data_5HNZ # _model_server_result.job_id kce61YXyAEpUJ_Fnr3yncg _model_server_result.datetime_utc '2024-11-05 01:27:48' _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 5hnz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":901}' # _entry.id 5HNZ # _exptl.entry_id 5HNZ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 _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 6 _struct_asym.id F _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 D _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 501 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id O1G _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 502 _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 2.449 _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 5HNZ _atom_sites.fract_transf_matrix[1][1] 0.001 _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] 0.001 _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] 0.001 _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 MG A 1 501 501 MG MG . E 5 GTP A 1 502 500 GTP GTP . F 6 GDP B 1 901 901 GDP GDP . G 7 TA1 B 1 902 902 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 . . . F 6 409.604 410.581 587.871 1 22.28 ? PB GDP 901 B 1 HETATM 2 O O1B GDP . . . F 6 409.723 409.685 589.038 1 23.59 ? O1B GDP 901 B 1 HETATM 3 O O2B GDP . . . F 6 410.62 411.527 587.715 1 23.44 ? O2B GDP 901 B 1 HETATM 4 O O3B GDP . . . F 6 409.339 409.663 586.544 1 25.3 ? O3B GDP 901 B 1 HETATM 5 O O3A GDP . . . F 6 408.302 411.436 588.112 1 19.52 ? O3A GDP 901 B 1 HETATM 6 P PA GDP . . . F 6 408.105 413.095 588.196 1 20.51 ? PA GDP 901 B 1 HETATM 7 O O1A GDP . . . F 6 408.817 413.61 589.397 1 23.36 ? O1A GDP 901 B 1 HETATM 8 O O2A GDP . . . F 6 408.589 413.645 586.864 1 18 ? O2A GDP 901 B 1 HETATM 9 O O5' GDP . . . F 6 406.575 413.2 588.443 1 16.66 ? O5' GDP 901 B 1 HETATM 10 C C5' GDP . . . F 6 405.829 414.404 588.084 1 7.65 ? C5' GDP 901 B 1 HETATM 11 C C4' GDP . . . F 6 405.122 415.034 589.183 1 2.51 ? C4' GDP 901 B 1 HETATM 12 O O4' GDP . . . F 6 406.117 415.512 590.173 1 2 ? O4' GDP 901 B 1 HETATM 13 C C3' GDP . . . F 6 404.381 416.373 588.823 1 3.46 ? C3' GDP 901 B 1 HETATM 14 O O3' GDP . . . F 6 403.13 416.363 589.603 1 2.32 ? O3' GDP 901 B 1 HETATM 15 C C2' GDP . . . F 6 405.237 417.573 589.295 1 2.23 ? C2' GDP 901 B 1 HETATM 16 O O2' GDP . . . F 6 404.579 418.773 589.74 1 2 ? O2' GDP 901 B 1 HETATM 17 C C1' GDP . . . F 6 406.05 416.981 590.445 1 2 ? C1' GDP 901 B 1 HETATM 18 N N9 GDP . . . F 6 407.42 417.479 590.54 1 5.88 ? N9 GDP 901 B 1 HETATM 19 C C8 GDP . . . F 6 408.422 417.073 589.497 1 9.42 ? C8 GDP 901 B 1 HETATM 20 N N7 GDP . . . F 6 409.468 417.798 590.097 1 10.36 ? N7 GDP 901 B 1 HETATM 21 C C5 GDP . . . F 6 409.259 418.497 591.208 1 10.45 ? C5 GDP 901 B 1 HETATM 22 C C6 GDP . . . F 6 409.829 419.347 592.177 1 13.51 ? C6 GDP 901 B 1 HETATM 23 O O6 GDP . . . F 6 411.136 419.623 592.027 1 11.34 ? O6 GDP 901 B 1 HETATM 24 N N1 GDP . . . F 6 409.167 419.86 593.238 1 10.31 ? N1 GDP 901 B 1 HETATM 25 C C2 GDP . . . F 6 407.723 419.529 593.391 1 5.81 ? C2 GDP 901 B 1 HETATM 26 N N2 GDP . . . F 6 407.282 420.146 594.467 1 6.23 ? N2 GDP 901 B 1 HETATM 27 N N3 GDP . . . F 6 407.145 418.786 592.542 1 4.23 ? N3 GDP 901 B 1 HETATM 28 C C4 GDP . . . F 6 407.856 418.27 591.524 1 7.64 ? C4 GDP 901 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #