data_7C9S # _model_server_result.job_id 8FPip7wdfAfh0Q9zpEP7KQ _model_server_result.datetime_utc '2025-03-06 02:52:20' _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 7c9s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":500}' # _entry.id 7C9S # _exptl.entry_id 7C9S _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 299.492 _entity.id 5 _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 ? 240-meric 240 'complete icosahedral assembly' 1 ? tetrameric 4 'icosahedral asymmetric unit' 2 ? eicosameric 20 'icosahedral pentamer' 3 ? 24-meric 24 'icosahedral 23 hexamer' 4 ? tetrameric 4 'icosahedral asymmetric unit, std point frame' 5 ? 240-meric 240 '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 1 (1-60) A,B,C,D,E 2 1 A,B,C,D,E 3 (1-5) A,B,C,D,E 4 (1,2,6,10,23,24) A,B,C,D,E 5 P A,B,C,D,E 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 0.262866 -0.809017 0.525731 -0.16246 0.5 0.850651 305.51743 4.95111 -288.08877 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 1 398.1289 -63.05744 0.00002 3 'point symmetry operation' ? ? -0.809017 -0.587785 0 0.587785 -0.809017 0 0 0 1 581.12869 296.09983 0.00002 4 'point symmetry operation' ? ? -0.809017 0.587785 0 -0.587785 -0.809017 0 0 0 1 296.09987 581.12867 0.00001 5 'point symmetry operation' ? ? 0.309017 0.951057 0 -0.951057 0.309017 0 0 0 1 -63.05741 398.12891 0 6 'point symmetry operation' ? ? -0.947214 -0.16246 -0.276393 -0.16246 -0.5 0.850651 -0.276393 0.850651 0.447214 578.52573 196.83122 -5.20588 7 'point symmetry operation' ? ? -0.447214 0.850651 -0.276393 -0.525731 0 0.850651 0.723607 0.525731 0.447214 211.65693 163.67998 -168.88588 8 'point symmetry operation' ? ? 0.67082 0.688191 -0.276393 -0.16246 0.5 0.850651 0.723607 -0.525731 0.447214 -20.0316 -45.62878 86.05164 9 'point symmetry operation' ? ? 0.861803 -0.425325 -0.276393 0.425325 0.309017 0.850651 -0.276393 -0.850651 0.447214 203.64582 -141.83746 407.29169 10 'point symmetry operation' ? ? -0.138197 -0.951057 -0.276393 0.425325 -0.309017 0.850651 -0.894427 0 0.447214 573.57459 8.01106 350.89144 11 'point symmetry operation' ? ? -0.861803 -0.425325 0.276393 -0.425325 0.309017 -0.850651 0.276393 -0.850651 -0.447214 487.52295 476.90892 490.12591 12 'point symmetry operation' ? ? -0.67082 0.688191 0.276393 0.16246 0.5 -0.850651 -0.723607 -0.525731 -0.447214 171.23403 288.08877 653.80588 13 'point symmetry operation' ? ? 0.447214 0.850651 0.276393 0.525731 0 -0.850651 -0.723607 0.525731 -0.447214 -139.2345 321.24002 398.86834 14 'point symmetry operation' ? ? 0.947214 -0.16246 0.276393 0.16246 -0.5 -0.850651 0.276393 0.850651 -0.447214 -14.82569 530.54877 77.62831 15 'point symmetry operation' ? ? 0.138197 -0.951057 0.276393 -0.425325 -0.309017 -0.850651 0.894427 0 -0.447214 372.53172 626.75744 134.02859 16 'point symmetry operation' ? ? 0.809017 0.587785 0 0.587785 -0.809017 0 0 0 -1 -96.20869 296.09984 484.91998 17 'point symmetry operation' ? ? 0.809017 -0.587785 0 -0.587785 -0.809017 0 0 0 -1 188.82013 581.12867 484.91999 18 'point symmetry operation' ? ? -0.309017 -0.951057 0 -0.951057 0.309017 0 0 0 -1 547.97741 398.1289 484.92001 19 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 484.92 0 484.92001 20 'point symmetry operation' ? ? -0.309017 0.951057 0 0.951057 0.309017 0 0 0 -1 86.79109 -63.05744 484.91999 21 'point symmetry operation' ? ? -0.138197 -0.425325 -0.894427 0.951057 -0.309017 0 -0.276393 -0.850651 0.447214 595.95435 86.79108 407.2917 22 'point symmetry operation' ? ? -0.447214 0 -0.894427 0 -1 0 -0.894427 0 0.447214 567.75422 484.91999 350.89143 23 'point symmetry operation' ? ? -0.138197 0.425325 -0.894427 -0.951057 -0.309017 0 -0.276393 0.850651 0.447214 389.70557 547.97743 -5.20589 24 'point symmetry operation' ? ? 0.361803 0.262866 -0.894427 -0.587785 0.809017 0 0.723607 0.525731 0.447214 307.86559 188.82016 -168.88587 25 'point symmetry operation' ? ? 0.361803 -0.262866 -0.894427 0.587785 0.809017 0 0.723607 -0.525731 0.447214 435.33434 -96.20868 86.05166 26 'point symmetry operation' ? ? 0.447214 -0.525731 -0.723607 -0.850651 0 -0.525731 0.276393 0.850651 -0.447214 436.94306 576.17756 77.62833 27 'point symmetry operation' ? ? -0.361803 -0.587785 -0.723607 -0.262866 0.809017 -0.525731 0.894427 0 -0.447214 648.14297 237.50888 134.0286 28 'point symmetry operation' ? ? -0.67082 0.16246 -0.723607 0.688191 0.5 -0.525731 0.276393 -0.850651 -0.447214 541.16279 81.83997 490.12591 29 'point symmetry operation' ? ? -0.052786 0.688191 -0.723607 0.688191 -0.5 -0.525731 -0.723607 -0.525731 -0.447214 263.8455 324.29997 653.80588 30 'point symmetry operation' ? ? 0.638197 0.262866 -0.723607 -0.262866 -0.809017 -0.525731 -0.723607 0.525731 -0.447214 199.43416 629.8174 398.86835 31 'point symmetry operation' ? ? 0.052786 0.688191 0.723607 -0.688191 -0.5 0.525731 0.723607 -0.525731 0.447214 -112.64306 403.08002 86.05163 32 'point symmetry operation' ? ? 0.67082 0.16246 0.723607 -0.688191 0.5 0.525731 -0.276393 -0.850651 0.447214 -135.02284 160.62002 407.29167 33 'point symmetry operation' ? ? 0.361803 -0.587785 0.723607 0.262866 0.809017 0.525731 -0.894427 0 0.447214 121.80585 -144.89741 350.89142 34 'point symmetry operation' ? ? -0.447214 -0.525731 0.723607 0.850651 0 0.525731 -0.276393 0.850651 0.447214 302.91448 -91.25757 -5.20589 35 'point symmetry operation' ? ? -0.638197 0.262866 0.723607 0.262866 -0.809017 0.525731 0.723607 0.525731 0.447214 158.01709 247.41111 -168.88588 36 'point symmetry operation' ? ? -0.361803 0.262866 0.894427 0.587785 0.809017 0 -0.723607 0.525731 -0.447214 49.58566 -96.20868 398.86835 37 'point symmetry operation' ? ? 0.138197 0.425325 0.894427 0.951057 -0.309017 0 0.276393 0.850651 -0.447214 -111.03435 86.79108 77.6283 38 'point symmetry operation' ? ? 0.447214 0 0.894427 0 -1 0 0.894427 0 -0.447214 -82.83422 484.91999 134.02857 39 'point symmetry operation' ? ? 0.138197 -0.425325 0.894427 -0.951057 -0.309017 0 0.276393 -0.850651 -0.447214 95.21443 547.97743 490.12589 40 'point symmetry operation' ? ? -0.361803 -0.262866 0.894427 -0.587785 0.809017 0 -0.723607 -0.525731 -0.447214 177.05441 188.82015 653.80588 41 'point symmetry operation' ? ? -0.138197 0.951057 -0.276393 -0.425325 -0.309017 -0.850651 -0.894427 0 0.447214 112.38828 626.75745 350.89142 42 'point symmetry operation' ? ? 0.861803 0.425325 -0.276393 -0.425325 0.309017 -0.850651 -0.276393 0.850651 0.447214 -2.60295 476.90893 -5.20591 43 'point symmetry operation' ? ? 0.67082 -0.688191 -0.276393 0.16246 0.5 -0.850651 0.723607 0.525731 0.447214 313.68597 288.08877 -168.88587 44 'point symmetry operation' ? ? -0.447214 -0.850651 -0.276393 0.525731 0 -0.850651 0.723607 -0.525731 0.447214 624.1545 321.24001 86.05166 45 'point symmetry operation' ? ? -0.947214 0.16246 -0.276393 0.16246 -0.5 -0.850651 -0.276393 -0.850651 0.447214 499.74569 530.54876 407.2917 46 'point symmetry operation' ? ? 0.052786 -0.688191 0.723607 0.688191 -0.5 -0.525731 0.723607 0.525731 0.447214 221.0745 324.29997 -168.88588 47 'point symmetry operation' ? ? -0.638197 -0.262866 0.723607 -0.262866 -0.809017 -0.525731 0.723607 -0.525731 0.447214 285.48584 629.8174 86.05165 48 'point symmetry operation' ? ? -0.447214 0.525731 0.723607 -0.850651 0 -0.525731 -0.276393 -0.850651 0.447214 47.97694 576.17756 407.29168 49 'point symmetry operation' ? ? 0.361803 0.587785 0.723607 -0.262866 0.809017 -0.525731 -0.894427 0 0.447214 -163.22297 237.50889 350.89141 50 'point symmetry operation' ? ? 0.67082 -0.16246 0.723607 0.688191 0.5 -0.525731 -0.276393 0.850651 0.447214 -56.24279 81.83997 -5.20591 51 'point symmetry operation' ? ? -0.361803 0.587785 -0.723607 0.262866 0.809017 0.525731 0.894427 0 -0.447214 363.11415 -144.89741 134.02859 52 'point symmetry operation' ? ? 0.447214 0.525731 -0.723607 0.850651 0 0.525731 0.276393 -0.850651 -0.447214 182.00551 -91.25757 490.1259 53 'point symmetry operation' ? ? 0.638197 -0.262866 -0.723607 0.262866 -0.809017 0.525731 -0.723607 -0.525731 -0.447214 326.90291 247.4111 653.80589 54 'point symmetry operation' ? ? -0.052786 -0.688191 -0.723607 -0.688191 -0.5 0.525731 -0.723607 0.525731 -0.447214 597.56306 403.08001 398.86837 55 'point symmetry operation' ? ? -0.67082 -0.16246 -0.723607 -0.688191 0.5 0.525731 0.276393 0.850651 -0.447214 619.94284 160.62002 77.62833 56 'point symmetry operation' ? ? 0.447214 -0.850651 0.276393 -0.525731 0 0.850651 -0.723607 -0.525731 -0.447214 273.26307 163.67997 653.80588 57 'point symmetry operation' ? ? -0.67082 -0.688191 0.276393 -0.16246 0.5 0.850651 -0.723607 0.525731 -0.447214 504.95159 -45.62878 398.86837 58 'point symmetry operation' ? ? -0.861803 0.425325 0.276393 0.425325 0.309017 0.850651 0.276393 0.850651 -0.447214 281.27417 -141.83746 77.62832 59 'point symmetry operation' ? ? 0.138197 0.951057 0.276393 0.425325 -0.309017 0.850651 0.894427 0 -0.447214 -88.6546 8.01106 134.02857 60 'point symmetry operation' ? ? 0.947214 0.16246 0.276393 -0.16246 -0.5 0.850651 0.276393 -0.850651 -0.447214 -93.60574 196.83122 490.12589 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id D _struct_conn.ptnr1_label_atom_id C1 _struct_conn.ptnr1_label_comp_id MYR _struct_conn.ptnr1_label_seq_id 1 _struct_conn.ptnr1_auth_asym_id D _struct_conn.ptnr1_auth_comp_id MYR _struct_conn.ptnr1_auth_seq_id 1 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id D _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id GLY _struct_conn.ptnr2_label_seq_id 2 _struct_conn.ptnr2_auth_asym_id D _struct_conn.ptnr2_auth_comp_id GLY _struct_conn.ptnr2_auth_seq_id 2 _struct_conn.ptnr2_symmetry 1_555 _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 1.506 _struct_conn.pdbx_value_order ? # _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 7C9S _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 E _pdbx_nonpoly_scheme.entity_id 5 _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 . . . E 5 206.79 248.814 368.298 1 20.1 ? C1 SPH 500 A 1 HETATM 2 O O1 SPH . . . E 5 205.938 247.848 367.73 1 20.1 ? O1 SPH 500 A 1 HETATM 3 C C2 SPH . . . E 5 208.192 248.653 367.731 1 20.1 ? C2 SPH 500 A 1 HETATM 4 N N2 SPH . . . E 5 208.711 249.972 367.432 1 20.1 ? N2 SPH 500 A 1 HETATM 5 C C3 SPH . . . E 5 209.118 247.983 368.735 1 20.1 ? C3 SPH 500 A 1 HETATM 6 O O3 SPH . . . E 5 208.401 247.291 369.73 1 20.1 ? O3 SPH 500 A 1 HETATM 7 C C4 SPH . . . E 5 210.131 247.086 368.085 1 20.1 ? C4 SPH 500 A 1 HETATM 8 C C5 SPH . . . E 5 210.868 246.135 368.932 1 20.1 ? C5 SPH 500 A 1 HETATM 9 C C6 SPH . . . E 5 211.854 245.157 368.344 1 20.1 ? C6 SPH 500 A 1 HETATM 10 C C7 SPH . . . E 5 211.63 243.782 368.955 1 20.1 ? C7 SPH 500 A 1 HETATM 11 C C8 SPH . . . E 5 212.811 242.844 368.733 1 20.1 ? C8 SPH 500 A 1 HETATM 12 C C9 SPH . . . E 5 212.565 241.517 369.435 1 20.1 ? C9 SPH 500 A 1 HETATM 13 C C10 SPH . . . E 5 213.802 240.624 369.488 1 20.1 ? C10 SPH 500 A 1 HETATM 14 C C11 SPH . . . E 5 214.989 241.345 370.107 1 20.1 ? C11 SPH 500 A 1 HETATM 15 C C12 SPH . . . E 5 215.589 240.589 371.285 1 20.1 ? C12 SPH 500 A 1 HETATM 16 C C13 SPH . . . E 5 216.73 239.661 370.886 1 20.1 ? C13 SPH 500 A 1 HETATM 17 C C14 SPH . . . E 5 217.977 239.94 371.722 1 20.1 ? C14 SPH 500 A 1 HETATM 18 C C15 SPH . . . E 5 218.965 238.779 371.723 1 20.1 ? C15 SPH 500 A 1 HETATM 19 C C16 SPH . . . E 5 219.572 238.636 373.11 1 20.1 ? C16 SPH 500 A 1 HETATM 20 C C17 SPH . . . E 5 220.596 237.515 373.19 1 20.1 ? C17 SPH 500 A 1 HETATM 21 C C18 SPH . . . E 5 220.882 237.184 374.653 1 20.1 ? C18 SPH 500 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 21 #