data_3EPD # _model_server_result.job_id 112rfV7sRjxxtIlefZKdvQ _model_server_result.datetime_utc '2025-03-05 19:49:41' _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 3epd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1000}' # _entry.id 3EPD # _exptl.entry_id 3EPD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 299.492 _entity.id 7 _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 90 _cell.angle_gamma 90 _cell.entry_id 3EPD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EPD _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 360-MERIC 360 'complete icosahedral assembly' 1 ? hexameric 6 'icosahedral asymmetric unit' 2 ? 30-meric 30 'icosahedral pentamer' 3 ? 36-meric 36 'icosahedral 23 hexamer' 4 ? hexameric 6 'icosahedral asymmetric unit, std point frame' 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 (1-60) A,B,C,D,E,F,G,H 2 1 A,B,C,D,E,F,G,H 3 (1-5) A,B,C,D,E,F,G,H 4 (1,2,6,10,23,24) A,B,C,D,E,F,G,H 5 P # 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] P 'transform to point frame' ? ? 0.5 0.809017 0.309017 -0.309017 0.5 -0.809017 -0.809017 0.309017 0.5 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.809017 -0.309017 0.5 -0.309017 0.5 0.809017 -0.5 -0.809017 0.309017 0 0 0 3 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 -0.809017 -0.309017 0.5 -0.309017 -0.5 -0.809017 0 0 0 4 'point symmetry operation' ? ? 0.5 -0.809017 -0.309017 -0.809017 -0.309017 -0.5 0.309017 0.5 -0.809017 0 0 0 5 'point symmetry operation' ? ? 0.809017 -0.309017 -0.5 -0.309017 0.5 -0.809017 0.5 0.809017 0.309017 0 0 0 6 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 -0.5 -0.809017 0.309017 -0.809017 0.309017 -0.5 0 0 0 7 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 -0.309017 -0.5 -0.809017 -0.5 0.809017 -0.309017 0 0 0 8 'point symmetry operation' ? ? 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 0 0 0 9 'point symmetry operation' ? ? 0.309017 -0.5 0.809017 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 0 0 0 10 'point symmetry operation' ? ? 0 -1 0 0 0 1 -1 0 0 0 0 0 11 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 -0.309017 -0.5 -0.809017 0.5 -0.809017 0.309017 0 0 0 12 'point symmetry operation' ? ? -0.809017 -0.309017 -0.5 0.309017 0.5 -0.809017 0.5 -0.809017 -0.309017 0 0 0 13 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 0.5 0.809017 0.309017 0.809017 -0.309017 -0.5 0 0 0 14 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 0 0 15 'point symmetry operation' ? ? -0.309017 0.5 0.809017 -0.5 -0.809017 0.309017 0.809017 -0.309017 0.5 0 0 0 16 'point symmetry operation' ? ? -0.5 0.809017 0.309017 0.809017 0.309017 0.5 0.309017 0.5 -0.809017 0 0 0 17 'point symmetry operation' ? ? -0.809017 0.309017 0.5 0.309017 -0.5 0.809017 0.5 0.809017 0.309017 0 0 0 18 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 0 0 0 19 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 0.309017 -0.5 -0.809017 -0.5 -0.809017 0.309017 0 0 0 20 'point symmetry operation' ? ? -0.5 0.809017 -0.309017 0.809017 0.309017 -0.5 -0.309017 -0.5 -0.809017 0 0 0 21 'point symmetry operation' ? ? -0.309017 -0.5 0.809017 -0.5 0.809017 0.309017 -0.809017 -0.309017 -0.5 0 0 0 22 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 -0.809017 0.309017 0.5 -0.309017 0.5 -0.809017 0 0 0 23 'point symmetry operation' ? ? 0 0 -1 -1 0 0 0 1 0 0 0 0 24 'point symmetry operation' ? ? 0.5 0.809017 -0.309017 -0.809017 0.309017 -0.5 -0.309017 0.5 0.809017 0 0 0 25 'point symmetry operation' ? ? 0.309017 0.5 0.809017 -0.5 0.809017 -0.309017 -0.809017 -0.309017 0.5 0 0 0 26 'point symmetry operation' ? ? -0.5 0.809017 -0.309017 -0.809017 -0.309017 0.5 0.309017 0.5 0.809017 0 0 0 27 'point symmetry operation' ? ? -0.5 0.809017 0.309017 -0.809017 -0.309017 -0.5 -0.309017 -0.5 0.809017 0 0 0 28 'point symmetry operation' ? ? -0.809017 0.309017 0.5 -0.309017 0.5 -0.809017 -0.5 -0.809017 -0.309017 0 0 0 29 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 0 0 0 30 'point symmetry operation' ? ? -0.809017 0.309017 -0.5 -0.309017 0.5 0.809017 0.5 0.809017 -0.309017 0 0 0 31 'point symmetry operation' ? ? 0.809017 -0.309017 0.5 0.309017 -0.5 -0.809017 0.5 0.809017 -0.309017 0 0 0 32 'point symmetry operation' ? ? 0.5 -0.809017 0.309017 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 0 0 0 33 'point symmetry operation' ? ? 0.5 -0.809017 -0.309017 0.809017 0.309017 0.5 -0.309017 -0.5 0.809017 0 0 0 34 'point symmetry operation' ? ? 0.809017 -0.309017 -0.5 0.309017 -0.5 0.809017 -0.5 -0.809017 -0.309017 0 0 0 35 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 0 0 36 'point symmetry operation' ? ? 0 0 -1 1 0 0 0 -1 0 0 0 0 37 'point symmetry operation' ? ? 0.5 0.809017 -0.309017 0.809017 -0.309017 0.5 0.309017 -0.5 -0.809017 0 0 0 38 'point symmetry operation' ? ? 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 0.809017 0.309017 -0.5 0 0 0 39 'point symmetry operation' ? ? -0.309017 -0.5 0.809017 0.5 -0.809017 -0.309017 0.809017 0.309017 0.5 0 0 0 40 'point symmetry operation' ? ? -0.5 -0.809017 -0.309017 0.809017 -0.309017 -0.5 0.309017 -0.5 0.809017 0 0 0 41 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 -0.5 0.809017 -0.309017 0.809017 0.309017 -0.5 0 0 0 42 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 -0.5 0.809017 0.309017 0.809017 0.309017 0.5 0 0 0 43 'point symmetry operation' ? ? 0.5 0.809017 0.309017 -0.809017 0.309017 0.5 0.309017 -0.5 0.809017 0 0 0 44 'point symmetry operation' ? ? 0 0 1 -1 0 0 0 -1 0 0 0 0 45 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 -0.809017 0.309017 -0.5 0.309017 -0.5 -0.809017 0 0 0 46 'point symmetry operation' ? ? 0.809017 0.309017 0.5 -0.309017 -0.5 0.809017 0.5 -0.809017 -0.309017 0 0 0 47 'point symmetry operation' ? ? 0.309017 -0.5 0.809017 -0.5 -0.809017 -0.309017 0.809017 -0.309017 -0.5 0 0 0 48 'point symmetry operation' ? ? 0 -1 0 0 0 -1 1 0 0 0 0 0 49 'point symmetry operation' ? ? 0.309017 -0.5 -0.809017 0.5 0.809017 -0.309017 0.809017 -0.309017 0.5 0 0 0 50 'point symmetry operation' ? ? 0.809017 0.309017 -0.5 0.309017 0.5 0.809017 0.5 -0.809017 0.309017 0 0 0 51 'point symmetry operation' ? ? 0 1 0 0 0 -1 -1 0 0 0 0 0 52 'point symmetry operation' ? ? -0.309017 0.5 0.809017 0.5 0.809017 -0.309017 -0.809017 0.309017 -0.5 0 0 0 53 'point symmetry operation' ? ? -0.809017 -0.309017 0.5 0.309017 0.5 0.809017 -0.5 0.809017 -0.309017 0 0 0 54 'point symmetry operation' ? ? -0.809017 -0.309017 -0.5 -0.309017 -0.5 0.809017 -0.5 0.809017 0.309017 0 0 0 55 'point symmetry operation' ? ? -0.309017 0.5 -0.809017 -0.5 -0.809017 -0.309017 -0.809017 0.309017 0.5 0 0 0 56 'point symmetry operation' ? ? -0.5 -0.809017 0.309017 0.809017 -0.309017 0.5 -0.309017 0.5 0.809017 0 0 0 57 'point symmetry operation' ? ? -0.309017 -0.5 -0.809017 0.5 -0.809017 0.309017 -0.809017 -0.309017 0.5 0 0 0 58 'point symmetry operation' ? ? 0.309017 0.5 -0.809017 0.5 -0.809017 -0.309017 -0.809017 -0.309017 -0.5 0 0 0 59 'point symmetry operation' ? ? 0.5 0.809017 0.309017 0.809017 -0.309017 -0.5 -0.309017 0.5 -0.809017 0 0 0 60 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _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 disulf ? disulf1 A SG CYS 20 R CYS 49 1_555 A SG CYS 94 R CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 137 R CYS 166 1_555 A SG CYS 192 R CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 H C1 MYR . 4 MYR 1 1_555 E N GLY 1 4 GLY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? # _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 331 n n C1 C2 SPH sing 332 n n C1 H11 SPH sing 333 n n C1 H12 SPH sing 334 n n O1 HO1 SPH sing 335 n n C2 N2 SPH sing 336 n n C2 C3 SPH sing 337 n n C2 H2 SPH sing 338 n n N2 HN21 SPH sing 339 n n N2 HN22 SPH sing 340 n n C3 O3 SPH sing 341 n n C3 C4 SPH sing 342 n n C3 H3 SPH sing 343 n n O3 HO3 SPH sing 344 n n C4 C5 SPH doub 345 z n C4 H4 SPH sing 346 n n C5 C6 SPH sing 347 n n C5 H5 SPH sing 348 n n C6 C7 SPH sing 349 n n C6 H61 SPH sing 350 n n C6 H62 SPH sing 351 n n C7 C8 SPH sing 352 n n C7 H71 SPH sing 353 n n C7 H72 SPH sing 354 n n C8 C9 SPH sing 355 n n C8 H81 SPH sing 356 n n C8 H82 SPH sing 357 n n C9 C10 SPH sing 358 n n C9 H91 SPH sing 359 n n C9 H92 SPH sing 360 n n C10 C11 SPH sing 361 n n C10 H101 SPH sing 362 n n C10 H102 SPH sing 363 n n C11 C12 SPH sing 364 n n C11 H111 SPH sing 365 n n C11 H112 SPH sing 366 n n C12 C13 SPH sing 367 n n C12 H121 SPH sing 368 n n C12 H122 SPH sing 369 n n C13 C14 SPH sing 370 n n C13 H131 SPH sing 371 n n C13 H132 SPH sing 372 n n C14 C15 SPH sing 373 n n C14 H141 SPH sing 374 n n C14 H142 SPH sing 375 n n C15 C16 SPH sing 376 n n C15 H151 SPH sing 377 n n C15 H152 SPH sing 378 n n C16 C17 SPH sing 379 n n C16 H161 SPH sing 380 n n C16 H162 SPH sing 381 n n C17 C18 SPH sing 382 n n C17 H171 SPH sing 383 n n C17 H172 SPH sing 384 n n C18 H181 SPH sing 385 n n C18 H182 SPH sing 386 n n C18 H183 SPH sing 387 n n # _atom_sites.entry_id 3EPD _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 G 7 SPH 1 1 1000 1000 SPH SPH . H 8 MYR 4 1 1 1 MYR MYR . # 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 . . . G 7 -113.676 52.07 34.664 1 38.01 ? C1 SPH 1000 1 1 HETATM 2 O O1 SPH . . . G 7 -113.318 51.385 35.875 1 36.51 ? O1 SPH 1000 1 1 HETATM 3 C C2 SPH . . . G 7 -115.071 51.618 34.095 1 37.25 ? C2 SPH 1000 1 1 HETATM 4 N N2 SPH . . . G 7 -116.098 52.349 34.815 1 37.51 ? N2 SPH 1000 1 1 HETATM 5 C C3 SPH . . . G 7 -115.525 51.923 32.584 1 35.68 ? C3 SPH 1000 1 1 HETATM 6 O O3 SPH . . . G 7 -115.944 50.638 32.213 1 37.03 ? O3 SPH 1000 1 1 HETATM 7 C C4 SPH . . . G 7 -114.698 52.358 31.374 1 33.43 ? C4 SPH 1000 1 1 HETATM 8 C C5 SPH . . . G 7 -115.258 52.607 30.161 1 29.85 ? C5 SPH 1000 1 1 HETATM 9 C C6 SPH . . . G 7 -114.562 53.064 28.893 1 26.6 ? C6 SPH 1000 1 1 HETATM 10 C C7 SPH . . . G 7 -114.336 54.579 28.905 1 23.48 ? C7 SPH 1000 1 1 HETATM 11 C C8 SPH . . . G 7 -113.377 55.255 27.902 1 20.28 ? C8 SPH 1000 1 1 HETATM 12 C C9 SPH . . . G 7 -113.116 56.63 28.556 1 18.04 ? C9 SPH 1000 1 1 HETATM 13 C C10 SPH . . . G 7 -112.319 57.695 27.801 1 14.47 ? C10 SPH 1000 1 1 HETATM 14 C C11 SPH . . . G 7 -112.335 59.037 28.562 1 12.2 ? C11 SPH 1000 1 1 HETATM 15 C C12 SPH . . . G 7 -111.659 60.238 27.858 1 9.98 ? C12 SPH 1000 1 1 HETATM 16 C C13 SPH . . . G 7 -112.394 60.832 26.635 1 9.14 ? C13 SPH 1000 1 1 HETATM 17 C C14 SPH . . . G 7 -111.661 61.991 25.953 1 7.09 ? C14 SPH 1000 1 1 HETATM 18 C C15 SPH . . . G 7 -112.425 62.581 24.755 1 7.83 ? C15 SPH 1000 1 1 HETATM 19 C C16 SPH . . . G 7 -111.625 63.754 24.165 1 7.99 ? C16 SPH 1000 1 1 HETATM 20 C C17 SPH . . . G 7 -112.378 64.581 23.106 1 7.77 ? C17 SPH 1000 1 1 HETATM 21 C C18 SPH . . . G 7 -111.568 65.854 22.669 1 5.06 ? C18 SPH 1000 1 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 21 #