data_3Q86 # _model_server_result.job_id l25Vv-WlWQV7Rdlqg_syVg _model_server_result.datetime_utc '2024-11-14 08:43:50' _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 3q86 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":158}' # _entry.id 3Q86 # _exptl.entry_id 3Q86 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 3Q86 _cell.length_a 75.302 _cell.length_b 75.302 _cell.length_c 154.712 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3Q86 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_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 1,2,3 B,E,F,H 2 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 37.651 -65.213445 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 75.302 0 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 E 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 C O2B GTP . A GTP 158 1_555 D MG MG . A MG 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc2 C O1A GTP . A GTP 158 1_555 D MG MG . A MG 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc3 C O5' GTP . A GTP 158 1_555 D MG MG . A MG 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? metalc ? metalc4 E O2A GTP . B GTP 158 1_555 F MG MG . B MG 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc5 E O2G GTP . B GTP 158 1_555 F MG MG . B MG 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc6 E O1B GTP . B GTP 158 1_555 F MG MG . B MG 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc7 F MG MG . B MG 159 1_555 H O HOH . B HOH 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc8 F MG MG . B MG 159 1_555 H O HOH . B HOH 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PG O1G GTP doub 116 n n PG O2G GTP sing 117 n n PG O3G GTP sing 118 n n PG O3B GTP sing 119 n n O2G HOG2 GTP sing 120 n n O3G HOG3 GTP sing 121 n n O3B PB GTP sing 122 n n PB O1B GTP doub 123 n n PB O2B GTP sing 124 n n PB O3A GTP sing 125 n n O2B HOB2 GTP sing 126 n n O3A PA GTP sing 127 n n PA O1A GTP doub 128 n n PA O2A GTP sing 129 n n PA O5' GTP sing 130 n n O2A HOA2 GTP sing 131 n n O5' C5' GTP sing 132 n n C5' C4' GTP sing 133 n n C5' H5' GTP sing 134 n n C5' "H5''" GTP sing 135 n n C4' O4' GTP sing 136 n n C4' C3' GTP sing 137 n n C4' H4' GTP sing 138 n n O4' C1' GTP sing 139 n n C3' O3' GTP sing 140 n n C3' C2' GTP sing 141 n n C3' H3' GTP sing 142 n n O3' HO3' GTP sing 143 n n C2' O2' GTP sing 144 n n C2' C1' GTP sing 145 n n C2' H2' GTP sing 146 n n O2' HO2' GTP sing 147 n n C1' N9 GTP sing 148 n n C1' H1' GTP sing 149 n n N9 C8 GTP sing 150 n y N9 C4 GTP sing 151 n y C8 N7 GTP doub 152 n y C8 H8 GTP sing 153 n n N7 C5 GTP sing 154 n y C5 C6 GTP sing 155 n n C5 C4 GTP doub 156 n y C6 O6 GTP doub 157 n n C6 N1 GTP sing 158 n n N1 C2 GTP sing 159 n n N1 HN1 GTP sing 160 n n C2 N2 GTP sing 161 n n C2 N3 GTP doub 162 n n N2 HN21 GTP sing 163 n n N2 HN22 GTP sing 164 n n N3 C4 GTP sing 165 n n # _atom_sites.entry_id 3Q86 _atom_sites.fract_transf_matrix[1][1] 0.01328 _atom_sites.fract_transf_matrix[1][2] 0.007667 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015334 _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] 0.006464 _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 GTP A 1 158 2 GTP GTP . D 3 MG A 1 159 2 MG MG . E 2 GTP B 1 158 1 GTP GTP . F 3 MG B 1 159 1 MG MG . G 4 HOH A 1 160 3 HOH HOH . G 4 HOH A 2 161 5 HOH HOH . G 4 HOH A 3 162 8 HOH HOH . G 4 HOH A 4 163 9 HOH HOH . G 4 HOH A 5 164 11 HOH HOH . G 4 HOH A 6 165 13 HOH HOH . G 4 HOH A 7 166 16 HOH HOH . G 4 HOH A 8 167 17 HOH HOH . G 4 HOH A 9 168 19 HOH HOH . G 4 HOH A 10 169 20 HOH HOH . G 4 HOH A 11 170 23 HOH HOH . G 4 HOH A 12 171 26 HOH HOH . G 4 HOH A 13 172 28 HOH HOH . G 4 HOH A 14 173 29 HOH HOH . G 4 HOH A 15 174 30 HOH HOH . G 4 HOH A 16 175 31 HOH HOH . G 4 HOH A 17 176 32 HOH HOH . G 4 HOH A 18 177 35 HOH HOH . G 4 HOH A 19 178 36 HOH HOH . G 4 HOH A 20 179 37 HOH HOH . G 4 HOH A 21 180 38 HOH HOH . G 4 HOH A 22 181 39 HOH HOH . G 4 HOH A 23 182 42 HOH HOH . G 4 HOH A 24 183 45 HOH HOH . G 4 HOH A 25 184 54 HOH HOH . G 4 HOH A 26 185 59 HOH HOH . G 4 HOH A 27 186 60 HOH HOH . G 4 HOH A 28 187 63 HOH HOH . G 4 HOH A 29 188 64 HOH HOH . G 4 HOH A 30 189 65 HOH HOH . G 4 HOH A 31 190 67 HOH HOH . G 4 HOH A 32 191 68 HOH HOH . G 4 HOH A 33 192 77 HOH HOH . G 4 HOH A 34 193 79 HOH HOH . G 4 HOH A 35 194 80 HOH HOH . G 4 HOH A 36 195 81 HOH HOH . G 4 HOH A 37 196 82 HOH HOH . G 4 HOH A 38 197 83 HOH HOH . G 4 HOH A 39 198 84 HOH HOH . G 4 HOH A 40 199 87 HOH HOH . G 4 HOH A 41 200 88 HOH HOH . G 4 HOH A 42 201 90 HOH HOH . G 4 HOH A 43 202 93 HOH HOH . G 4 HOH A 44 203 94 HOH HOH . G 4 HOH A 45 204 95 HOH HOH . G 4 HOH A 46 205 97 HOH HOH . G 4 HOH A 47 206 103 HOH HOH . G 4 HOH A 48 207 104 HOH HOH . G 4 HOH A 49 208 105 HOH HOH . G 4 HOH A 50 209 106 HOH HOH . G 4 HOH A 51 210 107 HOH HOH . G 4 HOH A 52 211 109 HOH HOH . G 4 HOH A 53 212 113 HOH HOH . G 4 HOH A 54 213 114 HOH HOH . G 4 HOH A 55 214 115 HOH HOH . G 4 HOH A 56 215 116 HOH HOH . G 4 HOH A 57 216 117 HOH HOH . G 4 HOH A 58 217 118 HOH HOH . G 4 HOH A 59 218 119 HOH HOH . G 4 HOH A 60 219 120 HOH HOH . G 4 HOH A 61 220 127 HOH HOH . G 4 HOH A 62 221 128 HOH HOH . G 4 HOH A 63 222 129 HOH HOH . G 4 HOH A 64 223 130 HOH HOH . G 4 HOH A 65 224 131 HOH HOH . G 4 HOH A 66 225 132 HOH HOH . G 4 HOH A 67 226 135 HOH HOH . G 4 HOH A 68 227 136 HOH HOH . G 4 HOH A 69 228 137 HOH HOH . G 4 HOH A 70 229 138 HOH HOH . H 4 HOH B 1 160 1 HOH HOH . H 4 HOH B 2 161 2 HOH HOH . H 4 HOH B 3 162 4 HOH HOH . H 4 HOH B 4 163 6 HOH HOH . H 4 HOH B 5 164 7 HOH HOH . H 4 HOH B 6 165 10 HOH HOH . H 4 HOH B 7 166 12 HOH HOH . H 4 HOH B 8 167 14 HOH HOH . H 4 HOH B 9 168 15 HOH HOH . H 4 HOH B 10 169 18 HOH HOH . H 4 HOH B 11 170 21 HOH HOH . H 4 HOH B 12 171 22 HOH HOH . H 4 HOH B 13 172 24 HOH HOH . H 4 HOH B 14 173 25 HOH HOH . H 4 HOH B 15 174 27 HOH HOH . H 4 HOH B 16 175 33 HOH HOH . H 4 HOH B 17 176 34 HOH HOH . H 4 HOH B 18 177 40 HOH HOH . H 4 HOH B 19 178 41 HOH HOH . H 4 HOH B 20 179 43 HOH HOH . H 4 HOH B 21 180 44 HOH HOH . H 4 HOH B 22 181 46 HOH HOH . H 4 HOH B 23 182 47 HOH HOH . H 4 HOH B 24 183 48 HOH HOH . H 4 HOH B 25 184 49 HOH HOH . H 4 HOH B 26 185 50 HOH HOH . H 4 HOH B 27 186 51 HOH HOH . H 4 HOH B 28 187 52 HOH HOH . H 4 HOH B 29 188 53 HOH HOH . H 4 HOH B 30 189 56 HOH HOH . H 4 HOH B 31 190 57 HOH HOH . H 4 HOH B 32 191 58 HOH HOH . H 4 HOH B 33 192 61 HOH HOH . H 4 HOH B 34 193 66 HOH HOH . H 4 HOH B 35 194 69 HOH HOH . H 4 HOH B 36 195 70 HOH HOH . H 4 HOH B 37 196 71 HOH HOH . H 4 HOH B 38 197 72 HOH HOH . H 4 HOH B 39 198 73 HOH HOH . H 4 HOH B 40 199 74 HOH HOH . H 4 HOH B 41 200 75 HOH HOH . H 4 HOH B 42 201 76 HOH HOH . H 4 HOH B 43 202 78 HOH HOH . H 4 HOH B 44 203 85 HOH HOH . H 4 HOH B 45 204 86 HOH HOH . H 4 HOH B 46 205 89 HOH HOH . H 4 HOH B 47 206 91 HOH HOH . H 4 HOH B 48 207 92 HOH HOH . H 4 HOH B 49 208 98 HOH HOH . H 4 HOH B 50 209 99 HOH HOH . H 4 HOH B 51 210 100 HOH HOH . H 4 HOH B 52 211 101 HOH HOH . H 4 HOH B 53 212 102 HOH HOH . H 4 HOH B 54 213 108 HOH HOH . H 4 HOH B 55 214 110 HOH HOH . H 4 HOH B 56 215 111 HOH HOH . H 4 HOH B 57 216 112 HOH HOH . H 4 HOH B 58 217 121 HOH HOH . H 4 HOH B 59 218 122 HOH HOH . H 4 HOH B 60 219 123 HOH HOH . H 4 HOH B 61 220 124 HOH HOH . H 4 HOH B 62 221 125 HOH HOH . H 4 HOH B 63 222 126 HOH HOH . H 4 HOH B 64 223 133 HOH HOH . H 4 HOH B 65 224 134 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 PG GTP . . . C 2 17.932 -27.124 -22.711 0.8 73.14 ? PG GTP 158 A 1 HETATM 2 O O1G GTP . . . C 2 16.879 -26.938 -21.653 0.8 73.84 ? O1G GTP 158 A 1 HETATM 3 O O2G GTP . . . C 2 18.964 -26.006 -22.786 0.8 73.75 ? O2G GTP 158 A 1 HETATM 4 O O3G GTP . . . C 2 18.557 -28.462 -22.392 0.8 74.35 ? O3G GTP 158 A 1 HETATM 5 O O3B GTP . . . C 2 17.203 -27.144 -24.139 0.8 73.82 ? O3B GTP 158 A 1 HETATM 6 P PB GTP . . . C 2 17.757 -28.292 -25.098 0.8 73.56 ? PB GTP 158 A 1 HETATM 7 O O1B GTP . . . C 2 17.035 -29.582 -24.766 0.8 72.58 ? O1B GTP 158 A 1 HETATM 8 O O2B GTP . . . C 2 19.255 -28.335 -24.822 0.8 74.39 ? O2B GTP 158 A 1 HETATM 9 O O3A GTP . . . C 2 17.487 -27.843 -26.612 0.8 71.39 ? O3A GTP 158 A 1 HETATM 10 P PA GTP . . . C 2 18.782 -27.841 -27.555 0.8 69.74 ? PA GTP 158 A 1 HETATM 11 O O1A GTP . . . C 2 19.539 -26.572 -27.197 0.8 68.16 ? O1A GTP 158 A 1 HETATM 12 O O2A GTP . . . C 2 18.446 -27.861 -29.03 0.8 70.22 ? O2A GTP 158 A 1 HETATM 13 O O5' GTP . . . C 2 19.553 -29.201 -27.094 0.8 66.29 ? O5' GTP 158 A 1 HETATM 14 C C5' GTP . . . C 2 18.989 -30.497 -26.908 0.8 62.33 ? C5' GTP 158 A 1 HETATM 15 C C4' GTP . . . C 2 18.758 -30.969 -25.449 0.8 60.78 ? C4' GTP 158 A 1 HETATM 16 O O4' GTP . . . C 2 18.055 -32.198 -25.472 0.8 60.19 ? O4' GTP 158 A 1 HETATM 17 C C3' GTP . . . C 2 19.979 -31.185 -24.545 0.8 59.57 ? C3' GTP 158 A 1 HETATM 18 O O3' GTP . . . C 2 19.99 -30.321 -23.429 0.8 57.98 ? O3' GTP 158 A 1 HETATM 19 C C2' GTP . . . C 2 19.838 -32.592 -24.035 0.8 58.68 ? C2' GTP 158 A 1 HETATM 20 O O2' GTP . . . C 2 19.363 -32.496 -22.717 0.8 58.51 ? O2' GTP 158 A 1 HETATM 21 C C1' GTP . . . C 2 18.834 -33.259 -24.966 0.8 57.96 ? C1' GTP 158 A 1 HETATM 22 N N9 GTP . . . C 2 19.502 -33.958 -26.101 0.8 56.07 ? N9 GTP 158 A 1 HETATM 23 C C8 GTP . . . C 2 19.867 -33.437 -27.326 0.8 54.42 ? C8 GTP 158 A 1 HETATM 24 N N7 GTP . . . C 2 20.454 -34.4 -28.083 0.8 55.6 ? N7 GTP 158 A 1 HETATM 25 C C5 GTP . . . C 2 20.463 -35.561 -27.357 0.8 55 ? C5 GTP 158 A 1 HETATM 26 C C6 GTP . . . C 2 20.935 -36.867 -27.625 0.8 54.28 ? C6 GTP 158 A 1 HETATM 27 O O6 GTP . . . C 2 21.468 -37.175 -28.699 0.8 53.11 ? O6 GTP 158 A 1 HETATM 28 N N1 GTP . . . C 2 20.806 -37.845 -26.656 0.8 54.05 ? N1 GTP 158 A 1 HETATM 29 C C2 GTP . . . C 2 20.203 -37.538 -25.45 0.8 53.53 ? C2 GTP 158 A 1 HETATM 30 N N2 GTP . . . C 2 20.071 -38.489 -24.55 0.8 51.98 ? N2 GTP 158 A 1 HETATM 31 N N3 GTP . . . C 2 19.744 -36.255 -25.176 0.8 54.14 ? N3 GTP 158 A 1 HETATM 32 C C4 GTP . . . C 2 19.876 -35.28 -26.111 0.8 54.88 ? C4 GTP 158 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 32 #