data_3KBR # _model_server_result.job_id PmvfmcLLMv7YwzCjsglTtQ _model_server_result.datetime_utc '2024-11-06 01:42:17' _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 3kbr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":263}' # _entry.id 3KBR # _exptl.entry_id 3KBR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 5 _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 3KBR _cell.length_a 126.39 _cell.length_b 126.39 _cell.length_c 88.981 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KBR _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 88.981 5 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 88.981 6 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 88.981 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N ? 4 F N N ? 4 H N N ? 4 I 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 disulf ? disulf1 A SG CYS 109 A CYS 131 1_555 A SG CYS 188 A CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A C ASP 43 A ASP 65 1_555 A N MSE 44 A MSE 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C MSE 44 A MSE 66 1_555 A N ALA 45 A ALA 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C LEU 66 A LEU 88 1_555 A N MSE 67 A MSE 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale4 A C MSE 67 A MSE 89 1_555 A N ARG 68 A ARG 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 A C ALA 78 A ALA 100 1_555 A N MSE 79 A MSE 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale6 A C MSE 79 A MSE 101 1_555 A N SER 80 A SER 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C LEU 169 A LEU 191 1_555 A N MSE 170 A MSE 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale8 A C MSE 170 A MSE 192 1_555 A N MSE 171 A MSE 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale9 A C MSE 171 A MSE 193 1_555 A N THR 172 A THR 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale10 A C ARG 231 A ARG 253 1_555 A N MSE 232 A MSE 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale11 A C MSE 232 A MSE 254 1_555 A N GLU 233 A GLU 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? metalc ? metalc1 B NI NI . A NI 1 1_555 A OE1 GLU 112 A GLU 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc2 B NI NI . A NI 1 1_555 A OE2 GLU 112 A GLU 134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc3 B NI NI . A NI 1 1_555 A NE2 HIS 191 A HIS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 166 n n C1 C2 GOL sing 167 n n C1 H11 GOL sing 168 n n C1 H12 GOL sing 169 n n O1 HO1 GOL sing 170 n n C2 O2 GOL sing 171 n n C2 C3 GOL sing 172 n n C2 H2 GOL sing 173 n n O2 HO2 GOL sing 174 n n C3 O3 GOL sing 175 n n C3 H31 GOL sing 176 n n C3 H32 GOL sing 177 n n O3 HO3 GOL sing 178 n n # _atom_sites.entry_id 3KBR _atom_sites.fract_transf_matrix[1][1] 0.007912 _atom_sites.fract_transf_matrix[1][2] 0.004568 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009136 _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] 0.011238 _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 NI A 1 1 1 NI NI . C 3 CL A 1 262 1 CL CL . D 4 GOL A 1 263 1 GOL GOL . E 4 GOL A 1 2 2 GOL GOL . F 4 GOL A 1 3 3 GOL GOL . G 5 FMT A 1 265 2 FMT FMT . H 4 GOL A 1 4 4 GOL GOL . I 4 GOL A 1 5 5 GOL GOL . J 5 FMT A 1 264 1 FMT FMT . K 6 EPE A 1 266 1 EPE EPE . L 7 HOH A 1 6 6 HOH HOH . L 7 HOH A 2 7 7 HOH HOH . L 7 HOH A 3 8 8 HOH HOH . L 7 HOH A 4 9 9 HOH HOH . L 7 HOH A 5 10 10 HOH HOH . L 7 HOH A 6 11 11 HOH HOH . L 7 HOH A 7 12 12 HOH HOH . L 7 HOH A 8 13 13 HOH HOH . L 7 HOH A 9 14 14 HOH HOH . L 7 HOH A 10 15 15 HOH HOH . L 7 HOH A 11 16 16 HOH HOH . L 7 HOH A 12 17 17 HOH HOH . L 7 HOH A 13 18 18 HOH HOH . L 7 HOH A 14 19 19 HOH HOH . L 7 HOH A 15 20 20 HOH HOH . L 7 HOH A 16 21 21 HOH HOH . L 7 HOH A 17 22 22 HOH HOH . L 7 HOH A 18 267 1 HOH HOH . L 7 HOH A 19 268 2 HOH HOH . L 7 HOH A 20 269 3 HOH HOH . L 7 HOH A 21 270 4 HOH HOH . L 7 HOH A 22 271 5 HOH HOH . L 7 HOH A 23 272 23 HOH HOH . L 7 HOH A 24 273 24 HOH HOH . L 7 HOH A 25 274 25 HOH HOH . L 7 HOH A 26 275 26 HOH HOH . L 7 HOH A 27 276 27 HOH HOH . L 7 HOH A 28 277 28 HOH HOH . L 7 HOH A 29 278 29 HOH HOH . L 7 HOH A 30 279 30 HOH HOH . L 7 HOH A 31 280 31 HOH HOH . L 7 HOH A 32 281 32 HOH HOH . L 7 HOH A 33 282 33 HOH HOH . L 7 HOH A 34 283 34 HOH HOH . L 7 HOH A 35 284 35 HOH HOH . L 7 HOH A 36 285 36 HOH HOH . L 7 HOH A 37 286 37 HOH HOH . L 7 HOH A 38 287 38 HOH HOH . L 7 HOH A 39 288 39 HOH HOH . L 7 HOH A 40 289 40 HOH HOH . L 7 HOH A 41 290 41 HOH HOH . L 7 HOH A 42 291 42 HOH HOH . L 7 HOH A 43 292 43 HOH HOH . L 7 HOH A 44 293 44 HOH HOH . L 7 HOH A 45 294 45 HOH HOH . L 7 HOH A 46 295 46 HOH HOH . L 7 HOH A 47 296 47 HOH HOH . L 7 HOH A 48 297 48 HOH HOH . L 7 HOH A 49 298 49 HOH HOH . L 7 HOH A 50 299 50 HOH HOH . L 7 HOH A 51 300 51 HOH HOH . L 7 HOH A 52 301 52 HOH HOH . L 7 HOH A 53 302 53 HOH HOH . L 7 HOH A 54 303 54 HOH HOH . L 7 HOH A 55 304 55 HOH HOH . L 7 HOH A 56 305 56 HOH HOH . L 7 HOH A 57 306 57 HOH HOH . L 7 HOH A 58 307 58 HOH HOH . L 7 HOH A 59 308 59 HOH HOH . L 7 HOH A 60 309 60 HOH HOH . L 7 HOH A 61 310 61 HOH HOH . L 7 HOH A 62 311 62 HOH HOH . L 7 HOH A 63 312 63 HOH HOH . L 7 HOH A 64 313 64 HOH HOH . L 7 HOH A 65 314 65 HOH HOH . L 7 HOH A 66 315 66 HOH HOH . L 7 HOH A 67 316 67 HOH HOH . L 7 HOH A 68 317 68 HOH HOH . L 7 HOH A 69 318 69 HOH HOH . L 7 HOH A 70 319 70 HOH HOH . L 7 HOH A 71 320 71 HOH HOH . L 7 HOH A 72 321 72 HOH HOH . L 7 HOH A 73 322 73 HOH HOH . L 7 HOH A 74 323 74 HOH HOH . L 7 HOH A 75 324 75 HOH HOH . L 7 HOH A 76 325 76 HOH HOH . L 7 HOH A 77 326 77 HOH HOH . L 7 HOH A 78 327 78 HOH HOH . L 7 HOH A 79 328 79 HOH HOH . L 7 HOH A 80 329 80 HOH HOH . L 7 HOH A 81 330 81 HOH HOH . L 7 HOH A 82 331 82 HOH HOH . L 7 HOH A 83 332 83 HOH HOH . L 7 HOH A 84 333 84 HOH HOH . L 7 HOH A 85 334 85 HOH HOH . L 7 HOH A 86 335 86 HOH HOH . L 7 HOH A 87 336 87 HOH HOH . L 7 HOH A 88 337 88 HOH HOH . L 7 HOH A 89 338 89 HOH HOH . L 7 HOH A 90 339 90 HOH HOH . L 7 HOH A 91 340 91 HOH HOH . L 7 HOH A 92 341 92 HOH HOH . L 7 HOH A 93 342 93 HOH HOH . L 7 HOH A 94 343 94 HOH HOH . L 7 HOH A 95 344 95 HOH HOH . L 7 HOH A 96 345 96 HOH HOH . L 7 HOH A 97 346 97 HOH HOH . L 7 HOH A 98 347 98 HOH HOH . L 7 HOH A 99 348 99 HOH HOH . L 7 HOH A 100 349 100 HOH HOH . L 7 HOH A 101 350 101 HOH HOH . L 7 HOH A 102 351 102 HOH HOH . L 7 HOH A 103 352 103 HOH HOH . L 7 HOH A 104 353 104 HOH HOH . L 7 HOH A 105 354 105 HOH HOH . L 7 HOH A 106 355 106 HOH HOH . L 7 HOH A 107 356 107 HOH HOH . L 7 HOH A 108 357 108 HOH HOH . L 7 HOH A 109 358 109 HOH HOH . L 7 HOH A 110 359 110 HOH HOH . L 7 HOH A 111 360 111 HOH HOH . L 7 HOH A 112 361 112 HOH HOH . L 7 HOH A 113 362 113 HOH HOH . L 7 HOH A 114 363 114 HOH HOH . L 7 HOH A 115 364 115 HOH HOH . L 7 HOH A 116 365 116 HOH HOH . L 7 HOH A 117 366 117 HOH HOH . L 7 HOH A 118 367 118 HOH HOH . L 7 HOH A 119 368 119 HOH HOH . L 7 HOH A 120 369 120 HOH HOH . L 7 HOH A 121 370 121 HOH HOH . L 7 HOH A 122 371 122 HOH HOH . L 7 HOH A 123 372 123 HOH HOH . L 7 HOH A 124 373 124 HOH HOH . L 7 HOH A 125 374 125 HOH HOH . L 7 HOH A 126 375 126 HOH HOH . L 7 HOH A 127 376 127 HOH HOH . L 7 HOH A 128 377 128 HOH HOH . L 7 HOH A 129 378 129 HOH HOH . L 7 HOH A 130 379 130 HOH HOH . L 7 HOH A 131 380 131 HOH HOH . L 7 HOH A 132 381 132 HOH HOH . L 7 HOH A 133 382 133 HOH HOH . L 7 HOH A 134 383 134 HOH HOH . L 7 HOH A 135 384 135 HOH HOH . L 7 HOH A 136 385 136 HOH HOH . L 7 HOH A 137 386 137 HOH HOH . L 7 HOH A 138 387 138 HOH HOH . L 7 HOH A 139 388 139 HOH HOH . L 7 HOH A 140 389 140 HOH HOH . L 7 HOH A 141 390 141 HOH HOH . L 7 HOH A 142 391 142 HOH HOH . L 7 HOH A 143 392 143 HOH HOH . L 7 HOH A 144 393 144 HOH HOH . L 7 HOH A 145 394 145 HOH HOH . L 7 HOH A 146 395 146 HOH HOH . L 7 HOH A 147 396 147 HOH HOH . L 7 HOH A 148 397 148 HOH HOH . L 7 HOH A 149 398 149 HOH HOH . L 7 HOH A 150 399 150 HOH HOH . L 7 HOH A 151 400 151 HOH HOH . L 7 HOH A 152 401 152 HOH HOH . L 7 HOH A 153 402 153 HOH HOH . L 7 HOH A 154 403 154 HOH HOH . L 7 HOH A 155 404 155 HOH HOH . L 7 HOH A 156 405 156 HOH HOH . L 7 HOH A 157 406 157 HOH HOH . L 7 HOH A 158 407 158 HOH HOH . L 7 HOH A 159 408 159 HOH HOH . L 7 HOH A 160 409 160 HOH HOH . L 7 HOH A 161 410 161 HOH HOH . L 7 HOH A 162 411 162 HOH HOH . L 7 HOH A 163 412 163 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 C C1 GOL . . . D 4 14.346 14.926 27.97 1 72.62 ? C1 GOL 263 A 1 HETATM 2 O O1 GOL . . . D 4 15.429 15.606 27.379 1 79.42 ? O1 GOL 263 A 1 HETATM 3 C C2 GOL . . . D 4 14.591 14.817 29.469 1 60.29 ? C2 GOL 263 A 1 HETATM 4 O O2 GOL . . . D 4 14.317 16.05 30.102 1 55.46 ? O2 GOL 263 A 1 HETATM 5 C C3 GOL . . . D 4 16.046 14.425 29.699 1 43.38 ? C3 GOL 263 A 1 HETATM 6 O O3 GOL . . . D 4 16.052 13.275 30.511 1 35.41 ? O3 GOL 263 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 224 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #