data_7C81 # _model_server_result.job_id GhJdpHxTIlOOI2ooID_j-A _model_server_result.datetime_utc '2025-03-06 02:40:44' _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 7c81 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":500}' # _entry.id 7C81 # _exptl.entry_id 7C81 _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' ? ? 0.587785 -0.809017 0 0.688191 0.5 0.525731 -0.425325 -0.309017 0.850651 0 0 0 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 0 0 1 0 0 0 3 'point symmetry operation' ? ? -0.809017 -0.587785 0 0.587785 -0.809017 0 0 0 1 0 0 0 4 'point symmetry operation' ? ? -0.809017 0.587785 0 -0.587785 -0.809017 0 0 0 1 0 0 0 5 'point symmetry operation' ? ? 0.309017 0.951057 0 -0.951057 0.309017 0 0 0 1 0 0 0 6 'point symmetry operation' ? ? -0.638197 0.262866 -0.723607 0.262866 -0.809017 -0.525731 -0.723607 -0.525731 0.447214 0 0 0 7 'point symmetry operation' ? ? 0.052786 0.688191 -0.723607 -0.688191 -0.5 -0.525731 -0.723607 0.525731 0.447214 0 0 0 8 'point symmetry operation' ? ? 0.67082 0.16246 -0.723607 -0.688191 0.5 -0.525731 0.276393 0.850651 0.447214 0 0 0 9 'point symmetry operation' ? ? 0.361803 -0.587785 -0.723607 0.262866 0.809017 -0.525731 0.894427 0 0.447214 0 0 0 10 'point symmetry operation' ? ? -0.447214 -0.525731 -0.723607 0.850651 0 -0.525731 0.276393 -0.850651 0.447214 0 0 0 11 'point symmetry operation' ? ? -0.052786 0.688191 0.723607 0.688191 -0.5 0.525731 0.723607 0.525731 -0.447214 0 0 0 12 'point symmetry operation' ? ? 0.638197 0.262866 0.723607 -0.262866 -0.809017 0.525731 0.723607 -0.525731 -0.447214 0 0 0 13 'point symmetry operation' ? ? 0.447214 -0.525731 0.723607 -0.850651 0 0.525731 -0.276393 -0.850651 -0.447214 0 0 0 14 'point symmetry operation' ? ? -0.361803 -0.587785 0.723607 -0.262866 0.809017 0.525731 -0.894427 0 -0.447214 0 0 0 15 'point symmetry operation' ? ? -0.67082 0.16246 0.723607 0.688191 0.5 0.525731 -0.276393 0.850651 -0.447214 0 0 0 16 'point symmetry operation' ? ? -0.309017 -0.951057 0 -0.951057 0.309017 0 0 0 -1 0 0 0 17 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 0 0 0 18 'point symmetry operation' ? ? -0.309017 0.951057 0 0.951057 0.309017 0 0 0 -1 0 0 0 19 'point symmetry operation' ? ? 0.809017 0.587785 0 0.587785 -0.809017 0 0 0 -1 0 0 0 20 'point symmetry operation' ? ? 0.809017 -0.587785 0 -0.587785 -0.809017 0 0 0 -1 0 0 0 21 'point symmetry operation' ? ? -0.138197 -0.951057 0.276393 0.425325 -0.309017 -0.850651 0.894427 0 0.447214 0 0 0 22 'point symmetry operation' ? ? -0.947214 -0.16246 0.276393 -0.16246 -0.5 -0.850651 0.276393 -0.850651 0.447214 0 0 0 23 'point symmetry operation' ? ? -0.447214 0.850651 0.276393 -0.525731 0 -0.850651 -0.723607 -0.525731 0.447214 0 0 0 24 'point symmetry operation' ? ? 0.67082 0.688191 0.276393 -0.16246 0.5 -0.850651 -0.723607 0.525731 0.447214 0 0 0 25 'point symmetry operation' ? ? 0.861803 -0.425325 0.276393 0.425325 0.309017 -0.850651 0.276393 0.850651 0.447214 0 0 0 26 'point symmetry operation' ? ? -0.361803 0.587785 0.723607 0.262866 0.809017 -0.525731 -0.894427 0 -0.447214 0 0 0 27 'point symmetry operation' ? ? 0.447214 0.525731 0.723607 0.850651 0 -0.525731 -0.276393 0.850651 -0.447214 0 0 0 28 'point symmetry operation' ? ? 0.638197 -0.262866 0.723607 0.262866 -0.809017 -0.525731 0.723607 0.525731 -0.447214 0 0 0 29 'point symmetry operation' ? ? -0.052786 -0.688191 0.723607 -0.688191 -0.5 -0.525731 0.723607 -0.525731 -0.447214 0 0 0 30 'point symmetry operation' ? ? -0.67082 -0.16246 0.723607 -0.688191 0.5 -0.525731 -0.276393 -0.850651 -0.447214 0 0 0 31 'point symmetry operation' ? ? -0.447214 0.525731 -0.723607 -0.850651 0 0.525731 0.276393 0.850651 0.447214 0 0 0 32 'point symmetry operation' ? ? 0.361803 0.587785 -0.723607 -0.262866 0.809017 0.525731 0.894427 0 0.447214 0 0 0 33 'point symmetry operation' ? ? 0.67082 -0.16246 -0.723607 0.688191 0.5 0.525731 0.276393 -0.850651 0.447214 0 0 0 34 'point symmetry operation' ? ? 0.052786 -0.688191 -0.723607 0.688191 -0.5 0.525731 -0.723607 -0.525731 0.447214 0 0 0 35 'point symmetry operation' ? ? -0.638197 -0.262866 -0.723607 -0.262866 -0.809017 0.525731 -0.723607 0.525731 0.447214 0 0 0 36 'point symmetry operation' ? ? 0.947214 -0.16246 -0.276393 0.16246 -0.5 0.850651 -0.276393 -0.850651 -0.447214 0 0 0 37 'point symmetry operation' ? ? 0.138197 -0.951057 -0.276393 -0.425325 -0.309017 0.850651 -0.894427 0 -0.447214 0 0 0 38 'point symmetry operation' ? ? -0.861803 -0.425325 -0.276393 -0.425325 0.309017 0.850651 -0.276393 0.850651 -0.447214 0 0 0 39 'point symmetry operation' ? ? -0.67082 0.688191 -0.276393 0.16246 0.5 0.850651 0.723607 0.525731 -0.447214 0 0 0 40 'point symmetry operation' ? ? 0.447214 0.850651 -0.276393 0.525731 0 0.850651 0.723607 -0.525731 -0.447214 0 0 0 41 'point symmetry operation' ? ? -0.138197 0.425325 0.894427 -0.951057 -0.309017 0 0.276393 -0.850651 0.447214 0 0 0 42 'point symmetry operation' ? ? 0.361803 0.262866 0.894427 -0.587785 0.809017 0 -0.723607 -0.525731 0.447214 0 0 0 43 'point symmetry operation' ? ? 0.361803 -0.262866 0.894427 0.587785 0.809017 0 -0.723607 0.525731 0.447214 0 0 0 44 'point symmetry operation' ? ? -0.138197 -0.425325 0.894427 0.951057 -0.309017 0 0.276393 0.850651 0.447214 0 0 0 45 'point symmetry operation' ? ? -0.447214 0 0.894427 0 -1 0 0.894427 0 0.447214 0 0 0 46 'point symmetry operation' ? ? -0.447214 -0.850651 0.276393 0.525731 0 0.850651 -0.723607 0.525731 0.447214 0 0 0 47 'point symmetry operation' ? ? -0.947214 0.16246 0.276393 0.16246 -0.5 0.850651 0.276393 0.850651 0.447214 0 0 0 48 'point symmetry operation' ? ? -0.138197 0.951057 0.276393 -0.425325 -0.309017 0.850651 0.894427 0 0.447214 0 0 0 49 'point symmetry operation' ? ? 0.861803 0.425325 0.276393 -0.425325 0.309017 0.850651 0.276393 -0.850651 0.447214 0 0 0 50 'point symmetry operation' ? ? 0.67082 -0.688191 0.276393 0.16246 0.5 0.850651 -0.723607 -0.525731 0.447214 0 0 0 51 'point symmetry operation' ? ? 0.947214 0.16246 -0.276393 -0.16246 -0.5 -0.850651 -0.276393 0.850651 -0.447214 0 0 0 52 'point symmetry operation' ? ? 0.447214 -0.850651 -0.276393 -0.525731 0 -0.850651 0.723607 0.525731 -0.447214 0 0 0 53 'point symmetry operation' ? ? -0.67082 -0.688191 -0.276393 -0.16246 0.5 -0.850651 0.723607 -0.525731 -0.447214 0 0 0 54 'point symmetry operation' ? ? -0.861803 0.425325 -0.276393 0.425325 0.309017 -0.850651 -0.276393 -0.850651 -0.447214 0 0 0 55 'point symmetry operation' ? ? 0.138197 0.951057 -0.276393 0.425325 -0.309017 -0.850651 -0.894427 0 -0.447214 0 0 0 56 'point symmetry operation' ? ? -0.361803 0.262866 -0.894427 0.587785 0.809017 0 0.723607 -0.525731 -0.447214 0 0 0 57 'point symmetry operation' ? ? 0.138197 0.425325 -0.894427 0.951057 -0.309017 0 -0.276393 -0.850651 -0.447214 0 0 0 58 'point symmetry operation' ? ? 0.447214 0 -0.894427 0 -1 0 -0.894427 0 -0.447214 0 0 0 59 'point symmetry operation' ? ? 0.138197 -0.425325 -0.894427 -0.951057 -0.309017 0 -0.276393 0.850651 -0.447214 0 0 0 60 'point symmetry operation' ? ? -0.361803 -0.262866 -0.894427 -0.587785 0.809017 0 0.723607 0.525731 -0.447214 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 E SG CYS 133 L CYS 133 1_555 E SG CYS 193 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 F SG CYS 22 H CYS 22 1_555 F SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 F SG CYS 143 H CYS 143 1_555 F SG CYS 198 H CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 D C1 MYR 1 D MYR 1 1_555 D N GLY 2 D GLY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? # _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 7C81 _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 -32.266 -16.995 126.72 1 18.88 ? C1 SPH 500 A 1 HETATM 2 O O1 SPH . . . G 7 -31.68 -18.272 126.602 1 18.88 ? O1 SPH 500 A 1 HETATM 3 C C2 SPH . . . G 7 -31.362 -15.943 126.086 1 18.88 ? C2 SPH 500 A 1 HETATM 4 N N2 SPH . . . G 7 -32.193 -14.941 125.447 1 18.88 ? N2 SPH 500 A 1 HETATM 5 C C3 SPH . . . G 7 -30.504 -15.235 127.123 1 18.88 ? C3 SPH 500 A 1 HETATM 6 O O3 SPH . . . G 7 -30.627 -15.839 128.391 1 18.88 ? O3 SPH 500 A 1 HETATM 7 C C4 SPH . . . G 7 -29.063 -15.235 126.72 1 18.88 ? C4 SPH 500 A 1 HETATM 8 C C5 SPH . . . G 7 -28.177 -16.24 127.317 1 18.88 ? C5 SPH 500 A 1 HETATM 9 C C6 SPH . . . G 7 -26.68 -16.071 127.272 1 18.88 ? C6 SPH 500 A 1 HETATM 10 C C7 SPH . . . G 7 -26.036 -17.142 126.402 1 18.88 ? C7 SPH 500 A 1 HETATM 11 C C8 SPH . . . G 7 -24.521 -17.159 126.57 1 18.88 ? C8 SPH 500 A 1 HETATM 12 C C9 SPH . . . G 7 -24.118 -17.187 128.039 1 18.88 ? C9 SPH 500 A 1 HETATM 13 C C10 SPH . . . G 7 -22.865 -18.023 128.261 1 18.88 ? C10 SPH 500 A 1 HETATM 14 C C11 SPH . . . G 7 -21.614 -17.161 128.197 1 18.88 ? C11 SPH 500 A 1 HETATM 15 C C12 SPH . . . G 7 -20.884 -17.12 129.532 1 18.88 ? C12 SPH 500 A 1 HETATM 16 C C13 SPH . . . G 7 -19.379 -17.24 129.335 1 18.88 ? C13 SPH 500 A 1 HETATM 17 C C14 SPH . . . G 7 -18.606 -16.119 130.025 1 18.88 ? C14 SPH 500 A 1 HETATM 18 C C15 SPH . . . G 7 -17.108 -16.402 129.998 1 18.88 ? C15 SPH 500 A 1 HETATM 19 C C16 SPH . . . G 7 -16.498 -16.235 131.381 1 18.88 ? C16 SPH 500 A 1 HETATM 20 C C17 SPH . . . G 7 -15.149 -16.934 131.47 1 18.88 ? C17 SPH 500 A 1 HETATM 21 C C18 SPH . . . G 7 -14.663 -16.985 132.916 1 18.88 ? C18 SPH 500 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 21 #