data_5OAM # _model_server_result.job_id 3dSQrR3uWkHIiw8_QCTbLA _model_server_result.datetime_utc '2024-12-12 15:47:35' _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 5oam # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":600}' # _entry.id 5OAM # _exptl.entry_id 5OAM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _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 ? # _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,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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id E _struct_conn.ptnr1_label_atom_id MG _struct_conn.ptnr1_label_comp_id MG _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id MG _struct_conn.ptnr1_auth_seq_id 502 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id F _struct_conn.ptnr2_label_atom_id O2G _struct_conn.ptnr2_label_comp_id GTP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id GTP _struct_conn.ptnr2_auth_seq_id 503 _struct_conn.ptnr2_symmetry 1_555 _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 2.448 _struct_conn.pdbx_value_order ? # _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 5OAM _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 4 ZN A 1 501 900 ZN ZN . E 5 MG A 1 502 501 MG MG . F 6 GTP A 1 503 500 GTP GTP . G 7 GDP B 1 600 600 GDP GDP . H 8 TA1 B 1 601 601 TA1 TA1 . # 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 7 190.593 317.952 282.643 1 22.28 ? PB GDP 600 B 1 HETATM 2 O O1B GDP . . . G 7 190.195 318.795 281.5 1 23.59 ? O1B GDP 600 B 1 HETATM 3 O O2B GDP . . . G 7 191.966 317.742 282.805 1 23.44 ? O2B GDP 600 B 1 HETATM 4 O O3B GDP . . . G 7 189.845 318.516 283.982 1 25.3 ? O3B GDP 600 B 1 HETATM 5 O O3A GDP . . . G 7 190.007 316.519 282.35 1 19.52 ? O3A GDP 600 B 1 HETATM 6 P PA GDP . . . G 7 190.784 315.044 282.227 1 20.51 ? PA GDP 600 B 1 HETATM 7 O O1A GDP . . . G 7 191.673 315.062 281.031 1 23.36 ? O1A GDP 600 B 1 HETATM 8 O O2A GDP . . . G 7 191.482 314.82 283.558 1 18 ? O2A GDP 600 B 1 HETATM 9 O O5' GDP . . . G 7 189.583 314.1 281.937 1 16.66 ? O5' GDP 600 B 1 HETATM 10 C C5' GDP . . . G 7 189.646 312.675 282.251 1 7.65 ? C5' GDP 600 B 1 HETATM 11 C C4' GDP . . . G 7 189.431 311.789 281.12 1 2.51 ? C4' GDP 600 B 1 HETATM 12 O O4' GDP . . . G 7 190.531 311.991 280.147 1 2 ? O4' GDP 600 B 1 HETATM 13 C C3' GDP . . . G 7 189.574 310.256 281.432 1 3.46 ? C3' GDP 600 B 1 HETATM 14 O O3' GDP . . . G 7 188.544 309.582 280.62 1 2.32 ? O3' GDP 600 B 1 HETATM 15 C C2' GDP . . . G 7 190.963 309.766 280.956 1 2.23 ? C2' GDP 600 B 1 HETATM 16 O O2' GDP . . . G 7 191.102 308.42 280.47 1 2 ? O2' GDP 600 B 1 HETATM 17 C C1' GDP . . . G 7 191.308 310.752 279.842 1 2 ? C1' GDP 600 B 1 HETATM 18 N N9 GDP . . . G 7 192.722 311.119 279.771 1 5.88 ? N9 GDP 600 B 1 HETATM 19 C C8 GDP . . . G 7 193.309 311.986 280.848 1 9.42 ? C8 GDP 600 B 1 HETATM 20 N N7 GDP . . . G 7 194.586 312 280.26 1 10.36 ? N7 GDP 600 B 1 HETATM 21 C C5 GDP . . . G 7 194.819 311.341 279.13 1 10.45 ? C5 GDP 600 B 1 HETATM 22 C C6 GDP . . . G 7 195.78 310.994 278.157 1 13.51 ? C6 GDP 600 B 1 HETATM 23 O O6 GDP . . . G 7 197.012 311.501 278.335 1 11.34 ? O6 GDP 600 B 1 HETATM 24 N N1 GDP . . . G 7 195.533 310.23 277.069 1 10.31 ? N1 GDP 600 B 1 HETATM 25 C C2 GDP . . . G 7 194.158 309.693 276.885 1 5.81 ? C2 GDP 600 B 1 HETATM 26 N N2 GDP . . . G 7 194.153 308.97 275.786 1 6.23 ? N2 GDP 600 B 1 HETATM 27 N N3 GDP . . . G 7 193.253 309.951 277.734 1 4.23 ? N3 GDP 600 B 1 HETATM 28 C C4 GDP . . . G 7 193.538 310.746 278.782 1 7.64 ? C4 GDP 600 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 44 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 1046 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 28 #