data_4JY5 # _model_server_result.job_id e_DJ57pm1glmh-XBYzxRdg _model_server_result.datetime_utc '2024-10-23 16:20:52' _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 4jy5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 4JY5 # _exptl.entry_id 4JY5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.32 _cell.angle_gamma 90 _cell.entry_id 4JY5 _cell.length_a 210.34 _cell.length_b 42.04 _cell.length_c 45.05 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JY5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 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 disulf ? disulf1 A SG CYS 15 L CYS 23 1_555 A SG CYS 83 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf2 A SG CYS 133 L CYS 135 1_555 A SG CYS 192 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 95 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf4 B SG CYS 159 H CYS 138 1_555 B SG CYS 215 H CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _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 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 4JY5 _atom_sites.fract_transf_matrix[1][1] 0.004754 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000866 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023787 _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] 0.022562 _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 GOL L 1 301 1 GOL GOL . D 3 GOL H 1 301 1 GOL GOL . E 3 GOL H 1 302 1 GOL GOL . F 4 HOH L 1 401 1 HOH HOH . F 4 HOH L 2 402 7 HOH HOH . F 4 HOH L 3 403 12 HOH HOH . F 4 HOH L 4 404 20 HOH HOH . F 4 HOH L 5 405 25 HOH HOH . F 4 HOH L 6 406 30 HOH HOH . F 4 HOH L 7 407 31 HOH HOH . F 4 HOH L 8 408 34 HOH HOH . F 4 HOH L 9 409 38 HOH HOH . F 4 HOH L 10 410 40 HOH HOH . F 4 HOH L 11 411 42 HOH HOH . F 4 HOH L 12 412 48 HOH HOH . F 4 HOH L 13 413 50 HOH HOH . F 4 HOH L 14 414 51 HOH HOH . F 4 HOH L 15 415 53 HOH HOH . F 4 HOH L 16 416 54 HOH HOH . F 4 HOH L 17 417 56 HOH HOH . F 4 HOH L 18 418 58 HOH HOH . F 4 HOH L 19 419 63 HOH HOH . F 4 HOH L 20 420 64 HOH HOH . F 4 HOH L 21 421 77 HOH HOH . F 4 HOH L 22 422 84 HOH HOH . F 4 HOH L 23 423 85 HOH HOH . F 4 HOH L 24 424 87 HOH HOH . F 4 HOH L 25 425 92 HOH HOH . F 4 HOH L 26 426 93 HOH HOH . F 4 HOH L 27 427 94 HOH HOH . F 4 HOH L 28 428 99 HOH HOH . F 4 HOH L 29 429 100 HOH HOH . F 4 HOH L 30 430 101 HOH HOH . F 4 HOH L 31 431 104 HOH HOH . F 4 HOH L 32 432 108 HOH HOH . F 4 HOH L 33 433 111 HOH HOH . F 4 HOH L 34 434 117 HOH HOH . F 4 HOH L 35 435 127 HOH HOH . F 4 HOH L 36 436 129 HOH HOH . F 4 HOH L 37 437 135 HOH HOH . F 4 HOH L 38 438 136 HOH HOH . F 4 HOH L 39 439 137 HOH HOH . F 4 HOH L 40 440 139 HOH HOH . F 4 HOH L 41 441 142 HOH HOH . F 4 HOH L 42 442 144 HOH HOH . F 4 HOH L 43 443 148 HOH HOH . F 4 HOH L 44 444 152 HOH HOH . F 4 HOH L 45 445 154 HOH HOH . F 4 HOH L 46 446 159 HOH HOH . F 4 HOH L 47 447 161 HOH HOH . F 4 HOH L 48 448 171 HOH HOH . F 4 HOH L 49 449 178 HOH HOH . F 4 HOH L 50 450 179 HOH HOH . F 4 HOH L 51 451 181 HOH HOH . F 4 HOH L 52 452 185 HOH HOH . F 4 HOH L 53 453 192 HOH HOH . F 4 HOH L 54 454 193 HOH HOH . F 4 HOH L 55 455 196 HOH HOH . F 4 HOH L 56 456 197 HOH HOH . F 4 HOH L 57 457 198 HOH HOH . F 4 HOH L 58 458 199 HOH HOH . F 4 HOH L 59 459 207 HOH HOH . F 4 HOH L 60 460 218 HOH HOH . F 4 HOH L 61 461 224 HOH HOH . F 4 HOH L 62 462 227 HOH HOH . F 4 HOH L 63 463 228 HOH HOH . F 4 HOH L 64 464 231 HOH HOH . F 4 HOH L 65 465 234 HOH HOH . F 4 HOH L 66 466 237 HOH HOH . F 4 HOH L 67 467 242 HOH HOH . F 4 HOH L 68 468 245 HOH HOH . F 4 HOH L 69 469 250 HOH HOH . F 4 HOH L 70 470 255 HOH HOH . F 4 HOH L 71 471 256 HOH HOH . F 4 HOH L 72 472 264 HOH HOH . F 4 HOH L 73 473 275 HOH HOH . F 4 HOH L 74 474 276 HOH HOH . F 4 HOH L 75 475 277 HOH HOH . F 4 HOH L 76 476 282 HOH HOH . F 4 HOH L 77 477 294 HOH HOH . F 4 HOH L 78 478 297 HOH HOH . F 4 HOH L 79 479 302 HOH HOH . G 4 HOH H 1 401 2 HOH HOH . G 4 HOH H 2 402 3 HOH HOH . G 4 HOH H 3 403 4 HOH HOH . G 4 HOH H 4 404 5 HOH HOH . G 4 HOH H 5 405 6 HOH HOH . G 4 HOH H 6 406 8 HOH HOH . G 4 HOH H 7 407 9 HOH HOH . G 4 HOH H 8 408 10 HOH HOH . G 4 HOH H 9 409 11 HOH HOH . G 4 HOH H 10 410 13 HOH HOH . G 4 HOH H 11 411 14 HOH HOH . G 4 HOH H 12 412 15 HOH HOH . G 4 HOH H 13 413 16 HOH HOH . G 4 HOH H 14 414 17 HOH HOH . G 4 HOH H 15 415 18 HOH HOH . G 4 HOH H 16 416 19 HOH HOH . G 4 HOH H 17 417 21 HOH HOH . G 4 HOH H 18 418 22 HOH HOH . G 4 HOH H 19 419 23 HOH HOH . G 4 HOH H 20 420 24 HOH HOH . G 4 HOH H 21 421 26 HOH HOH . G 4 HOH H 22 422 27 HOH HOH . G 4 HOH H 23 423 28 HOH HOH . G 4 HOH H 24 424 29 HOH HOH . G 4 HOH H 25 425 32 HOH HOH . G 4 HOH H 26 426 33 HOH HOH . G 4 HOH H 27 427 35 HOH HOH . G 4 HOH H 28 428 36 HOH HOH . G 4 HOH H 29 429 37 HOH HOH . G 4 HOH H 30 430 39 HOH HOH . G 4 HOH H 31 431 41 HOH HOH . G 4 HOH H 32 432 43 HOH HOH . G 4 HOH H 33 433 46 HOH HOH . G 4 HOH H 34 434 47 HOH HOH . G 4 HOH H 35 435 49 HOH HOH . G 4 HOH H 36 436 55 HOH HOH . G 4 HOH H 37 437 57 HOH HOH . G 4 HOH H 38 438 59 HOH HOH . G 4 HOH H 39 439 60 HOH HOH . G 4 HOH H 40 440 61 HOH HOH . G 4 HOH H 41 441 62 HOH HOH . G 4 HOH H 42 442 65 HOH HOH . G 4 HOH H 43 443 66 HOH HOH . G 4 HOH H 44 444 67 HOH HOH . G 4 HOH H 45 445 68 HOH HOH . G 4 HOH H 46 446 69 HOH HOH . G 4 HOH H 47 447 70 HOH HOH . G 4 HOH H 48 448 71 HOH HOH . G 4 HOH H 49 449 72 HOH HOH . G 4 HOH H 50 450 73 HOH HOH . G 4 HOH H 51 451 74 HOH HOH . G 4 HOH H 52 452 75 HOH HOH . G 4 HOH H 53 453 76 HOH HOH . G 4 HOH H 54 454 78 HOH HOH . G 4 HOH H 55 455 79 HOH HOH . G 4 HOH H 56 456 80 HOH HOH . G 4 HOH H 57 457 81 HOH HOH . G 4 HOH H 58 458 82 HOH HOH . G 4 HOH H 59 459 83 HOH HOH . G 4 HOH H 60 460 86 HOH HOH . G 4 HOH H 61 461 88 HOH HOH . G 4 HOH H 62 462 89 HOH HOH . G 4 HOH H 63 463 90 HOH HOH . G 4 HOH H 64 464 91 HOH HOH . G 4 HOH H 65 465 95 HOH HOH . G 4 HOH H 66 466 96 HOH HOH . G 4 HOH H 67 467 97 HOH HOH . G 4 HOH H 68 468 98 HOH HOH . G 4 HOH H 69 469 103 HOH HOH . G 4 HOH H 70 470 105 HOH HOH . G 4 HOH H 71 471 109 HOH HOH . G 4 HOH H 72 472 110 HOH HOH . G 4 HOH H 73 473 112 HOH HOH . G 4 HOH H 74 474 113 HOH HOH . G 4 HOH H 75 475 114 HOH HOH . G 4 HOH H 76 476 115 HOH HOH . G 4 HOH H 77 477 116 HOH HOH . G 4 HOH H 78 478 118 HOH HOH . G 4 HOH H 79 479 119 HOH HOH . G 4 HOH H 80 480 120 HOH HOH . G 4 HOH H 81 481 121 HOH HOH . G 4 HOH H 82 482 122 HOH HOH . G 4 HOH H 83 483 123 HOH HOH . G 4 HOH H 84 484 124 HOH HOH . G 4 HOH H 85 485 125 HOH HOH . G 4 HOH H 86 486 126 HOH HOH . G 4 HOH H 87 487 128 HOH HOH . G 4 HOH H 88 488 130 HOH HOH . G 4 HOH H 89 489 131 HOH HOH . G 4 HOH H 90 490 132 HOH HOH . G 4 HOH H 91 491 133 HOH HOH . G 4 HOH H 92 492 134 HOH HOH . G 4 HOH H 93 493 138 HOH HOH . G 4 HOH H 94 494 140 HOH HOH . G 4 HOH H 95 495 141 HOH HOH . G 4 HOH H 96 496 143 HOH HOH . G 4 HOH H 97 497 145 HOH HOH . G 4 HOH H 98 498 147 HOH HOH . G 4 HOH H 99 499 149 HOH HOH . G 4 HOH H 100 500 150 HOH HOH . G 4 HOH H 101 501 153 HOH HOH . G 4 HOH H 102 502 155 HOH HOH . G 4 HOH H 103 503 156 HOH HOH . G 4 HOH H 104 504 157 HOH HOH . G 4 HOH H 105 505 162 HOH HOH . G 4 HOH H 106 506 164 HOH HOH . G 4 HOH H 107 507 165 HOH HOH . G 4 HOH H 108 508 166 HOH HOH . G 4 HOH H 109 509 167 HOH HOH . G 4 HOH H 110 510 169 HOH HOH . G 4 HOH H 111 511 170 HOH HOH . G 4 HOH H 112 512 172 HOH HOH . G 4 HOH H 113 513 173 HOH HOH . G 4 HOH H 114 514 174 HOH HOH . G 4 HOH H 115 515 175 HOH HOH . G 4 HOH H 116 516 176 HOH HOH . G 4 HOH H 117 517 177 HOH HOH . G 4 HOH H 118 518 180 HOH HOH . G 4 HOH H 119 519 182 HOH HOH . G 4 HOH H 120 520 183 HOH HOH . G 4 HOH H 121 521 186 HOH HOH . G 4 HOH H 122 522 187 HOH HOH . G 4 HOH H 123 523 188 HOH HOH . G 4 HOH H 124 524 189 HOH HOH . G 4 HOH H 125 525 190 HOH HOH . G 4 HOH H 126 526 191 HOH HOH . G 4 HOH H 127 527 194 HOH HOH . G 4 HOH H 128 528 195 HOH HOH . G 4 HOH H 129 529 203 HOH HOH . G 4 HOH H 130 530 204 HOH HOH . G 4 HOH H 131 531 209 HOH HOH . G 4 HOH H 132 532 214 HOH HOH . G 4 HOH H 133 533 215 HOH HOH . G 4 HOH H 134 534 216 HOH HOH . G 4 HOH H 135 535 217 HOH HOH . G 4 HOH H 136 536 219 HOH HOH . G 4 HOH H 137 537 223 HOH HOH . G 4 HOH H 138 538 226 HOH HOH . G 4 HOH H 139 539 229 HOH HOH . G 4 HOH H 140 540 230 HOH HOH . G 4 HOH H 141 541 233 HOH HOH . G 4 HOH H 142 542 238 HOH HOH . G 4 HOH H 143 543 243 HOH HOH . G 4 HOH H 144 544 244 HOH HOH . G 4 HOH H 145 545 246 HOH HOH . G 4 HOH H 146 546 247 HOH HOH . G 4 HOH H 147 547 249 HOH HOH . G 4 HOH H 148 548 251 HOH HOH . G 4 HOH H 149 549 252 HOH HOH . G 4 HOH H 150 550 253 HOH HOH . G 4 HOH H 151 551 254 HOH HOH . G 4 HOH H 152 552 257 HOH HOH . G 4 HOH H 153 553 258 HOH HOH . G 4 HOH H 154 554 259 HOH HOH . G 4 HOH H 155 555 260 HOH HOH . G 4 HOH H 156 556 262 HOH HOH . G 4 HOH H 157 557 263 HOH HOH . G 4 HOH H 158 558 272 HOH HOH . G 4 HOH H 159 559 278 HOH HOH . G 4 HOH H 160 560 279 HOH HOH . G 4 HOH H 161 561 283 HOH HOH . G 4 HOH H 162 562 284 HOH HOH . G 4 HOH H 163 563 285 HOH HOH . G 4 HOH H 164 564 286 HOH HOH . G 4 HOH H 165 565 290 HOH HOH . G 4 HOH H 166 566 293 HOH HOH . G 4 HOH H 167 567 299 HOH HOH . G 4 HOH H 168 568 300 HOH HOH . G 4 HOH H 169 569 301 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 3 -34.157 18.719 -6.707 1 44.96 ? C1 GOL 301 H 1 HETATM 2 O O1 GOL . . . D 3 -33.88 20.083 -6.921 1 44.77 ? O1 GOL 301 H 1 HETATM 3 C C2 GOL . . . D 3 -32.854 17.95 -6.549 1 51.63 ? C2 GOL 301 H 1 HETATM 4 O O2 GOL . . . D 3 -32.514 17.413 -7.807 1 57.14 ? O2 GOL 301 H 1 HETATM 5 C C3 GOL . . . D 3 -33.084 16.817 -5.552 1 50.38 ? C3 GOL 301 H 1 HETATM 6 O O3 GOL . . . D 3 -31.897 16.478 -4.866 1 55.58 ? O3 GOL 301 H 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #