data_5MI9 # _model_server_result.job_id w-sgGyYkVjo6x8H2OCRMvA _model_server_result.datetime_utc '2024-11-23 11:17:57' _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 5mi9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 5MI9 # _exptl.entry_id 5MI9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 ? # _cell.angle_alpha 109.25 _cell.angle_beta 106 _cell.angle_gamma 88.15 _cell.entry_id 5MI9 _cell.length_a 58.12 _cell.length_b 62.1 _cell.length_c 65.47 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MI9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 x,y,z _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 ? 3 D N N ? 3 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 metalc ? metalc1 A OG1 THR 34 A THR 26 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc2 C MG MG . A MG 401 1_555 D O3B GDP . A GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc3 C MG MG . A MG 401 1_555 D O2B GDP . A GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? metalc ? metalc4 C MG MG . A MG 401 1_555 G O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc5 C MG MG . A MG 401 1_555 G O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc6 C MG MG . A MG 401 1_555 G O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.975 ? metalc ? metalc7 B OG1 THR 34 B THR 26 1_555 E MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc8 E MG MG . B MG 401 1_555 F O1B GDP . B GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc9 E MG MG . B MG 401 1_555 F O1A GDP . B GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc10 E MG MG . B MG 401 1_555 F O2A GDP . B GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc11 E MG MG . B MG 401 1_555 H O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc12 E MG MG . B MG 401 1_555 H O HOH . B HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? # _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 5MI9 _atom_sites.fract_transf_matrix[1][1] 0.017206 _atom_sites.fract_transf_matrix[1][2] -0.000556 _atom_sites.fract_transf_matrix[1][3] 0.005037 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016111 _atom_sites.fract_transf_matrix[2][3] 0.005707 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.016857 _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 MG A 1 401 1 MG MG . D 3 GDP A 1 402 1 GDP GDP . E 2 MG B 1 401 2 MG MG . F 3 GDP B 1 402 2 GDP GDP . G 4 HOH A 1 501 9 HOH HOH . G 4 HOH A 2 502 10 HOH HOH . G 4 HOH A 3 503 8 HOH HOH . G 4 HOH A 4 504 1 HOH HOH . G 4 HOH A 5 505 11 HOH HOH . H 4 HOH B 1 501 2 HOH HOH . H 4 HOH B 2 502 5 HOH HOH . H 4 HOH B 3 503 7 HOH HOH . H 4 HOH B 4 504 6 HOH HOH . H 4 HOH B 5 505 3 HOH HOH . H 4 HOH B 6 506 4 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 . . . F 3 -28.569 -16.702 29.643 1 106.02 ? PB GDP 402 B 1 HETATM 2 O O1B GDP . . . F 3 -28.338 -16.823 28.169 1 106.87 ? O1B GDP 402 B 1 HETATM 3 O O2B GDP . . . F 3 -27.731 -17.76 30.371 1 105.1 ? O2B GDP 402 B 1 HETATM 4 O O3B GDP . . . F 3 -30.029 -16.727 30 1 103.1 ? O3B GDP 402 B 1 HETATM 5 O O3A GDP . . . F 3 -27.913 -15.308 30.043 1 109.73 ? O3A GDP 402 B 1 HETATM 6 P PA GDP . . . F 3 -28.192 -13.815 29.568 1 113.65 ? PA GDP 402 B 1 HETATM 7 O O1A GDP . . . F 3 -27.469 -13.571 28.302 1 113.97 ? O1A GDP 402 B 1 HETATM 8 O O2A GDP . . . F 3 -29.706 -13.658 29.35 1 114.6 ? O2A GDP 402 B 1 HETATM 9 O O5' GDP . . . F 3 -27.726 -12.833 30.736 1 118.3 ? O5' GDP 402 B 1 HETATM 10 C C5' GDP . . . F 3 -28.513 -12.608 31.922 1 124.57 ? C5' GDP 402 B 1 HETATM 11 C C4' GDP . . . F 3 -27.906 -11.494 32.738 1 130.89 ? C4' GDP 402 B 1 HETATM 12 O O4' GDP . . . F 3 -26.483 -11.7 32.866 1 133.02 ? O4' GDP 402 B 1 HETATM 13 C C3' GDP . . . F 3 -28.112 -10.072 32.205 1 133.5 ? C3' GDP 402 B 1 HETATM 14 O O3' GDP . . . F 3 -28.783 -9.262 33.165 1 134.33 ? O3' GDP 402 B 1 HETATM 15 C C2' GDP . . . F 3 -26.69 -9.574 31.908 1 134.01 ? C2' GDP 402 B 1 HETATM 16 O O2' GDP . . . F 3 -26.527 -8.199 32.237 1 134.14 ? O2' GDP 402 B 1 HETATM 17 C C1' GDP . . . F 3 -25.844 -10.445 32.834 1 134.2 ? C1' GDP 402 B 1 HETATM 18 N N9 GDP . . . F 3 -24.456 -10.646 32.379 1 136.16 ? N9 GDP 402 B 1 HETATM 19 C C8 GDP . . . F 3 -24.036 -11.235 31.215 1 135.78 ? C8 GDP 402 B 1 HETATM 20 N N7 GDP . . . F 3 -22.732 -11.282 31.09 1 137.31 ? N7 GDP 402 B 1 HETATM 21 C C5 GDP . . . F 3 -22.258 -10.694 32.25 1 139.12 ? C5 GDP 402 B 1 HETATM 22 C C6 GDP . . . F 3 -20.91 -10.459 32.728 1 139.57 ? C6 GDP 402 B 1 HETATM 23 O O6 GDP . . . F 3 -19.863 -10.736 32.159 1 137.05 ? O6 GDP 402 B 1 HETATM 24 N N1 GDP . . . F 3 -20.891 -9.845 33.968 1 143.02 ? N1 GDP 402 B 1 HETATM 25 C C2 GDP . . . F 3 -22.001 -9.477 34.687 1 145.35 ? C2 GDP 402 B 1 HETATM 26 N N2 GDP . . . F 3 -21.79 -8.872 35.859 1 146.54 ? N2 GDP 402 B 1 HETATM 27 N N3 GDP . . . F 3 -23.252 -9.683 34.266 1 144.28 ? N3 GDP 402 B 1 HETATM 28 C C4 GDP . . . F 3 -23.311 -10.293 33.055 1 140.25 ? C4 GDP 402 B 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #