data_7C80 # _model_server_result.job_id QaVO-3Uvrx6hOWUJ1S8XwA _model_server_result.datetime_utc '2025-03-06 02:42:34' _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 7c80 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":500}' # _entry.id 7C80 # _exptl.entry_id 7C80 _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 ? # 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 ? 360-meric 360 'crystal asymmetric unit, crystal frame' 6 # 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 1 (1-60) A,B,C,D,E,F,G 2 1 A,B,C,D,E,F,G 3 (1-5) A,B,C,D,E,F,G 4 (1,2,6,10,23,24) A,B,C,D,E,F,G 5 P A,B,C,D,E,F,G 6 (X0)(1-60) # 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' ? ? -0.951057 0.309017 -0.000001 -0.262866 -0.809017 0.525731 0.162459 0.5 0.850651 193.88971 164.93244 -456.94414 X0 'transform to crystal frame' ? ? 1 0 0 0 1 0 0 0 1 0 0 0 1 'point symmetry operation' ? ? 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.309017 -0.951057 0 0.951057 0.309017 0.000001 0 -0.000001 1 495.87966 -78.53979 0.00034 3 'point symmetry operation' ? ? -0.809017 -0.587785 -0.000001 0.587785 -0.809017 0 -0.000001 0 1 723.81068 368.79966 0.0005 4 'point symmetry operation' ? ? -0.809017 0.587785 -0.000001 -0.587785 -0.809017 0 -0.000001 0 1 368.80014 723.81044 0.00025 5 'point symmetry operation' ? ? 0.309017 0.951057 0 -0.951057 0.309017 -0.000001 0 0.000001 1 -78.53946 495.87971 -0.00006 6 'point symmetry operation' ? ? -0.947214 0.162459 0.276392 0.162459 -0.5 0.850651 0.276392 0.850651 0.447214 455.51038 147.03586 -173.41992 7 'point symmetry operation' ? ? -0.138197 0.951057 0.276393 -0.425326 -0.309017 0.850651 0.894427 0.000001 0.447214 -26.95319 266.86629 -103.17242 8 'point symmetry operation' ? ? 0.861803 0.425326 0.276393 -0.425326 0.309017 0.850651 0.276393 -0.850651 0.447214 -170.17816 80.22621 340.35573 9 'point symmetry operation' ? ? 0.670821 -0.688191 0.276393 0.162459 0.5 0.850651 -0.723607 -0.525732 0.447213 223.7675 -154.95414 544.22371 10 'point symmetry operation' ? ? -0.447213 -0.850651 0.276393 0.525731 0 0.850651 -0.723607 0.525731 0.447213 610.46429 -113.6635 226.6929 11 'point symmetry operation' ? ? -0.861803 0.425326 -0.276393 0.425326 0.309017 -0.850651 -0.276393 -0.850651 -0.447214 517.26975 337.11371 777.40016 12 'point symmetry operation' ? ? 0.138197 0.951057 -0.276393 0.425326 -0.309017 -0.850651 -0.894427 0.000001 -0.447214 56.51406 523.7538 707.15201 13 'point symmetry operation' ? ? 0.947214 0.162459 -0.276392 -0.162459 -0.5 -0.850651 -0.276392 0.850651 -0.447214 50.34747 758.93415 263.62376 14 'point symmetry operation' ? ? 0.447213 -0.850651 -0.276393 -0.525731 0 -0.850651 0.723607 0.525731 -0.447213 507.292 717.64351 59.75637 15 'point symmetry operation' ? ? -0.670821 -0.688191 -0.276393 -0.162459 0.5 -0.850651 0.723607 -0.525732 -0.447213 795.86584 456.94414 377.28765 16 'point symmetry operation' ? ? 0.809017 -0.587785 0.000001 -0.587785 -0.809017 0 0.000001 0 -1 235.17984 723.81044 603.97974 17 'point symmetry operation' ? ? -0.309017 -0.951057 0 -0.951057 0.309017 -0.000001 0 -0.000001 -1 682.51945 495.87971 603.98005 18 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 603.97999 0 603.97999 19 'point symmetry operation' ? ? -0.309017 0.951057 0 0.951057 0.309017 0.000001 0 0.000001 -1 108.10033 -78.53979 603.97965 20 'point symmetry operation' ? ? 0.809017 0.587785 0.000001 0.587785 -0.809017 0 0.000001 0 -1 -119.83069 368.79966 603.97949 21 'point symmetry operation' ? ? 0.052787 -0.688191 -0.723607 0.688191 -0.5 0.525732 -0.723607 -0.525732 0.447213 712.3975 86.39265 544.22405 22 'point symmetry operation' ? ? -0.638196 -0.262866 -0.723608 -0.262866 -0.809017 0.525731 -0.723608 0.525731 0.447213 792.6238 466.92244 226.69302 23 'point symmetry operation' ? ? -0.447213 0.525731 -0.723607 -0.850651 0 0.525731 0.276393 0.850651 0.447213 496.80077 400.11279 -173.41989 24 'point symmetry operation' ? ? 0.361803 0.587785 -0.723607 -0.262866 0.809017 0.525731 0.894427 0 0.447214 233.74579 -21.70765 -103.17224 25 'point symmetry operation' ? ? 0.670821 -0.162459 -0.723607 0.688191 0.5 0.525732 0.276393 -0.850651 0.447213 366.99189 -215.59736 340.3561 26 'point symmetry operation' ? ? -0.361803 -0.262866 -0.894427 -0.587785 0.809017 0 0.723607 0.525731 -0.447214 760.74189 235.18035 59.75655 27 'point symmetry operation' ? ? -0.361803 0.262866 -0.894427 0.587785 0.809017 0 0.723607 -0.525731 -0.447214 601.97613 -119.83043 377.28752 28 'point symmetry operation' ? ? 0.138197 0.425326 -0.894427 0.951057 -0.309017 0.000001 -0.276393 -0.850651 -0.447214 401.9195 108.10029 777.40008 29 'point symmetry operation' ? ? 0.447215 0 -0.894427 0 -1 0 -0.894427 0 -0.447215 437.04346 603.98001 707.15228 30 'point symmetry operation' ? ? 0.138197 -0.425326 -0.894427 -0.951057 -0.309017 -0.000001 -0.276393 0.850651 -0.447214 658.80789 682.5198 263.62418 31 'point symmetry operation' ? ? -0.138197 0.425326 0.894427 -0.951057 -0.309017 -0.000001 0.276393 -0.850651 0.447214 -54.82791 682.5198 340.35581 32 'point symmetry operation' ? ? 0.361803 0.262866 0.894427 -0.587785 0.809017 0 -0.723607 -0.525731 0.447214 -156.7619 235.18035 544.22344 33 'point symmetry operation' ? ? 0.361803 -0.262866 0.894427 0.587785 0.809017 0 -0.723607 0.525731 0.447214 2.00386 -119.83043 226.69248 34 'point symmetry operation' ? ? -0.138197 -0.425326 0.894427 0.951057 -0.309017 0.000001 0.276393 0.850651 0.447214 202.06049 108.10029 -173.42009 35 'point symmetry operation' ? ? -0.447215 0 0.894427 0 -1 0 0.894427 0 0.447215 166.93652 603.98001 -103.17229 36 'point symmetry operation' ? ? 0.447213 0.525731 0.723607 0.850651 0 -0.525731 -0.276393 0.850651 -0.447213 -210.3515 203.86722 263.62358 37 'point symmetry operation' ? ? 0.638196 -0.262866 0.723608 0.262866 -0.809017 -0.525731 0.723608 0.525731 -0.447213 -29.87805 625.68765 59.756 38 'point symmetry operation' ? ? -0.052787 -0.688191 0.723607 -0.688191 -0.5 -0.525732 0.723607 -0.525732 -0.447213 307.23584 819.57736 377.28731 39 'point symmetry operation' ? ? -0.670821 -0.162459 0.723607 -0.688191 0.5 -0.525732 -0.276393 -0.850651 -0.447213 335.11024 517.58736 777.40004 40 'point symmetry operation' ? ? -0.361803 0.587785 0.723607 0.262866 0.809017 -0.525731 -0.894427 0 -0.447214 15.22367 137.05756 707.15199 41 'point symmetry operation' ? ? 0.052787 0.688191 -0.723607 -0.688191 -0.5 -0.525732 -0.723607 0.525732 0.447213 296.74414 819.57736 226.69268 42 'point symmetry operation' ? ? 0.670821 0.162459 -0.723607 -0.688191 0.5 -0.525732 0.276393 0.850651 0.447213 268.86975 517.58736 -173.42005 43 'point symmetry operation' ? ? 0.361803 -0.587785 -0.723607 0.262866 0.809017 -0.525731 0.894427 0 0.447214 588.75632 137.05756 -103.172 44 'point symmetry operation' ? ? -0.447213 -0.525731 -0.723607 0.850651 0 -0.525731 0.276393 -0.850651 0.447213 814.33149 203.86722 340.35641 45 'point symmetry operation' ? ? -0.638196 0.262866 -0.723608 0.262866 -0.809017 -0.525731 -0.723608 -0.525731 0.447213 633.85804 625.68765 544.22399 46 'point symmetry operation' ? ? -0.138197 -0.951057 0.276393 0.425326 -0.309017 -0.850651 0.894427 -0.000001 0.447214 547.46593 523.7538 -103.17203 47 'point symmetry operation' ? ? -0.947214 -0.162459 0.276392 -0.162459 -0.5 -0.850651 0.276392 -0.850651 0.447214 553.63252 758.93415 340.35623 48 'point symmetry operation' ? ? -0.447213 0.850651 0.276393 -0.525731 0 -0.850651 -0.723607 -0.525731 0.447213 96.68799 717.64351 544.22362 49 'point symmetry operation' ? ? 0.670821 0.688191 0.276393 -0.162459 0.5 -0.850651 -0.723607 0.525732 0.447213 -191.88585 456.94414 226.69234 50 'point symmetry operation' ? ? 0.861803 -0.425326 0.276393 0.425326 0.309017 -0.850651 0.276393 0.850651 0.447214 86.71023 337.11371 -173.42017 51 'point symmetry operation' ? ? 0.447213 0.850651 -0.276393 0.525731 0 0.850651 0.723607 -0.525731 -0.447213 -6.4843 -113.6635 377.2871 52 'point symmetry operation' ? ? 0.947214 -0.162459 -0.276392 0.162459 -0.5 0.850651 -0.276392 -0.850651 -0.447214 148.46961 147.03586 777.39991 53 'point symmetry operation' ? ? 0.138197 -0.951057 -0.276393 -0.425326 -0.309017 0.850651 -0.894427 -0.000001 -0.447214 630.93317 266.8663 707.15241 54 'point symmetry operation' ? ? -0.861803 -0.425326 -0.276393 -0.425326 0.309017 0.850651 -0.276393 0.850651 -0.447214 774.15815 80.22621 263.62426 55 'point symmetry operation' ? ? -0.670821 0.688191 -0.276393 0.162459 0.5 0.850651 0.723607 0.525732 -0.447213 380.21249 -154.95414 59.75628 56 'point symmetry operation' ? ? -0.361803 -0.587785 0.723607 -0.262866 0.809017 0.525731 -0.894427 0 -0.447214 370.2342 -21.70764 707.15223 57 'point symmetry operation' ? ? -0.670821 0.162459 0.723607 0.688191 0.5 0.525732 -0.276393 0.850651 -0.447213 236.9881 -215.59736 263.62389 58 'point symmetry operation' ? ? -0.052787 0.688191 0.723607 0.688191 -0.5 0.525732 0.723607 0.525732 -0.447213 -108.41751 86.39265 59.75595 59 'point symmetry operation' ? ? 0.638196 0.262866 0.723608 -0.262866 -0.809017 0.525731 0.723608 -0.525731 -0.447213 -188.64381 466.92244 377.28697 60 'point symmetry operation' ? ? 0.447213 -0.525731 0.723607 -0.850651 0 0.525731 -0.276393 -0.850651 -0.447213 107.17922 400.11279 777.39988 # _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 23 L CYS 23 1_555 A SG CYS 92 L CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 133 H CYS 133 1_555 B SG CYS 188 H CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 F C1 MYR 1 D MYR 1 1_555 F N GLY 2 D GLY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.532 ? # _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 ? # _atom_sites.entry_id 7C80 _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 # _pdbx_nonpoly_scheme.asym_id G _pdbx_nonpoly_scheme.entity_id 7 _pdbx_nonpoly_scheme.mon_id SPH _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 500 _pdbx_nonpoly_scheme.auth_seq_num 500 _pdbx_nonpoly_scheme.pdb_mon_id SPH _pdbx_nonpoly_scheme.auth_mon_id SPH _pdbx_nonpoly_scheme.pdb_ins_code . # 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 7 275.84 327.856 427.573 1 54.04 ? C1 SPH 500 A 1 HETATM 2 O O1 SPH . . . G 7 274.63 327.545 426.911 1 54.04 ? O1 SPH 500 A 1 HETATM 3 C C2 SPH . . . G 7 276.939 326.902 427.115 1 54.04 ? C2 SPH 500 A 1 HETATM 4 N N2 SPH . . . G 7 278.061 327.69 426.639 1 54.04 ? N2 SPH 500 A 1 HETATM 5 C C3 SPH . . . G 7 277.391 325.986 428.251 1 54.04 ? C3 SPH 500 A 1 HETATM 6 O O3 SPH . . . G 7 276.371 325.885 429.214 1 54.04 ? O3 SPH 500 A 1 HETATM 7 C C4 SPH . . . G 7 277.763 324.618 427.756 1 54.04 ? C4 SPH 500 A 1 HETATM 8 C C5 SPH . . . G 7 276.934 323.896 426.786 1 54.04 ? C5 SPH 500 A 1 HETATM 9 C C6 SPH . . . G 7 276.84 322.389 426.825 1 54.04 ? C6 SPH 500 A 1 HETATM 10 C C7 SPH . . . G 7 278.193 321.789 426.478 1 54.04 ? C7 SPH 500 A 1 HETATM 11 C C8 SPH . . . G 7 278.21 320.27 426.593 1 54.04 ? C8 SPH 500 A 1 HETATM 12 C C9 SPH . . . G 7 278.585 319.839 428.005 1 54.04 ? C9 SPH 500 A 1 HETATM 13 C C10 SPH . . . G 7 279.248 318.468 428.058 1 54.04 ? C10 SPH 500 A 1 HETATM 14 C C11 SPH . . . G 7 278.357 317.46 428.774 1 54.04 ? C11 SPH 500 A 1 HETATM 15 C C12 SPH . . . G 7 278.931 316.048 428.748 1 54.04 ? C12 SPH 500 A 1 HETATM 16 C C13 SPH . . . G 7 279.601 315.68 430.069 1 54.04 ? C13 SPH 500 A 1 HETATM 17 C C14 SPH . . . G 7 280.832 314.79 429.895 1 54.04 ? C14 SPH 500 A 1 HETATM 18 C C15 SPH . . . G 7 280.494 313.345 429.56 1 54.04 ? C15 SPH 500 A 1 HETATM 19 C C16 SPH . . . G 7 281.656 312.416 429.89 1 54.04 ? C16 SPH 500 A 1 HETATM 20 C C17 SPH . . . G 7 281.244 311.356 430.906 1 54.04 ? C17 SPH 500 A 1 HETATM 21 C C18 SPH . . . G 7 280.982 311.965 432.277 1 54.04 ? C18 SPH 500 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 21 #