data_2EVD # _model_server_result.job_id jVZgypP5BVly6QWatchvMA _model_server_result.datetime_utc '2024-11-27 02:48:26' _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 2evd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 2EVD # _exptl.entry_id 2EVD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 299.492 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPHINGOSINE _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 122.38 _cell.angle_gamma 90 _cell.entry_id 2EVD _cell.length_a 75.592 _cell.length_b 49.36 _cell.length_c 68.632 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2EVD _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 GAL _pdbx_entity_branch_link.comp_id_2 BGC _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B BGC 1 B 1 BGC B 300 LAT 2 n B GAL 2 B 2 GAL B 300 LAT # 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 C N2 SPH . A SPH 301 1_555 D C1 DAO . A DAO 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.26 ? covale ? covale2 C C1 SPH . A SPH 301 1_555 B O1 BGC . B BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale3 B O4 BGC . B BGC 1 1_555 B C1 GAL . B GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 sing # _chem_comp.formula 'C18 H37 N O2' _chem_comp.formula_weight 299.492 _chem_comp.id SPH _chem_comp.mon_nstd_flag . _chem_comp.name SPHINGOSINE _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 C1 O1 SPH sing 431 n n C1 C2 SPH sing 432 n n C1 H11 SPH sing 433 n n C1 H12 SPH sing 434 n n O1 HO1 SPH sing 435 n n C2 N2 SPH sing 436 n n C2 C3 SPH sing 437 n n C2 H2 SPH sing 438 n n N2 HN21 SPH sing 439 n n N2 HN22 SPH sing 440 n n C3 O3 SPH sing 441 n n C3 C4 SPH sing 442 n n C3 H3 SPH sing 443 n n O3 HO3 SPH sing 444 n n C4 C5 SPH doub 445 z n C4 H4 SPH sing 446 n n C5 C6 SPH sing 447 n n C5 H5 SPH sing 448 n n C6 C7 SPH sing 449 n n C6 H61 SPH sing 450 n n C6 H62 SPH sing 451 n n C7 C8 SPH sing 452 n n C7 H71 SPH sing 453 n n C7 H72 SPH sing 454 n n C8 C9 SPH sing 455 n n C8 H81 SPH sing 456 n n C8 H82 SPH sing 457 n n C9 C10 SPH sing 458 n n C9 H91 SPH sing 459 n n C9 H92 SPH sing 460 n n C10 C11 SPH sing 461 n n C10 H101 SPH sing 462 n n C10 H102 SPH sing 463 n n C11 C12 SPH sing 464 n n C11 H111 SPH sing 465 n n C11 H112 SPH sing 466 n n C12 C13 SPH sing 467 n n C12 H121 SPH sing 468 n n C12 H122 SPH sing 469 n n C13 C14 SPH sing 470 n n C13 H131 SPH sing 471 n n C13 H132 SPH sing 472 n n C14 C15 SPH sing 473 n n C14 H141 SPH sing 474 n n C14 H142 SPH sing 475 n n C15 C16 SPH sing 476 n n C15 H151 SPH sing 477 n n C15 H152 SPH sing 478 n n C16 C17 SPH sing 479 n n C16 H161 SPH sing 480 n n C16 H162 SPH sing 481 n n C17 C18 SPH sing 482 n n C17 H171 SPH sing 483 n n C17 H172 SPH sing 484 n n C18 H181 SPH sing 485 n n C18 H182 SPH sing 486 n n C18 H183 SPH sing 487 n n # _atom_sites.entry_id 2EVD _atom_sites.fract_transf_matrix[1][1] 0.013229 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008389 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020259 _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] 0.017253 _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 SPH A 1 301 301 SPH SPH . D 4 DAO A 1 302 302 DAO LAU . E 5 OCT A 1 303 303 OCT OCT . F 6 D10 A 1 304 304 D10 D10 . G 7 HOH A 1 305 1 HOH HOH . G 7 HOH A 2 306 2 HOH HOH . G 7 HOH A 3 307 3 HOH HOH . G 7 HOH A 4 308 4 HOH HOH . G 7 HOH A 5 309 5 HOH HOH . G 7 HOH A 6 310 6 HOH HOH . G 7 HOH A 7 311 7 HOH HOH . G 7 HOH A 8 312 8 HOH HOH . G 7 HOH A 9 313 9 HOH HOH . G 7 HOH A 10 314 10 HOH HOH . G 7 HOH A 11 315 11 HOH HOH . G 7 HOH A 12 316 12 HOH HOH . G 7 HOH A 13 317 13 HOH HOH . G 7 HOH A 14 318 14 HOH HOH . G 7 HOH A 15 319 15 HOH HOH . G 7 HOH A 16 320 16 HOH HOH . G 7 HOH A 17 321 17 HOH HOH . G 7 HOH A 18 322 18 HOH HOH . G 7 HOH A 19 323 19 HOH HOH . G 7 HOH A 20 324 20 HOH HOH . G 7 HOH A 21 325 21 HOH HOH . G 7 HOH A 22 326 22 HOH HOH . G 7 HOH A 23 327 23 HOH HOH . G 7 HOH A 24 328 24 HOH HOH . G 7 HOH A 25 329 25 HOH HOH . G 7 HOH A 26 330 26 HOH HOH . G 7 HOH A 27 331 27 HOH HOH . G 7 HOH A 28 332 28 HOH HOH . G 7 HOH A 29 333 29 HOH HOH . G 7 HOH A 30 334 30 HOH HOH . G 7 HOH A 31 335 31 HOH HOH . G 7 HOH A 32 336 32 HOH HOH . G 7 HOH A 33 337 33 HOH HOH . G 7 HOH A 34 338 34 HOH HOH . G 7 HOH A 35 339 35 HOH HOH . G 7 HOH A 36 340 36 HOH HOH . G 7 HOH A 37 341 37 HOH HOH . G 7 HOH A 38 342 38 HOH HOH . G 7 HOH A 39 343 39 HOH HOH . G 7 HOH A 40 344 40 HOH HOH . G 7 HOH A 41 345 41 HOH HOH . G 7 HOH A 42 346 42 HOH HOH . G 7 HOH A 43 347 44 HOH HOH . G 7 HOH A 44 348 45 HOH HOH . G 7 HOH A 45 349 46 HOH HOH . G 7 HOH A 46 350 47 HOH HOH . G 7 HOH A 47 351 48 HOH HOH . G 7 HOH A 48 352 49 HOH HOH . G 7 HOH A 49 353 50 HOH HOH . G 7 HOH A 50 354 51 HOH HOH . G 7 HOH A 51 355 52 HOH HOH . G 7 HOH A 52 356 53 HOH HOH . G 7 HOH A 53 357 54 HOH HOH . G 7 HOH A 54 358 55 HOH HOH . G 7 HOH A 55 359 56 HOH HOH . G 7 HOH A 56 360 57 HOH HOH . G 7 HOH A 57 361 59 HOH HOH . G 7 HOH A 58 362 62 HOH HOH . G 7 HOH A 59 363 63 HOH HOH . G 7 HOH A 60 364 64 HOH HOH . G 7 HOH A 61 365 65 HOH HOH . G 7 HOH A 62 366 66 HOH HOH . G 7 HOH A 63 367 67 HOH HOH . G 7 HOH A 64 368 68 HOH HOH . G 7 HOH A 65 369 69 HOH HOH . G 7 HOH A 66 370 70 HOH HOH . G 7 HOH A 67 371 72 HOH HOH . G 7 HOH A 68 372 73 HOH HOH . G 7 HOH A 69 373 74 HOH HOH . G 7 HOH A 70 374 76 HOH HOH . G 7 HOH A 71 375 77 HOH HOH . G 7 HOH A 72 376 78 HOH HOH . G 7 HOH A 73 377 79 HOH HOH . G 7 HOH A 74 378 80 HOH HOH . G 7 HOH A 75 379 81 HOH HOH . G 7 HOH A 76 380 82 HOH HOH . G 7 HOH A 77 381 83 HOH HOH . G 7 HOH A 78 382 84 HOH HOH . G 7 HOH A 79 383 85 HOH HOH . G 7 HOH A 80 384 86 HOH HOH . G 7 HOH A 81 385 87 HOH HOH . G 7 HOH A 82 386 88 HOH HOH . G 7 HOH A 83 387 91 HOH HOH . G 7 HOH A 84 388 92 HOH HOH . G 7 HOH A 85 389 93 HOH HOH . G 7 HOH A 86 390 94 HOH HOH . G 7 HOH A 87 391 96 HOH HOH . G 7 HOH A 88 392 101 HOH HOH . G 7 HOH A 89 393 102 HOH HOH . G 7 HOH A 90 394 103 HOH HOH . G 7 HOH A 91 395 105 HOH HOH . G 7 HOH A 92 396 106 HOH HOH . G 7 HOH A 93 397 107 HOH HOH . G 7 HOH A 94 398 108 HOH HOH . G 7 HOH A 95 399 109 HOH HOH . G 7 HOH A 96 400 111 HOH HOH . G 7 HOH A 97 401 112 HOH HOH . G 7 HOH A 98 402 113 HOH HOH . G 7 HOH A 99 403 116 HOH HOH . G 7 HOH A 100 404 118 HOH HOH . G 7 HOH A 101 405 122 HOH HOH . G 7 HOH A 102 406 124 HOH HOH . G 7 HOH A 103 407 125 HOH HOH . G 7 HOH A 104 408 129 HOH HOH . G 7 HOH A 105 409 131 HOH HOH . G 7 HOH A 106 410 132 HOH HOH . G 7 HOH A 107 411 134 HOH HOH . G 7 HOH A 108 412 136 HOH HOH . G 7 HOH A 109 413 137 HOH HOH . G 7 HOH A 110 414 140 HOH HOH . G 7 HOH A 111 415 144 HOH HOH . G 7 HOH A 112 416 148 HOH HOH . G 7 HOH A 113 417 149 HOH HOH . G 7 HOH A 114 418 151 HOH HOH . G 7 HOH A 115 419 153 HOH HOH . G 7 HOH A 116 420 154 HOH HOH . G 7 HOH A 117 421 155 HOH HOH . G 7 HOH A 118 422 157 HOH HOH . G 7 HOH A 119 423 159 HOH HOH . G 7 HOH A 120 424 166 HOH HOH . G 7 HOH A 121 425 167 HOH HOH . G 7 HOH A 122 426 168 HOH HOH . G 7 HOH A 123 427 169 HOH HOH . G 7 HOH A 124 428 170 HOH HOH . G 7 HOH A 125 429 172 HOH HOH . G 7 HOH A 126 430 173 HOH HOH . G 7 HOH A 127 431 174 HOH HOH . G 7 HOH A 128 432 175 HOH HOH . G 7 HOH A 129 433 176 HOH HOH . G 7 HOH A 130 434 177 HOH HOH . G 7 HOH A 131 435 180 HOH HOH . G 7 HOH A 132 436 181 HOH HOH . G 7 HOH A 133 437 183 HOH HOH . G 7 HOH A 134 438 200 HOH HOH . G 7 HOH A 135 439 203 HOH HOH . G 7 HOH A 136 440 204 HOH HOH . G 7 HOH A 137 441 207 HOH HOH . G 7 HOH A 138 442 208 HOH HOH . G 7 HOH A 139 443 211 HOH HOH . G 7 HOH A 140 444 212 HOH HOH . G 7 HOH A 141 445 213 HOH HOH . G 7 HOH A 142 446 216 HOH HOH . G 7 HOH A 143 447 217 HOH HOH . G 7 HOH A 144 448 218 HOH HOH . G 7 HOH A 145 449 219 HOH HOH . G 7 HOH A 146 450 220 HOH HOH . G 7 HOH A 147 451 221 HOH HOH . G 7 HOH A 148 452 222 HOH HOH . G 7 HOH A 149 453 223 HOH HOH . G 7 HOH A 150 454 224 HOH HOH . G 7 HOH A 151 455 225 HOH HOH . G 7 HOH A 152 456 226 HOH HOH . G 7 HOH A 153 457 227 HOH HOH . G 7 HOH A 154 458 229 HOH HOH . G 7 HOH A 155 459 230 HOH HOH . G 7 HOH A 156 460 231 HOH HOH . G 7 HOH A 157 461 232 HOH HOH . G 7 HOH A 158 462 233 HOH HOH . G 7 HOH A 159 463 234 HOH HOH . G 7 HOH A 160 464 235 HOH HOH . G 7 HOH A 161 465 236 HOH HOH . G 7 HOH A 162 466 238 HOH HOH . G 7 HOH A 163 467 239 HOH HOH . G 7 HOH A 164 468 241 HOH HOH . G 7 HOH A 165 469 242 HOH HOH . G 7 HOH A 166 470 243 HOH HOH . G 7 HOH A 167 471 244 HOH HOH . G 7 HOH A 168 472 245 HOH HOH . G 7 HOH A 169 473 246 HOH HOH . G 7 HOH A 170 474 247 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 SPH . . . C 3 22.618 -1.986 18.974 1 33.83 ? C1 SPH 301 A 1 HETATM 2 C C2 SPH . . . C 3 21.473 -2.762 19.628 1 34.62 ? C2 SPH 301 A 1 HETATM 3 N N2 SPH . . . C 3 20.187 -2.275 19.144 1 31.8 ? N2 SPH 301 A 1 HETATM 4 C C3 SPH . . . C 3 21.576 -2.66 21.151 1 35.32 ? C3 SPH 301 A 1 HETATM 5 O O3 SPH . . . C 3 22.856 -3.187 21.535 1 33.01 ? O3 SPH 301 A 1 HETATM 6 C C4 SPH . . . C 3 20.475 -3.423 21.885 1 36.26 ? C4 SPH 301 A 1 HETATM 7 C C5 SPH . . . C 3 19.752 -2.862 22.86 1 38.23 ? C5 SPH 301 A 1 HETATM 8 C C6 SPH . . . C 3 18.936 -3.706 23.858 1 39.94 ? C6 SPH 301 A 1 HETATM 9 C C7 SPH . . . C 3 19.719 -4.117 25.121 1 38.52 ? C7 SPH 301 A 1 HETATM 10 C C8 SPH . . . C 3 20.375 -5.513 25.097 1 39.74 ? C8 SPH 301 A 1 HETATM 11 C C9 SPH . . . C 3 21.522 -5.71 26.096 1 37.44 ? C9 SPH 301 A 1 HETATM 12 C C10 SPH . . . C 3 21.09 -6.119 27.499 1 38.52 ? C10 SPH 301 A 1 HETATM 13 C C11 SPH . . . C 3 22.24 -6.371 28.474 1 38.88 ? C11 SPH 301 A 1 HETATM 14 C C12 SPH . . . C 3 21.696 -6.398 29.907 1 40.7 ? C12 SPH 301 A 1 HETATM 15 C C13 SPH . . . C 3 22.537 -7.215 30.892 1 39.65 ? C13 SPH 301 A 1 HETATM 16 C C14 SPH . . . C 3 22.081 -6.939 32.316 1 42.37 ? C14 SPH 301 A 1 HETATM 17 C C15 SPH . . . C 3 22.734 -7.8 33.401 1 42.93 ? C15 SPH 301 A 1 HETATM 18 C C16 SPH . . . C 3 21.696 -8.27 34.429 1 45.15 ? C16 SPH 301 A 1 HETATM 19 C C17 SPH . . . C 3 21.622 -7.472 35.738 1 45.2 ? C17 SPH 301 A 1 HETATM 20 C C18 SPH . . . C 3 22.93 -7.523 36.505 1 43.67 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #