301 301 MG MG . L 4 GDP F 1 302 302 GDP GDP . M 3 MG G 1 301 301 MG MG . N 4 GDP G 1 302 302 GDP GDP . O 3 MG H 1 301 301 MG MG . P 4 GDP H 1 302 302 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 . . . N 4 67.186 109.616 120.746 1 162.49 ? PB GDP 302 G 1 HETATM 2 O O1B GDP . . . N 4 68.371 110.166 119.99 1 162.49 ? O1B GDP 302 G 1 HETATM 3 O O2B GDP . . . N 4 67.299 109.987 122.203 1 162.49 ? O2B GDP 302 G 1 HETATM 4 O O3B GDP . . . N 4 67.163 108.112 120.618 1 162.49 ? O3B GDP 302 G 1 HETATM 5 O O3A GDP . . . N 4 65.823 110.218 120.136 1 162.49 ? O3A GDP 302 G 1 HETATM 6 P PA GDP . . . N 4 65.516 110.026 118.57 1 162.49 ? PA GDP 302 G 1 HETATM 7 O O1A GDP . . . N 4 65.891 111.275 117.81 1 162.49 ? O1A GDP 302 G 1 HETATM 8 O O2A GDP . . . N 4 66.277 108.839 118.031 1 162.49 ? O2A GDP 302 G 1 HETATM 9 O O5' GDP . . . N 4 63.924 109.776 118.503 1 162.49 ? O5' GDP 302 G 1 HETATM 10 C C5' GDP . . . N 4 63.45 108.537 117.978 1 162.49 ? C5' GDP 302 G 1 HETATM 11 C C4' GDP . . . N 4 62.045 108.638 117.388 1 162.49 ? C4' GDP 302 G 1 HETATM 12 O O4' GDP . . . N 4 61.256 109.635 118.04 1 162.49 ? O4' GDP 302 G 1 HETATM 13 C C3' GDP . . . N 4 62.08 109.028 115.916 1 162.49 ? C3' GDP 302 G 1 HETATM 14 O O3' GDP . . . N 4 62.01 107.877 115.065 1 162.49 ? O3' GDP 302 G 1 HETATM 15 C C2' GDP . . . N 4 60.903 109.971 115.714 1 162.49 ? C2' GDP 302 G 1 HETATM 16 O O2' GDP . . . N 4 59.857 109.461 114.888 1 162.49 ? O2' GDP 302 G 1 HETATM 17 C C1' GDP . . . N 4 60.307 110.146 117.094 1 162.49 ? C1' GDP 302 G 1 HETATM 18 N N9 GDP . . . N 4 60.007 111.579 117.288 1 162.49 ? N9 GDP 302 G 1 HETATM 19 C C8 GDP . . . N 4 60.859 112.492 117.787 1 162.49 ? C8 GDP 302 G 1 HETATM 20 N N7 GDP . . . N 4 60.27 113.715 117.826 1 162.49 ? N7 GDP 302 G 1 HETATM 21 C C5 GDP . . . N 4 59.021 113.587 117.341 1 162.49 ? C5 GDP 302 G 1 HETATM 22 C C6 GDP . . . N 4 57.866 114.485 117.105 1 162.49 ? C6 GDP 302 G 1 HETATM 23 O O6 GDP . . . N 4 57.939 115.7 117.385 1 162.49 ? O6 GDP 302 G 1 HETATM 24 N N1 GDP . . . N 4 56.748 113.96 116.585 1 162.49 ? N1 GDP 302 G 1 HETATM 25 C C2 GDP . . . N 4 56.649 112.653 116.275 1 162.49 ? C2 GDP 302 G 1 HETATM 26 N N2 GDP . . . N 4 55.482 112.2 115.752 1 162.49 ? N2 GDP 302 G 1 HETATM 27 N N3 GDP . . . N 4 57.666 111.77 116.464 1 162.49 ? N3 GDP 302 G 1 HETATM 28 C C4 GDP . . . N 4 58.852 112.174 116.982 1 162.49 ? C4 GDP 302 G 1 HETATM 29 H H5' GDP . . . N 4 63.455 107.786 118.769 1 162.48 ? H5' GDP 302 G 1 HETATM 30 H "H5''" GDP . . . N 4 64.138 108.199 117.2 1 162.48 ? "H5''" GDP 302 G 1 HETATM 31 H H4' GDP . . . N 4 61.559 107.657 117.479 1 162.48 ? H4' GDP 302 G 1 HETATM 32 H H3' GDP . . . N 4 63.015 109.582 115.74 1 162.48 ? H3' GDP 302 G 1 HETATM 33 H HO3' GDP . . . N 4 62.237 108.127 114.157 1 162.48 ? HO3' GDP 302 G 1 HETATM 34 H H2' GDP . . . N 4 61.266 110.94 115.337 1 162.48 ? H2' GDP 302 G 1 HETATM 35 H HO2' GDP . . . N 4 60.158 109.344 113.989 1 162.48 ? HO2' GDP 302 G 1 HETATM 36 H H1' GDP . . . N 4 59.381 109.558 117.139 1 162.48 ? H1' GDP 302 G 1 HETATM 37 H H8 GDP . . . N 4 61.869 112.275 118.111 1 162.48 ? H8 GDP 302 G 1 HETATM 38 H HN1 GDP . . . N 4 55.933 114.581 116.416 1 162.48 ? HN1 GDP 302 G 1 HETATM 39 H HN21 GDP . . . N 4 54.712 112.836 115.603 1 162.48 ? HN21 GDP 302 G 1 HETATM 40 H HN22 GDP . . . N 4 55.38 111.224 115.511 1 162.48 ? HN22 GDP 302 G 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 22 _model_server_stats.element_count 40 #