data_3RAP # _model_server_result.job_id GLecDLUmDbUEGgX8LgW3Lw _model_server_result.datetime_utc '2024-11-14 12:49:11' _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 3rap # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":180}' # _entry.id 3RAP # _exptl.entry_id 3RAP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 3 _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 97.07 _cell.angle_gamma 90 _cell.entry_id 3RAP _cell.length_a 41.01 _cell.length_b 59.83 _cell.length_c 68.44 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RAP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 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 OG SER 17 R SER 17 1_555 C MG MG . R MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.892 ? metalc ? metalc2 A OG1 THR 35 R THR 35 1_555 C MG MG . R MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.76 ? metalc ? metalc3 D O3G GTP . R GTP 180 1_555 C MG MG . R MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc4 D O2B GTP . R GTP 180 1_555 C MG MG . R MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc5 C MG MG . R MG 200 1_555 G O HOH . R HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc6 C MG MG . R MG 200 1_555 G O HOH . R HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? metalc ? metalc7 B OG SER 17 S SER 17 1_555 E MG MG . S MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc8 B OG1 THR 35 S THR 35 1_555 E MG MG . S MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? metalc ? metalc9 F O3G GTP . S GTP 181 1_555 E MG MG . S MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc10 F O1B GTP . S GTP 181 1_555 E MG MG . S MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc11 E MG MG . S MG 201 1_555 H O HOH . S HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? metalc ? metalc12 E MG MG . S MG 201 1_555 H O HOH . S HOH 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? # _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 129 n n PG O2G GTP sing 130 n n PG O3G GTP sing 131 n n PG O3B GTP sing 132 n n O2G HOG2 GTP sing 133 n n O3G HOG3 GTP sing 134 n n O3B PB GTP sing 135 n n PB O1B GTP doub 136 n n PB O2B GTP sing 137 n n PB O3A GTP sing 138 n n O2B HOB2 GTP sing 139 n n O3A PA GTP sing 140 n n PA O1A GTP doub 141 n n PA O2A GTP sing 142 n n PA O5' GTP sing 143 n n O2A HOA2 GTP sing 144 n n O5' C5' GTP sing 145 n n C5' C4' GTP sing 146 n n C5' H5' GTP sing 147 n n C5' "H5''" GTP sing 148 n n C4' O4' GTP sing 149 n n C4' C3' GTP sing 150 n n C4' H4' GTP sing 151 n n O4' C1' GTP sing 152 n n C3' O3' GTP sing 153 n n C3' C2' GTP sing 154 n n C3' H3' GTP sing 155 n n O3' HO3' GTP sing 156 n n C2' O2' GTP sing 157 n n C2' C1' GTP sing 158 n n C2' H2' GTP sing 159 n n O2' HO2' GTP sing 160 n n C1' N9 GTP sing 161 n n C1' H1' GTP sing 162 n n N9 C8 GTP sing 163 n y N9 C4 GTP sing 164 n y C8 N7 GTP doub 165 n y C8 H8 GTP sing 166 n n N7 C5 GTP sing 167 n y C5 C6 GTP sing 168 n n C5 C4 GTP doub 169 n y C6 O6 GTP doub 170 n n C6 N1 GTP sing 171 n n N1 C2 GTP sing 172 n n N1 HN1 GTP sing 173 n n C2 N2 GTP sing 174 n n C2 N3 GTP doub 175 n n N2 HN21 GTP sing 176 n n N2 HN22 GTP sing 177 n n N3 C4 GTP sing 178 n n # _atom_sites.entry_id 3RAP _atom_sites.fract_transf_matrix[1][1] 0.024384 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003024 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016714 _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] 0.014723 _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 R 1 200 200 MG MG . D 3 GTP R 1 180 180 GTP GTP . E 2 MG S 1 201 201 MG MG . F 3 GTP S 1 181 181 GTP GTP . G 4 HOH R 1 201 1 HOH HOH . G 4 HOH R 2 202 2 HOH HOH . G 4 HOH R 3 203 5 HOH HOH . G 4 HOH R 4 204 7 HOH HOH . G 4 HOH R 5 205 8 HOH HOH . G 4 HOH R 6 206 9 HOH HOH . G 4 HOH R 7 207 10 HOH HOH . G 4 HOH R 8 208 11 HOH HOH . G 4 HOH R 9 209 12 HOH HOH . G 4 HOH R 10 210 16 HOH HOH . G 4 HOH R 11 211 20 HOH HOH . G 4 HOH R 12 212 21 HOH HOH . G 4 HOH R 13 213 25 HOH HOH . G 4 HOH R 14 214 26 HOH HOH . G 4 HOH R 15 215 27 HOH HOH . G 4 HOH R 16 216 28 HOH HOH . G 4 HOH R 17 217 29 HOH HOH . G 4 HOH R 18 218 30 HOH HOH . G 4 HOH R 19 219 32 HOH HOH . G 4 HOH R 20 220 33 HOH HOH . G 4 HOH R 21 221 34 HOH HOH . G 4 HOH R 22 222 35 HOH HOH . G 4 HOH R 23 223 36 HOH HOH . G 4 HOH R 24 224 37 HOH HOH . G 4 HOH R 25 225 38 HOH HOH . G 4 HOH R 26 226 39 HOH HOH . G 4 HOH R 27 227 40 HOH HOH . G 4 HOH R 28 228 41 HOH HOH . G 4 HOH R 29 229 42 HOH HOH . G 4 HOH R 30 230 43 HOH HOH . G 4 HOH R 31 231 44 HOH HOH . G 4 HOH R 32 232 45 HOH HOH . G 4 HOH R 33 233 46 HOH HOH . G 4 HOH R 34 234 47 HOH HOH . G 4 HOH R 35 235 48 HOH HOH . G 4 HOH R 36 236 49 HOH HOH . G 4 HOH R 37 237 62 HOH HOH . G 4 HOH R 38 238 63 HOH HOH . G 4 HOH R 39 239 64 HOH HOH . G 4 HOH R 40 240 65 HOH HOH . G 4 HOH R 41 241 66 HOH HOH . G 4 HOH R 42 242 71 HOH HOH . G 4 HOH R 43 243 72 HOH HOH . G 4 HOH R 44 244 73 HOH HOH . G 4 HOH R 45 245 74 HOH HOH . G 4 HOH R 46 246 77 HOH HOH . G 4 HOH R 47 247 79 HOH HOH . G 4 HOH R 48 248 80 HOH HOH . G 4 HOH R 49 249 81 HOH HOH . G 4 HOH R 50 250 82 HOH HOH . G 4 HOH R 51 251 83 HOH HOH . G 4 HOH R 52 252 84 HOH HOH . G 4 HOH R 53 253 91 HOH HOH . G 4 HOH R 54 254 93 HOH HOH . H 4 HOH S 1 202 3 HOH HOH . H 4 HOH S 2 203 4 HOH HOH . H 4 HOH S 3 204 6 HOH HOH . H 4 HOH S 4 205 13 HOH HOH . H 4 HOH S 5 206 14 HOH HOH . H 4 HOH S 6 207 15 HOH HOH . H 4 HOH S 7 208 17 HOH HOH . H 4 HOH S 8 209 18 HOH HOH . H 4 HOH S 9 210 19 HOH HOH . H 4 HOH S 10 211 22 HOH HOH . H 4 HOH S 11 212 23 HOH HOH . H 4 HOH S 12 213 24 HOH HOH . H 4 HOH S 13 214 31 HOH HOH . H 4 HOH S 14 215 50 HOH HOH . H 4 HOH S 15 216 51 HOH HOH . H 4 HOH S 16 217 52 HOH HOH . H 4 HOH S 17 218 53 HOH HOH . H 4 HOH S 18 219 54 HOH HOH . H 4 HOH S 19 220 55 HOH HOH . H 4 HOH S 20 221 56 HOH HOH . H 4 HOH S 21 222 57 HOH HOH . H 4 HOH S 22 223 58 HOH HOH . H 4 HOH S 23 224 59 HOH HOH . H 4 HOH S 24 225 60 HOH HOH . H 4 HOH S 25 226 61 HOH HOH . H 4 HOH S 26 227 67 HOH HOH . H 4 HOH S 27 228 68 HOH HOH . H 4 HOH S 28 229 69 HOH HOH . H 4 HOH S 29 230 70 HOH HOH . H 4 HOH S 30 231 75 HOH HOH . H 4 HOH S 31 232 76 HOH HOH . H 4 HOH S 32 233 78 HOH HOH . H 4 HOH S 33 234 85 HOH HOH . H 4 HOH S 34 235 86 HOH HOH . H 4 HOH S 35 236 87 HOH HOH . H 4 HOH S 36 237 88 HOH HOH . H 4 HOH S 37 238 89 HOH HOH . H 4 HOH S 38 239 90 HOH HOH . H 4 HOH S 39 240 92 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 . . . D 3 -9.412 0.546 34.139 1 13.22 ? PG GTP 180 R 1 HETATM 2 O O1G GTP . . . D 3 -10.815 0.967 34.173 1 8.71 ? O1G GTP 180 R 1 HETATM 3 O O2G GTP . . . D 3 -8.463 1.597 34.52 1 8.58 ? O2G GTP 180 R 1 HETATM 4 O O3G GTP . . . D 3 -9.202 -0.732 34.856 1 8.91 ? O3G GTP 180 R 1 HETATM 5 O O3B GTP . . . D 3 -9.099 0.215 32.587 1 14.09 ? O3B GTP 180 R 1 HETATM 6 P PB GTP . . . D 3 -7.898 -0.621 31.928 1 14.01 ? PB GTP 180 R 1 HETATM 7 O O1B GTP . . . D 3 -6.832 0.329 31.543 1 12.89 ? O1B GTP 180 R 1 HETATM 8 O O2B GTP . . . D 3 -7.572 -1.783 32.797 1 8.31 ? O2B GTP 180 R 1 HETATM 9 O O3A GTP . . . D 3 -8.551 -1.2 30.581 1 14.39 ? O3A GTP 180 R 1 HETATM 10 P PA GTP . . . D 3 -8.82 -2.721 30.152 1 10.48 ? PA GTP 180 R 1 HETATM 11 O O1A GTP . . . D 3 -9.966 -3.229 30.923 1 12.54 ? O1A GTP 180 R 1 HETATM 12 O O2A GTP . . . D 3 -7.535 -3.456 30.184 1 12.97 ? O2A GTP 180 R 1 HETATM 13 O O5' GTP . . . D 3 -9.266 -2.55 28.615 1 21.41 ? O5' GTP 180 R 1 HETATM 14 C C5' GTP . . . D 3 -10.415 -1.772 28.294 1 12.15 ? C5' GTP 180 R 1 HETATM 15 C C4' GTP . . . D 3 -11.04 -2.145 26.954 1 13.93 ? C4' GTP 180 R 1 HETATM 16 O O4' GTP . . . D 3 -10.091 -1.92 25.889 1 15.94 ? O4' GTP 180 R 1 HETATM 17 C C3' GTP . . . D 3 -11.427 -3.619 26.907 1 13.65 ? C3' GTP 180 R 1 HETATM 18 O O3' GTP . . . D 3 -12.531 -3.805 26.047 1 17.25 ? O3' GTP 180 R 1 HETATM 19 C C2' GTP . . . D 3 -10.181 -4.232 26.296 1 12.73 ? C2' GTP 180 R 1 HETATM 20 O O2' GTP . . . D 3 -10.482 -5.457 25.67 1 13.9 ? O2' GTP 180 R 1 HETATM 21 C C1' GTP . . . D 3 -9.74 -3.186 25.343 1 7 ? C1' GTP 180 R 1 HETATM 22 N N9 GTP . . . D 3 -8.302 -3.251 25.073 1 12.28 ? N9 GTP 180 R 1 HETATM 23 C C8 GTP . . . D 3 -7.222 -3.216 25.918 1 15.06 ? C8 GTP 180 R 1 HETATM 24 N N7 GTP . . . D 3 -6.066 -3.318 25.315 1 11.58 ? N7 GTP 180 R 1 HETATM 25 C C5 GTP . . . D 3 -6.414 -3.445 23.978 1 14.77 ? C5 GTP 180 R 1 HETATM 26 C C6 GTP . . . D 3 -5.592 -3.596 22.825 1 13.97 ? C6 GTP 180 R 1 HETATM 27 O O6 GTP . . . D 3 -4.359 -3.627 22.765 1 10.29 ? O6 GTP 180 R 1 HETATM 28 N N1 GTP . . . D 3 -6.362 -3.691 21.671 1 12.01 ? N1 GTP 180 R 1 HETATM 29 C C2 GTP . . . D 3 -7.74 -3.632 21.618 1 16.64 ? C2 GTP 180 R 1 HETATM 30 N N2 GTP . . . D 3 -8.337 -3.801 20.447 1 14.77 ? N2 GTP 180 R 1 HETATM 31 N N3 GTP . . . D 3 -8.505 -3.489 22.703 1 17.32 ? N3 GTP 180 R 1 HETATM 32 C C4 GTP . . . D 3 -7.781 -3.401 23.826 1 12.91 ? C4 GTP 180 R 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 32 #