data_3KB2 # _model_server_result.job_id xaJEngC7X3YyW-PsNqbAtg _model_server_result.datetime_utc '2024-11-15 22:48:09' _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 3kb2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":180}' # _entry.id 3KB2 # _exptl.entry_id 3KB2 _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-3'-MONOPHOSPHATE-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 90 _cell.angle_beta 91.57 _cell.angle_gamma 90 _cell.entry_id 3KB2 _cell.length_a 45.478 _cell.length_b 63.05 _cell.length_c 70.456 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KB2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? dimeric 2 author_defined_assembly 1 PISA dimeric 2 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,B,C,D,E,F,G,H 1 1 A,C,D,G 2 1 B,E,F,H 2 2 # 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' 1_554 x,y,z-1 1 0 0 0 1 0 0 0 1 1.93037 0 -70.429551 # 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 covale ? covale1 A C VAL 135 A VAL 135 1_555 A N MSE 136 A MSE 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale2 A C MSE 136 A MSE 136 1_555 A N SER 137 A SER 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 B C VAL 135 B VAL 135 1_555 B N MSE 136 B MSE 136 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 B C MSE 136 B MSE 136 1_555 B N SER 137 B SER 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 A OG SER 15 A SER 15 1_555 D MG MG . A MG 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 B OG SER 15 B SER 15 1_555 F MG MG . B MG 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc3 C O3B G3D . A G3D 180 1_555 D MG MG . A MG 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc4 D MG MG . A MG 181 1_555 G O HOH . A HOH 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc5 D MG MG . A MG 181 1_555 H O HOH . B HOH 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc6 D MG MG . A MG 181 1_555 G O HOH . A HOH 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc7 D MG MG . A MG 181 1_555 G O HOH . A HOH 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc8 E O3B G3D . B G3D 180 1_555 F MG MG . B MG 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc9 F MG MG . B MG 181 1_555 H O HOH . B HOH 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id G3D _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3KB2 _atom_sites.fract_transf_matrix[1][1] 0.021989 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000603 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01586 _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] 0.014199 _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 G3D A 1 180 180 G3D G3D . D 3 MG A 1 181 181 MG MG . E 2 G3D B 1 180 180 G3D G3D . F 3 MG B 1 181 181 MG MG . G 4 HOH A 1 174 174 HOH HOH . G 4 HOH A 2 175 5 HOH HOH . G 4 HOH A 3 176 8 HOH HOH . G 4 HOH A 4 177 9 HOH HOH . G 4 HOH A 5 178 12 HOH HOH . G 4 HOH A 6 179 17 HOH HOH . G 4 HOH A 7 182 18 HOH HOH . G 4 HOH A 8 183 21 HOH HOH . G 4 HOH A 9 184 22 HOH HOH . G 4 HOH A 10 185 24 HOH HOH . G 4 HOH A 11 186 25 HOH HOH . G 4 HOH A 12 187 28 HOH HOH . G 4 HOH A 13 188 30 HOH HOH . G 4 HOH A 14 189 31 HOH HOH . G 4 HOH A 15 190 32 HOH HOH . G 4 HOH A 16 191 33 HOH HOH . G 4 HOH A 17 192 35 HOH HOH . G 4 HOH A 18 193 37 HOH HOH . G 4 HOH A 19 194 38 HOH HOH . G 4 HOH A 20 195 39 HOH HOH . G 4 HOH A 21 196 40 HOH HOH . G 4 HOH A 22 197 41 HOH HOH . G 4 HOH A 23 198 43 HOH HOH . G 4 HOH A 24 199 45 HOH HOH . G 4 HOH A 25 200 46 HOH HOH . G 4 HOH A 26 201 52 HOH HOH . G 4 HOH A 27 202 53 HOH HOH . G 4 HOH A 28 203 57 HOH HOH . G 4 HOH A 29 204 58 HOH HOH . G 4 HOH A 30 205 61 HOH HOH . G 4 HOH A 31 206 64 HOH HOH . G 4 HOH A 32 207 65 HOH HOH . G 4 HOH A 33 208 66 HOH HOH . G 4 HOH A 34 209 67 HOH HOH . G 4 HOH A 35 210 68 HOH HOH . G 4 HOH A 36 211 69 HOH HOH . G 4 HOH A 37 213 73 HOH HOH . G 4 HOH A 38 214 76 HOH HOH . G 4 HOH A 39 215 78 HOH HOH . G 4 HOH A 40 216 81 HOH HOH . G 4 HOH A 41 217 83 HOH HOH . G 4 HOH A 42 218 85 HOH HOH . G 4 HOH A 43 219 89 HOH HOH . G 4 HOH A 44 220 91 HOH HOH . G 4 HOH A 45 221 93 HOH HOH . G 4 HOH A 46 222 94 HOH HOH . G 4 HOH A 47 223 95 HOH HOH . G 4 HOH A 48 224 97 HOH HOH . G 4 HOH A 49 225 98 HOH HOH . G 4 HOH A 50 226 99 HOH HOH . G 4 HOH A 51 227 100 HOH HOH . G 4 HOH A 52 228 104 HOH HOH . G 4 HOH A 53 229 105 HOH HOH . G 4 HOH A 54 230 106 HOH HOH . G 4 HOH A 55 231 107 HOH HOH . G 4 HOH A 56 232 108 HOH HOH . G 4 HOH A 57 233 109 HOH HOH . G 4 HOH A 58 234 111 HOH HOH . G 4 HOH A 59 235 113 HOH HOH . G 4 HOH A 60 236 114 HOH HOH . G 4 HOH A 61 237 115 HOH HOH . G 4 HOH A 62 238 116 HOH HOH . G 4 HOH A 63 239 117 HOH HOH . G 4 HOH A 64 240 121 HOH HOH . G 4 HOH A 65 241 122 HOH HOH . G 4 HOH A 66 242 123 HOH HOH . G 4 HOH A 67 243 124 HOH HOH . G 4 HOH A 68 244 126 HOH HOH . G 4 HOH A 69 245 127 HOH HOH . G 4 HOH A 70 246 128 HOH HOH . G 4 HOH A 71 247 130 HOH HOH . G 4 HOH A 72 248 132 HOH HOH . G 4 HOH A 73 249 133 HOH HOH . G 4 HOH A 74 250 134 HOH HOH . G 4 HOH A 75 251 135 HOH HOH . G 4 HOH A 76 253 137 HOH HOH . G 4 HOH A 77 254 138 HOH HOH . G 4 HOH A 78 255 140 HOH HOH . G 4 HOH A 79 256 141 HOH HOH . G 4 HOH A 80 257 142 HOH HOH . G 4 HOH A 81 258 143 HOH HOH . G 4 HOH A 82 259 144 HOH HOH . G 4 HOH A 83 260 145 HOH HOH . G 4 HOH A 84 261 146 HOH HOH . G 4 HOH A 85 262 147 HOH HOH . G 4 HOH A 86 263 148 HOH HOH . G 4 HOH A 87 264 149 HOH HOH . G 4 HOH A 88 265 150 HOH HOH . G 4 HOH A 89 266 151 HOH HOH . G 4 HOH A 90 267 152 HOH HOH . G 4 HOH A 91 268 171 HOH HOH . G 4 HOH A 92 269 172 HOH HOH . G 4 HOH A 93 270 173 HOH HOH . H 4 HOH B 1 174 1 HOH HOH . H 4 HOH B 2 175 175 HOH HOH . H 4 HOH B 3 176 176 HOH HOH . H 4 HOH B 4 177 2 HOH HOH . H 4 HOH B 5 178 3 HOH HOH . H 4 HOH B 6 179 4 HOH HOH . H 4 HOH B 7 182 6 HOH HOH . H 4 HOH B 8 183 7 HOH HOH . H 4 HOH B 9 184 10 HOH HOH . H 4 HOH B 10 185 11 HOH HOH . H 4 HOH B 11 186 13 HOH HOH . H 4 HOH B 12 187 14 HOH HOH . H 4 HOH B 13 188 15 HOH HOH . H 4 HOH B 14 189 16 HOH HOH . H 4 HOH B 15 190 19 HOH HOH . H 4 HOH B 16 191 20 HOH HOH . H 4 HOH B 17 192 23 HOH HOH . H 4 HOH B 18 193 26 HOH HOH . H 4 HOH B 19 194 27 HOH HOH . H 4 HOH B 20 195 29 HOH HOH . H 4 HOH B 21 196 34 HOH HOH . H 4 HOH B 22 197 36 HOH HOH . H 4 HOH B 23 198 42 HOH HOH . H 4 HOH B 24 199 44 HOH HOH . H 4 HOH B 25 200 47 HOH HOH . H 4 HOH B 26 201 48 HOH HOH . H 4 HOH B 27 202 49 HOH HOH . H 4 HOH B 28 203 50 HOH HOH . H 4 HOH B 29 204 51 HOH HOH . H 4 HOH B 30 205 54 HOH HOH . H 4 HOH B 31 206 55 HOH HOH . H 4 HOH B 32 207 56 HOH HOH . H 4 HOH B 33 208 59 HOH HOH . H 4 HOH B 34 209 60 HOH HOH . H 4 HOH B 35 210 62 HOH HOH . H 4 HOH B 36 211 63 HOH HOH . H 4 HOH B 37 212 72 HOH HOH . H 4 HOH B 38 213 71 HOH HOH . H 4 HOH B 39 214 74 HOH HOH . H 4 HOH B 40 215 75 HOH HOH . H 4 HOH B 41 216 77 HOH HOH . H 4 HOH B 42 217 79 HOH HOH . H 4 HOH B 43 218 80 HOH HOH . H 4 HOH B 44 219 82 HOH HOH . H 4 HOH B 45 220 84 HOH HOH . H 4 HOH B 46 221 86 HOH HOH . H 4 HOH B 47 222 87 HOH HOH . H 4 HOH B 48 223 88 HOH HOH . H 4 HOH B 49 224 90 HOH HOH . H 4 HOH B 50 225 92 HOH HOH . H 4 HOH B 51 226 96 HOH HOH . H 4 HOH B 52 227 101 HOH HOH . H 4 HOH B 53 228 102 HOH HOH . H 4 HOH B 54 229 103 HOH HOH . H 4 HOH B 55 230 110 HOH HOH . H 4 HOH B 56 231 112 HOH HOH . H 4 HOH B 57 232 118 HOH HOH . H 4 HOH B 58 233 119 HOH HOH . H 4 HOH B 59 234 120 HOH HOH . H 4 HOH B 60 235 125 HOH HOH . H 4 HOH B 61 236 129 HOH HOH . H 4 HOH B 62 237 131 HOH HOH . H 4 HOH B 63 238 139 HOH HOH . H 4 HOH B 64 239 153 HOH HOH . H 4 HOH B 65 240 154 HOH HOH . H 4 HOH B 66 241 155 HOH HOH . H 4 HOH B 67 242 156 HOH HOH . H 4 HOH B 68 243 157 HOH HOH . H 4 HOH B 69 244 158 HOH HOH . H 4 HOH B 70 245 159 HOH HOH . H 4 HOH B 71 246 160 HOH HOH . H 4 HOH B 72 247 161 HOH HOH . H 4 HOH B 73 248 162 HOH HOH . H 4 HOH B 74 249 163 HOH HOH . H 4 HOH B 75 250 164 HOH HOH . H 4 HOH B 76 251 165 HOH HOH . H 4 HOH B 77 252 136 HOH HOH . H 4 HOH B 78 253 167 HOH HOH . H 4 HOH B 79 254 168 HOH HOH . H 4 HOH B 80 255 169 HOH HOH . H 4 HOH B 81 256 170 HOH HOH . H 4 HOH B 82 257 70 HOH HOH . H 4 HOH B 83 258 166 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 G3D . . . E 2 -18.407 54.343 79.412 1 27.59 ? PB G3D 180 B 1 HETATM 2 O O1B G3D . . . E 2 -17.765 54.713 78.073 1 27.65 ? O1B G3D 180 B 1 HETATM 3 O O2B G3D . . . E 2 -17.529 54.287 80.585 1 29.78 ? O2B G3D 180 B 1 HETATM 4 O O3B G3D . . . E 2 -19.647 55.402 79.694 1 24.43 ? O3B G3D 180 B 1 HETATM 5 P PA G3D . . . E 2 -20.664 52.611 79.779 1 34.04 ? PA G3D 180 B 1 HETATM 6 O O3A G3D . . . E 2 -19.185 53 79.282 1 40.37 ? O3A G3D 180 B 1 HETATM 7 O O1A G3D . . . E 2 -20.82 52.783 81.216 1 44.06 ? O1A G3D 180 B 1 HETATM 8 O O2A G3D . . . E 2 -21.639 53.329 78.835 1 49.78 ? O2A G3D 180 B 1 HETATM 9 O O5' G3D . . . E 2 -20.658 50.968 79.528 1 34.55 ? O5' G3D 180 B 1 HETATM 10 C C5' G3D . . . E 2 -19.694 50.612 78.453 1 34.58 ? C5' G3D 180 B 1 HETATM 11 C C4' G3D . . . E 2 -20.154 49.08 78.311 1 42.55 ? C4' G3D 180 B 1 HETATM 12 O O4' G3D . . . E 2 -19.733 48.208 79.372 1 35.48 ? O4' G3D 180 B 1 HETATM 13 C C3' G3D . . . E 2 -21.548 48.781 78.122 1 47.54 ? C3' G3D 180 B 1 HETATM 14 O O3' G3D . . . E 2 -21.764 47.836 77.104 1 63.83 ? O3' G3D 180 B 1 HETATM 15 C C2' G3D . . . E 2 -22.196 48.419 79.489 1 53 ? C2' G3D 180 B 1 HETATM 16 O O2' G3D . . . E 2 -23.21 47.587 79.37 1 51.93 ? O2' G3D 180 B 1 HETATM 17 C C1' G3D . . . E 2 -20.832 47.47 79.917 1 37.2 ? C1' G3D 180 B 1 HETATM 18 N N9 G3D . . . E 2 -20.913 47.222 81.406 1 37.76 ? N9 G3D 180 B 1 HETATM 19 C C8 G3D . . . E 2 -21.65 48.013 82.275 1 39.4 ? C8 G3D 180 B 1 HETATM 20 N N7 G3D . . . E 2 -21.357 47.352 83.418 1 41.71 ? N7 G3D 180 B 1 HETATM 21 C C5 G3D . . . E 2 -20.635 46.167 83.269 1 44.85 ? C5 G3D 180 B 1 HETATM 22 C C6 G3D . . . E 2 -20.262 45.366 84.164 1 36.84 ? C6 G3D 180 B 1 HETATM 23 O O6 G3D . . . E 2 -20.307 45.227 85.426 1 38.85 ? O6 G3D 180 B 1 HETATM 24 N N1 G3D . . . E 2 -19.395 44.29 83.569 1 39.97 ? N1 G3D 180 B 1 HETATM 25 C C2 G3D . . . E 2 -19.233 44.369 82.298 1 42.78 ? C2 G3D 180 B 1 HETATM 26 N N2 G3D . . . E 2 -18.305 43.332 81.74 1 42.59 ? N2 G3D 180 B 1 HETATM 27 N N3 G3D . . . E 2 -19.554 45.261 81.376 1 43.54 ? N3 G3D 180 B 1 HETATM 28 C C4 G3D . . . E 2 -20.343 46.138 81.992 1 47.8 ? C4 G3D 180 B 1 HETATM 29 P P1 G3D . . . E 2 -22.549 47.658 75.886 1 69.87 ? P1 G3D 180 B 1 HETATM 30 O O4P G3D . . . E 2 -23.855 47.133 76.14 1 76.98 ? O4P G3D 180 B 1 HETATM 31 O O5P G3D . . . E 2 -21.81 46.687 74.838 1 75.48 ? O5P G3D 180 B 1 HETATM 32 O O6P G3D . . . E 2 -22.491 48.956 75.075 1 68.53 ? O6P G3D 180 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 32 #