data_3P41 # _model_server_result.job_id ncO1-8XYHhzfY7vw1OhAmQ _model_server_result.datetime_utc '2024-11-05 23:12:27' _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 3p41 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":302}' # _entry.id 3P41 # _exptl.entry_id 3P41 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _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 3P41 _cell.length_a 48.362 _cell.length_b 48.362 _cell.length_c 208.592 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3P41 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 69.530667 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id H _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 ALA 24 A ALA 16 1_555 A N MSE 25 A MSE 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 A C MSE 25 A MSE 17 1_555 A N HIS 26 A HIS 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C ALA 42 A ALA 34 1_555 A N MSE 43 A MSE 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MSE 43 A MSE 35 1_555 A N ARG 44 A ARG 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 A C VAL 47 A VAL 39 1_555 A N MSE 48 A MSE 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale6 A C MSE 48 A MSE 40 1_555 A N ASN 49 A ASN 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale7 A C ALA 95 A ALA 87 1_555 A N MSE 96 A MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale8 A C MSE 96 A MSE 88 1_555 A N ASP 97 A ASP 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 A C ALA 115 A ALA 107 1_555 A N SCY 116 A SCY 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.361 ? covale ? covale10 A C SCY 116 A SCY 108 1_555 A N ALA 117 A ALA 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? covale ? covale11 A C ARG 147 A ARG 139 1_555 A N MSE 148 A MSE 140 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.331 ? covale ? covale12 A C ARG 147 A ARG 139 1_555 A N MSE 148 A MSE 140 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.331 ? covale ? covale13 A C MSE 148 A MSE 140 1_555 A N VAL 149 A VAL 141 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.331 ? covale ? covale14 A C MSE 148 A MSE 140 1_555 A N VAL 149 A VAL 141 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.321 ? covale ? covale15 A C GLY 160 A GLY 152 1_555 A N MSE 161 A MSE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale16 A C MSE 161 A MSE 153 1_555 A N VAL 162 A VAL 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale17 A C TYR 183 A TYR 175 1_555 A N MSE 184 A MSE 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale18 A C MSE 184 A MSE 176 1_555 A N HIS 185 A HIS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? metalc ? metalc1 A OD1 ASP 91 A ASP 83 1_555 C MG MG . A MG 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 A OD2 ASP 91 A ASP 83 1_555 D MG MG . A MG 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc3 A OD1 ASP 97 A ASP 89 1_555 C MG MG . A MG 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc4 A OD1 ASP 97 A ASP 89 1_555 D MG MG . A MG 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc5 A OD1 ASP 231 A ASP 223 1_555 B MG MG . A MG 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc6 B MG MG . A MG 296 1_555 G O4 POP . A POP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc7 B MG MG . A MG 296 1_555 J O HOH . A HOH 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc8 B MG MG . A MG 296 1_555 J O HOH . A HOH 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc9 B MG MG . A MG 296 1_555 J O HOH . A HOH 375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc10 B MG MG . A MG 296 1_555 J O HOH . A HOH 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc11 C MG MG . A MG 297 1_555 F O2A DMA . A DMA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc12 C MG MG . A MG 297 1_555 J O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc13 C MG MG . A MG 297 1_555 J O HOH . A HOH 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc14 C MG MG . A MG 297 1_555 J O HOH . A HOH 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc15 D MG MG . A MG 298 1_555 F O2B DMA . A DMA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.795 ? metalc ? metalc16 D MG MG . A MG 298 1_555 F O2A DMA . A DMA 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc17 D MG MG . A MG 298 1_555 J O HOH . A HOH 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc18 D MG MG . A MG 298 1_555 J O HOH . A HOH 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? # _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 154 n n C1 C2 GOL sing 155 n n C1 H11 GOL sing 156 n n C1 H12 GOL sing 157 n n O1 HO1 GOL sing 158 n n C2 O2 GOL sing 159 n n C2 C3 GOL sing 160 n n C2 H2 GOL sing 161 n n O2 HO2 GOL sing 162 n n C3 O3 GOL sing 163 n n C3 H31 GOL sing 164 n n C3 H32 GOL sing 165 n n O3 HO3 GOL sing 166 n n # _atom_sites.entry_id 3P41 _atom_sites.fract_transf_matrix[1][1] 0.020677 _atom_sites.fract_transf_matrix[1][2] 0.011938 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023876 _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] 0.004794 _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 MG A 1 296 1 MG MG . C 2 MG A 1 297 1 MG MG . D 2 MG A 1 298 1 MG MG . E 3 DMA A 1 299 1 DMA IPE . F 3 DMA A 1 300 1 DMA IPE . G 4 POP A 1 301 1 POP POP . H 5 GOL A 1 302 1 GOL GOL . I 6 CL A 1 303 1 CL CL . J 7 HOH A 1 304 1 HOH HOH . J 7 HOH A 2 305 2 HOH HOH . J 7 HOH A 3 306 3 HOH HOH . J 7 HOH A 4 307 4 HOH HOH . J 7 HOH A 5 308 5 HOH HOH . J 7 HOH A 6 309 6 HOH HOH . J 7 HOH A 7 310 7 HOH HOH . J 7 HOH A 8 311 8 HOH HOH . J 7 HOH A 9 312 9 HOH HOH . J 7 HOH A 10 313 10 HOH HOH . J 7 HOH A 11 314 12 HOH HOH . J 7 HOH A 12 315 13 HOH HOH . J 7 HOH A 13 316 14 HOH HOH . J 7 HOH A 14 317 15 HOH HOH . J 7 HOH A 15 318 16 HOH HOH . J 7 HOH A 16 319 17 HOH HOH . J 7 HOH A 17 320 18 HOH HOH . J 7 HOH A 18 321 19 HOH HOH . J 7 HOH A 19 322 20 HOH HOH . J 7 HOH A 20 323 21 HOH HOH . J 7 HOH A 21 324 22 HOH HOH . J 7 HOH A 22 325 23 HOH HOH . J 7 HOH A 23 326 24 HOH HOH . J 7 HOH A 24 327 25 HOH HOH . J 7 HOH A 25 328 26 HOH HOH . J 7 HOH A 26 329 27 HOH HOH . J 7 HOH A 27 330 29 HOH HOH . J 7 HOH A 28 331 30 HOH HOH . J 7 HOH A 29 332 32 HOH HOH . J 7 HOH A 30 333 33 HOH HOH . J 7 HOH A 31 334 34 HOH HOH . J 7 HOH A 32 335 35 HOH HOH . J 7 HOH A 33 336 36 HOH HOH . J 7 HOH A 34 337 37 HOH HOH . J 7 HOH A 35 338 38 HOH HOH . J 7 HOH A 36 339 39 HOH HOH . J 7 HOH A 37 340 41 HOH HOH . J 7 HOH A 38 341 42 HOH HOH . J 7 HOH A 39 342 44 HOH HOH . J 7 HOH A 40 343 46 HOH HOH . J 7 HOH A 41 344 47 HOH HOH . J 7 HOH A 42 345 48 HOH HOH . J 7 HOH A 43 346 49 HOH HOH . J 7 HOH A 44 347 50 HOH HOH . J 7 HOH A 45 348 51 HOH HOH . J 7 HOH A 46 349 52 HOH HOH . J 7 HOH A 47 350 53 HOH HOH . J 7 HOH A 48 351 54 HOH HOH . J 7 HOH A 49 352 55 HOH HOH . J 7 HOH A 50 353 56 HOH HOH . J 7 HOH A 51 354 57 HOH HOH . J 7 HOH A 52 355 59 HOH HOH . J 7 HOH A 53 356 60 HOH HOH . J 7 HOH A 54 357 61 HOH HOH . J 7 HOH A 55 358 62 HOH HOH . J 7 HOH A 56 359 65 HOH HOH . J 7 HOH A 57 360 66 HOH HOH . J 7 HOH A 58 361 67 HOH HOH . J 7 HOH A 59 362 68 HOH HOH . J 7 HOH A 60 363 69 HOH HOH . J 7 HOH A 61 364 70 HOH HOH . J 7 HOH A 62 365 72 HOH HOH . J 7 HOH A 63 366 73 HOH HOH . J 7 HOH A 64 367 74 HOH HOH . J 7 HOH A 65 368 75 HOH HOH . J 7 HOH A 66 369 76 HOH HOH . J 7 HOH A 67 370 77 HOH HOH . J 7 HOH A 68 371 78 HOH HOH . J 7 HOH A 69 372 79 HOH HOH . J 7 HOH A 70 373 80 HOH HOH . J 7 HOH A 71 374 81 HOH HOH . J 7 HOH A 72 375 82 HOH HOH . J 7 HOH A 73 376 83 HOH HOH . J 7 HOH A 74 377 85 HOH HOH . J 7 HOH A 75 378 86 HOH HOH . J 7 HOH A 76 379 87 HOH HOH . J 7 HOH A 77 380 88 HOH HOH . J 7 HOH A 78 381 89 HOH HOH . J 7 HOH A 79 382 92 HOH HOH . J 7 HOH A 80 383 93 HOH HOH . J 7 HOH A 81 384 94 HOH HOH . J 7 HOH A 82 385 95 HOH HOH . J 7 HOH A 83 386 96 HOH HOH . J 7 HOH A 84 387 97 HOH HOH . J 7 HOH A 85 388 98 HOH HOH . J 7 HOH A 86 389 99 HOH HOH . J 7 HOH A 87 390 101 HOH HOH . J 7 HOH A 88 391 102 HOH HOH . J 7 HOH A 89 392 103 HOH HOH . J 7 HOH A 90 393 104 HOH HOH . J 7 HOH A 91 394 105 HOH HOH . J 7 HOH A 92 395 106 HOH HOH . J 7 HOH A 93 396 107 HOH HOH . J 7 HOH A 94 397 108 HOH HOH . J 7 HOH A 95 398 110 HOH HOH . J 7 HOH A 96 399 111 HOH HOH . J 7 HOH A 97 400 113 HOH HOH . J 7 HOH A 98 401 114 HOH HOH . J 7 HOH A 99 402 115 HOH HOH . J 7 HOH A 100 403 116 HOH HOH . J 7 HOH A 101 404 117 HOH HOH . J 7 HOH A 102 405 118 HOH HOH . J 7 HOH A 103 406 119 HOH HOH . J 7 HOH A 104 407 120 HOH HOH . J 7 HOH A 105 408 121 HOH HOH . J 7 HOH A 106 409 122 HOH HOH . J 7 HOH A 107 410 123 HOH HOH . J 7 HOH A 108 411 124 HOH HOH . J 7 HOH A 109 412 125 HOH HOH . J 7 HOH A 110 413 126 HOH HOH . J 7 HOH A 111 414 127 HOH HOH . J 7 HOH A 112 415 128 HOH HOH . J 7 HOH A 113 416 130 HOH HOH . J 7 HOH A 114 417 131 HOH HOH . J 7 HOH A 115 418 132 HOH HOH . J 7 HOH A 116 419 133 HOH HOH . J 7 HOH A 117 420 134 HOH HOH . J 7 HOH A 118 421 136 HOH HOH . J 7 HOH A 119 422 137 HOH HOH . J 7 HOH A 120 423 138 HOH HOH . J 7 HOH A 121 424 139 HOH HOH . J 7 HOH A 122 425 140 HOH HOH . J 7 HOH A 123 426 141 HOH HOH . J 7 HOH A 124 427 142 HOH HOH . J 7 HOH A 125 428 143 HOH HOH . J 7 HOH A 126 429 144 HOH HOH . J 7 HOH A 127 430 145 HOH HOH . J 7 HOH A 128 431 146 HOH HOH . J 7 HOH A 129 432 147 HOH HOH . J 7 HOH A 130 433 148 HOH HOH . J 7 HOH A 131 434 149 HOH HOH . J 7 HOH A 132 435 150 HOH HOH . J 7 HOH A 133 436 151 HOH HOH . J 7 HOH A 134 437 152 HOH HOH . J 7 HOH A 135 438 153 HOH HOH . J 7 HOH A 136 439 154 HOH HOH . J 7 HOH A 137 440 155 HOH HOH . J 7 HOH A 138 441 156 HOH HOH . J 7 HOH A 139 442 157 HOH HOH . J 7 HOH A 140 443 158 HOH HOH . J 7 HOH A 141 444 159 HOH HOH . J 7 HOH A 142 445 160 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 . . . H 5 -28.653 24.074 23.207 1 55.76 ? C1 GOL 302 A 1 HETATM 2 O O1 GOL . . . H 5 -28.642 22.721 22.804 1 63.22 ? O1 GOL 302 A 1 HETATM 3 C C2 GOL . . . H 5 -27.569 24.295 24.252 1 55.05 ? C2 GOL 302 A 1 HETATM 4 O O2 GOL . . . H 5 -27.22 23.059 24.833 1 46.43 ? O2 GOL 302 A 1 HETATM 5 C C3 GOL . . . H 5 -28.079 25.23 25.336 1 58.55 ? C3 GOL 302 A 1 HETATM 6 O O3 GOL . . . H 5 -27.009 26.05 25.755 1 51.71 ? O3 GOL 302 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 6 #