data_5TAR # _model_server_result.job_id xmJxcCWQqM6ngH_-zLPTwA _model_server_result.datetime_utc '2024-11-04 20:19:11' _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 5tar # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 5TAR # _exptl.entry_id 5TAR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5TAR _cell.length_a 58.14 _cell.length_b 70.495 _cell.length_c 84.684 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TAR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A C LYS 184 A LYS 184 1_555 A N CMT 185 A CMT 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.276 ? covale ? covale2 A SG CMT 185 A CMT 185 1_555 C C1 FAR . A FAR 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.774 ? # _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 148 n n PB O2B GDP sing 149 n n PB O3B GDP sing 150 n n PB O3A GDP sing 151 n n O2B HOB2 GDP sing 152 n n O3B HOB3 GDP sing 153 n n O3A PA GDP sing 154 n n PA O1A GDP doub 155 n n PA O2A GDP sing 156 n n PA O5' GDP sing 157 n n O2A HOA2 GDP sing 158 n n O5' C5' GDP sing 159 n n C5' C4' GDP sing 160 n n C5' H5' GDP sing 161 n n C5' "H5''" GDP sing 162 n n C4' O4' GDP sing 163 n n C4' C3' GDP sing 164 n n C4' H4' GDP sing 165 n n O4' C1' GDP sing 166 n n C3' O3' GDP sing 167 n n C3' C2' GDP sing 168 n n C3' H3' GDP sing 169 n n O3' HO3' GDP sing 170 n n C2' O2' GDP sing 171 n n C2' C1' GDP sing 172 n n C2' H2' GDP sing 173 n n O2' HO2' GDP sing 174 n n C1' N9 GDP sing 175 n n C1' H1' GDP sing 176 n n N9 C8 GDP sing 177 n y N9 C4 GDP sing 178 n y C8 N7 GDP doub 179 n y C8 H8 GDP sing 180 n n N7 C5 GDP sing 181 n y C5 C6 GDP sing 182 n n C5 C4 GDP doub 183 n y C6 O6 GDP doub 184 n n C6 N1 GDP sing 185 n n N1 C2 GDP sing 186 n n N1 HN1 GDP sing 187 n n C2 N2 GDP sing 188 n n C2 N3 GDP doub 189 n n N2 HN21 GDP sing 190 n n N2 HN22 GDP sing 191 n n N3 C4 GDP sing 192 n n # _atom_sites.entry_id 5TAR _atom_sites.fract_transf_matrix[1][1] 0.0172 _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] 0.014185 _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] 0.011809 _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 3 FAR A 1 201 186 FAR FAR . D 4 GDP A 1 202 201 GDP GDP . E 5 EDO B 1 201 1 EDO EDO . F 6 HOH A 1 301 22 HOH HOH . F 6 HOH A 2 302 20 HOH HOH . F 6 HOH A 3 303 38 HOH HOH . F 6 HOH A 4 304 32 HOH HOH . F 6 HOH A 5 305 30 HOH HOH . F 6 HOH A 6 306 18 HOH HOH . F 6 HOH A 7 307 39 HOH HOH . F 6 HOH A 8 308 7 HOH HOH . F 6 HOH A 9 309 25 HOH HOH . F 6 HOH A 10 310 16 HOH HOH . F 6 HOH A 11 311 24 HOH HOH . F 6 HOH A 12 312 15 HOH HOH . F 6 HOH A 13 313 14 HOH HOH . F 6 HOH A 14 314 36 HOH HOH . F 6 HOH A 15 315 37 HOH HOH . F 6 HOH A 16 316 11 HOH HOH . F 6 HOH A 17 317 13 HOH HOH . F 6 HOH A 18 318 29 HOH HOH . F 6 HOH A 19 319 1 HOH HOH . F 6 HOH A 20 320 33 HOH HOH . F 6 HOH A 21 321 21 HOH HOH . F 6 HOH A 22 322 26 HOH HOH . F 6 HOH A 23 323 34 HOH HOH . F 6 HOH A 24 324 23 HOH HOH . G 6 HOH B 1 301 10 HOH HOH . G 6 HOH B 2 302 31 HOH HOH . G 6 HOH B 3 303 3 HOH HOH . G 6 HOH B 4 304 28 HOH HOH . G 6 HOH B 5 305 19 HOH HOH . G 6 HOH B 6 306 12 HOH HOH . G 6 HOH B 7 307 2 HOH HOH . G 6 HOH B 8 308 6 HOH HOH . G 6 HOH B 9 309 9 HOH HOH . G 6 HOH B 10 310 4 HOH HOH . G 6 HOH B 11 311 5 HOH HOH . G 6 HOH B 12 312 27 HOH HOH . G 6 HOH B 13 313 35 HOH HOH . G 6 HOH B 14 314 8 HOH HOH . G 6 HOH B 15 315 17 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 . . . D 4 25.959 66.795 95.642 1 27.59 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . D 4 25.499 66.968 94.222 1 26.36 ? O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . D 4 25.021 67.262 96.718 1 26.57 -1 O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . D 4 27.391 67.23 95.817 1 25.56 ? O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . D 4 26.055 65.195 95.867 1 27.72 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . D 4 24.981 64.245 96.575 1 28.59 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . D 4 23.676 64.291 95.864 1 30.46 ? O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . D 4 25.031 64.325 98.077 1 30.78 -1 O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . D 4 25.654 62.819 96.234 1 29.08 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . D 4 25.884 62.381 94.902 1 28.54 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . D 4 25.935 60.861 94.842 1 28.9 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . D 4 27.096 60.37 95.523 1 27.81 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . D 4 24.737 60.202 95.497 1 30.01 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . D 4 24.382 59.026 94.758 1 32.17 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . D 4 25.227 59.815 96.87 1 29.58 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . D 4 24.548 58.682 97.422 1 32.78 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . D 4 26.682 59.506 96.579 1 28.46 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . D 4 27.551 59.707 97.749 1 26.71 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . D 4 27.624 60.819 98.511 1 28.58 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . D 4 28.532 60.67 99.505 1 26.9 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . D 4 29.052 59.432 99.361 1 27.13 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . D 4 30.075 58.631 100.06 1 27.04 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . D 4 30.664 59.099 101.058 1 25.39 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . D 4 30.343 57.392 99.599 1 27.95 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . D 4 29.713 56.854 98.527 1 28.33 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . D 4 30.047 55.598 98.139 1 27.26 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . D 4 28.763 57.539 97.822 1 27.05 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . D 4 28.407 58.805 98.198 1 26.95 ? C4 GDP 202 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #