data_3GAJ # _model_server_result.job_id sfNynsE7NRPxuxI0W7boyA _model_server_result.datetime_utc '2024-10-27 08:31:38' _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 3gaj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":999}' # _entry.id 3GAJ # _exptl.entry_id 3GAJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 120 _cell.entry_id 3GAJ _cell.length_a 67.679 _cell.length_b 67.679 _cell.length_c 111.18 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GAJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -33.8395 58.611733 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -67.679 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 metalc ? metalc1 A O ILE 9 A ILE 3 1_555 D K K . A K 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc2 A OD1 ASN 162 A ASN 156 1_555 E MG MG . A MG 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc3 D K K . A K 182 1_555 B O1G ATP . A ATP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? metalc ? metalc4 D K K . A K 182 1_555 B O2G ATP . A ATP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc5 D K K . A K 182 1_555 B O2A ATP . A ATP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? metalc ? metalc6 D K K . A K 182 1_555 B O1A ATP . A ATP 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.362 ? metalc ? metalc7 E MG MG . A MG 183 1_555 F O HOH . A HOH 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc8 E MG MG . A MG 183 1_555 F O HOH . A HOH 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-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 ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 3GAJ _atom_sites.fract_transf_matrix[1][1] 0.014776 _atom_sites.fract_transf_matrix[1][2] 0.008531 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017061 _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] 0.008994 _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 B 2 ATP A 1 999 999 ATP ATP . C 3 B12 A 1 800 800 B12 B12 . D 4 K A 1 182 1 K K . E 5 MG A 1 183 1 MG MG . F 6 HOH A 1 184 4 HOH HOH . F 6 HOH A 2 185 5 HOH HOH . F 6 HOH A 3 186 6 HOH HOH . F 6 HOH A 4 187 7 HOH HOH . F 6 HOH A 5 188 8 HOH HOH . F 6 HOH A 6 189 9 HOH HOH . F 6 HOH A 7 190 10 HOH HOH . F 6 HOH A 8 191 12 HOH HOH . F 6 HOH A 9 192 13 HOH HOH . F 6 HOH A 10 193 14 HOH HOH . F 6 HOH A 11 194 194 HOH HOH . F 6 HOH A 12 195 195 HOH HOH . F 6 HOH A 13 196 196 HOH HOH . F 6 HOH A 14 197 15 HOH HOH . F 6 HOH A 15 198 198 HOH HOH . F 6 HOH A 16 199 199 HOH HOH . F 6 HOH A 17 200 200 HOH HOH . F 6 HOH A 18 201 201 HOH HOH . F 6 HOH A 19 202 16 HOH HOH . F 6 HOH A 20 203 17 HOH HOH . F 6 HOH A 21 204 18 HOH HOH . F 6 HOH A 22 205 19 HOH HOH . F 6 HOH A 23 206 20 HOH HOH . F 6 HOH A 24 207 207 HOH HOH . F 6 HOH A 25 208 208 HOH HOH . F 6 HOH A 26 209 209 HOH HOH . F 6 HOH A 27 210 210 HOH HOH . F 6 HOH A 28 211 211 HOH HOH . F 6 HOH A 29 212 212 HOH HOH . F 6 HOH A 30 213 213 HOH HOH . F 6 HOH A 31 214 214 HOH HOH . F 6 HOH A 32 215 215 HOH HOH . F 6 HOH A 33 216 216 HOH HOH . F 6 HOH A 34 217 217 HOH HOH . F 6 HOH A 35 218 218 HOH HOH . F 6 HOH A 36 219 219 HOH HOH . F 6 HOH A 37 220 220 HOH HOH . F 6 HOH A 38 221 221 HOH HOH . F 6 HOH A 39 222 222 HOH HOH . F 6 HOH A 40 223 223 HOH HOH . F 6 HOH A 41 224 224 HOH HOH . F 6 HOH A 42 225 21 HOH HOH . F 6 HOH A 43 226 22 HOH HOH . F 6 HOH A 44 227 23 HOH HOH . F 6 HOH A 45 228 24 HOH HOH . F 6 HOH A 46 229 25 HOH HOH . F 6 HOH A 47 230 26 HOH HOH . F 6 HOH A 48 231 27 HOH HOH . F 6 HOH A 49 232 28 HOH HOH . F 6 HOH A 50 233 29 HOH HOH . F 6 HOH A 51 234 30 HOH HOH . F 6 HOH A 52 235 31 HOH HOH . F 6 HOH A 53 236 33 HOH HOH . F 6 HOH A 54 237 34 HOH HOH . F 6 HOH A 55 238 35 HOH HOH . F 6 HOH A 56 239 37 HOH HOH . F 6 HOH A 57 240 38 HOH HOH . F 6 HOH A 58 241 39 HOH HOH . F 6 HOH A 59 242 40 HOH HOH . F 6 HOH A 60 243 41 HOH HOH . F 6 HOH A 61 244 42 HOH HOH . F 6 HOH A 62 245 43 HOH HOH . F 6 HOH A 63 246 44 HOH HOH . F 6 HOH A 64 247 45 HOH HOH . F 6 HOH A 65 248 46 HOH HOH . F 6 HOH A 66 249 47 HOH HOH . F 6 HOH A 67 250 48 HOH HOH . F 6 HOH A 68 251 49 HOH HOH . F 6 HOH A 69 252 50 HOH HOH . F 6 HOH A 70 253 51 HOH HOH . F 6 HOH A 71 254 52 HOH HOH . F 6 HOH A 72 255 53 HOH HOH . F 6 HOH A 73 256 54 HOH HOH . F 6 HOH A 74 257 55 HOH HOH . F 6 HOH A 75 258 56 HOH HOH . F 6 HOH A 76 259 57 HOH HOH . F 6 HOH A 77 260 58 HOH HOH . F 6 HOH A 78 261 60 HOH HOH . F 6 HOH A 79 262 61 HOH HOH . F 6 HOH A 80 263 62 HOH HOH . F 6 HOH A 81 264 63 HOH HOH . F 6 HOH A 82 265 64 HOH HOH . F 6 HOH A 83 266 65 HOH HOH . F 6 HOH A 84 267 66 HOH HOH . F 6 HOH A 85 268 67 HOH HOH . F 6 HOH A 86 269 68 HOH HOH . F 6 HOH A 87 270 69 HOH HOH . F 6 HOH A 88 271 70 HOH HOH . F 6 HOH A 89 272 71 HOH HOH . F 6 HOH A 90 273 72 HOH HOH . F 6 HOH A 91 274 73 HOH HOH . F 6 HOH A 92 275 74 HOH HOH . F 6 HOH A 93 276 75 HOH HOH . F 6 HOH A 94 277 76 HOH HOH . F 6 HOH A 95 278 77 HOH HOH . F 6 HOH A 96 279 78 HOH HOH . F 6 HOH A 97 280 79 HOH HOH . F 6 HOH A 98 281 80 HOH HOH . F 6 HOH A 99 282 81 HOH HOH . F 6 HOH A 100 283 82 HOH HOH . F 6 HOH A 101 284 83 HOH HOH . F 6 HOH A 102 285 84 HOH HOH . F 6 HOH A 103 286 85 HOH HOH . F 6 HOH A 104 287 86 HOH HOH . F 6 HOH A 105 288 88 HOH HOH . F 6 HOH A 106 289 89 HOH HOH . F 6 HOH A 107 290 90 HOH HOH . F 6 HOH A 108 291 91 HOH HOH . F 6 HOH A 109 292 92 HOH HOH . F 6 HOH A 110 293 93 HOH HOH . F 6 HOH A 111 294 94 HOH HOH . F 6 HOH A 112 295 95 HOH HOH . F 6 HOH A 113 296 96 HOH HOH . F 6 HOH A 114 297 97 HOH HOH . F 6 HOH A 115 298 98 HOH HOH . F 6 HOH A 116 299 99 HOH HOH . F 6 HOH A 117 300 100 HOH HOH . F 6 HOH A 118 301 101 HOH HOH . F 6 HOH A 119 302 102 HOH HOH . F 6 HOH A 120 303 104 HOH HOH . F 6 HOH A 121 304 105 HOH HOH . F 6 HOH A 122 305 106 HOH HOH . F 6 HOH A 123 306 107 HOH HOH . F 6 HOH A 124 307 108 HOH HOH . F 6 HOH A 125 308 109 HOH HOH . F 6 HOH A 126 309 111 HOH HOH . F 6 HOH A 127 310 112 HOH HOH . F 6 HOH A 128 311 113 HOH HOH . F 6 HOH A 129 312 114 HOH HOH . F 6 HOH A 130 313 115 HOH HOH . F 6 HOH A 131 314 116 HOH HOH . F 6 HOH A 132 315 117 HOH HOH . F 6 HOH A 133 316 118 HOH HOH . F 6 HOH A 134 317 119 HOH HOH . F 6 HOH A 135 318 120 HOH HOH . F 6 HOH A 136 319 121 HOH HOH . F 6 HOH A 137 320 122 HOH HOH . F 6 HOH A 138 321 124 HOH HOH . F 6 HOH A 139 322 125 HOH HOH . F 6 HOH A 140 323 126 HOH HOH . F 6 HOH A 141 324 127 HOH HOH . F 6 HOH A 142 325 128 HOH HOH . F 6 HOH A 143 326 129 HOH HOH . F 6 HOH A 144 327 130 HOH HOH . F 6 HOH A 145 328 131 HOH HOH . F 6 HOH A 146 329 132 HOH HOH . F 6 HOH A 147 330 133 HOH HOH . F 6 HOH A 148 331 134 HOH HOH . F 6 HOH A 149 332 135 HOH HOH . F 6 HOH A 150 333 138 HOH HOH . F 6 HOH A 151 334 140 HOH HOH . F 6 HOH A 152 335 141 HOH HOH . F 6 HOH A 153 336 142 HOH HOH . F 6 HOH A 154 337 143 HOH HOH . F 6 HOH A 155 338 145 HOH HOH . F 6 HOH A 156 339 147 HOH HOH . F 6 HOH A 157 340 148 HOH HOH . F 6 HOH A 158 341 149 HOH HOH . F 6 HOH A 159 342 152 HOH HOH . F 6 HOH A 160 343 155 HOH HOH . F 6 HOH A 161 344 157 HOH HOH . F 6 HOH A 162 345 159 HOH HOH . F 6 HOH A 163 346 162 HOH HOH . F 6 HOH A 164 347 166 HOH HOH . F 6 HOH A 165 348 168 HOH HOH . F 6 HOH A 166 349 169 HOH HOH . F 6 HOH A 167 350 175 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 ATP . . . B 2 -27.386 39.944 -6.917 1 7.82 ? PG ATP 999 A 1 HETATM 2 O O1G ATP . . . B 2 -26.48 40.889 -6.171 1 9.01 ? O1G ATP 999 A 1 HETATM 3 O O2G ATP . . . B 2 -28.028 38.885 -6.026 1 8.03 ? O2G ATP 999 A 1 HETATM 4 O O3G ATP . . . B 2 -28.386 40.592 -7.83 1 8.11 ? O3G ATP 999 A 1 HETATM 5 P PB ATP . . . B 2 -26.461 37.665 -8.42 1 7.97 ? PB ATP 999 A 1 HETATM 6 O O1B ATP . . . B 2 -27.819 37.127 -8.124 1 7.99 ? O1B ATP 999 A 1 HETATM 7 O O2B ATP . . . B 2 -25.971 37.627 -9.833 1 8.6 ? O2B ATP 999 A 1 HETATM 8 O O3B ATP . . . B 2 -26.361 39.15 -7.835 1 8.57 ? O3B ATP 999 A 1 HETATM 9 P PA ATP . . . B 2 -25.407 36.488 -5.977 1 7.87 ? PA ATP 999 A 1 HETATM 10 O O1A ATP . . . B 2 -26.811 36.295 -5.541 1 7.54 ? O1A ATP 999 A 1 HETATM 11 O O2A ATP . . . B 2 -24.549 37.494 -5.281 1 8.6 ? O2A ATP 999 A 1 HETATM 12 O O3A ATP . . . B 2 -25.375 36.843 -7.555 1 7.96 ? O3A ATP 999 A 1 HETATM 13 O O5' ATP . . . B 2 -24.696 35.071 -6.005 1 8.53 ? O5' ATP 999 A 1 HETATM 14 C C5' ATP . . . B 2 -23.28 34.915 -5.845 1 9.39 ? C5' ATP 999 A 1 HETATM 15 C C4' ATP . . . B 2 -22.747 34.013 -6.939 1 8.04 ? C4' ATP 999 A 1 HETATM 16 O O4' ATP . . . B 2 -23.489 32.779 -6.957 1 8.39 ? O4' ATP 999 A 1 HETATM 17 C C3' ATP . . . B 2 -22.991 34.578 -8.323 1 8.24 ? C3' ATP 999 A 1 HETATM 18 O O3' ATP . . . B 2 -21.878 35.392 -8.696 1 10 ? O3' ATP 999 A 1 HETATM 19 C C2' ATP . . . B 2 -23.135 33.36 -9.203 1 8.86 ? C2' ATP 999 A 1 HETATM 20 O O2' ATP . . . B 2 -21.867 32.752 -9.458 1 8.9 ? O2' ATP 999 A 1 HETATM 21 C C1' ATP . . . B 2 -23.858 32.399 -8.288 1 9.09 ? C1' ATP 999 A 1 HETATM 22 N N9 ATP . . . B 2 -25.349 32.486 -8.33 1 7.47 ? N9 ATP 999 A 1 HETATM 23 C C8 ATP . . . B 2 -26.167 33.565 -8.433 1 7.85 ? C8 ATP 999 A 1 HETATM 24 N N7 ATP . . . B 2 -27.478 33.228 -8.368 1 7.91 ? N7 ATP 999 A 1 HETATM 25 C C5 ATP . . . B 2 -27.491 31.879 -8.203 1 7.73 ? C5 ATP 999 A 1 HETATM 26 C C6 ATP . . . B 2 -28.514 30.854 -8.053 1 6.35 ? C6 ATP 999 A 1 HETATM 27 N N6 ATP . . . B 2 -29.826 31.188 -8.055 1 7.57 ? N6 ATP 999 A 1 HETATM 28 N N1 ATP . . . B 2 -28.117 29.571 -7.896 1 7.81 ? N1 ATP 999 A 1 HETATM 29 C C2 ATP . . . B 2 -26.815 29.243 -7.87 1 8.04 ? C2 ATP 999 A 1 HETATM 30 N N3 ATP . . . B 2 -25.795 30.114 -7.999 1 8.29 ? N3 ATP 999 A 1 HETATM 31 C C4 ATP . . . B 2 -26.118 31.414 -8.159 1 6.85 ? C4 ATP 999 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 377 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #