data_6ILJ # _model_server_result.job_id gk449ut7fOtbLT746E0mbA _model_server_result.datetime_utc '2024-11-08 01:28:25' _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 6ilj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 6ILJ # _exptl.entry_id 6ILJ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 299.492 _entity.id 6 _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 6ILJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ILJ _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 ? 300-meric 300 'complete icosahedral assembly' 1 ? pentameric 5 'icosahedral asymmetric unit' 2 ? 25-meric 25 'icosahedral pentamer' 3 ? 30-meric 30 'icosahedral 23 hexamer' 4 ? pentameric 5 '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 1 (1-60) A,B,C,D,E,F 2 1 A,B,C,D,E,F 3 (1-5) A,B,C,D,E,F 4 (1,2,6,10,23,24) A,B,C,D,E,F 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' ? ? -0.010649 -0.999932 0.004726 0.025304 0.004455 0.99967 -0.999623 0.010765 0.025254 270.35636 -275.27901 260.14694 1 'point symmetry operation' ? ? 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.79313 -0.526917 -0.305456 0.513615 0.309108 0.800407 -0.327329 -0.791713 0.515796 279.10995 -166.91591 430.57555 3 'point symmetry operation' ? ? 0.458407 -0.338955 -0.821567 0.304129 -0.808778 0.503372 -0.835086 -0.480612 -0.267663 456.90951 269.47981 693.45326 4 'point symmetry operation' ? ? 0.458407 0.304129 -0.835086 -0.338955 -0.808778 -0.480612 -0.821567 0.503372 -0.267663 287.68572 706.1031 425.34506 5 'point symmetry operation' ? ? 0.79313 0.513615 -0.327329 -0.526917 0.309108 -0.791713 -0.305456 0.800407 0.515796 5.30012 539.55542 -3.23262 6 'point symmetry operation' ? ? 0.998493 -0.021522 -0.05049 -0.021522 -0.999768 0.000544 -0.05049 0.000544 -0.998724 19.68916 543.12892 547.82085 7 'point symmetry operation' ? ? 0.797407 -0.492802 -0.348264 -0.530744 -0.298127 -0.793367 0.287146 0.817476 -0.49928 280.23117 704.2332 103.6116 8 'point symmetry operation' ? ? 0.493334 -0.296771 -0.817648 -0.314379 0.815624 -0.485719 0.811041 0.496673 0.309076 435.0979 264.25493 -167.67056 9 'point symmetry operation' ? ? 0.506492 0.295663 -0.809969 0.328564 0.802318 0.498328 0.79719 -0.518526 0.309224 270.2688 -168.77088 108.87711 10 'point symmetry operation' ? ? 0.818697 0.465776 -0.335839 0.509559 -0.319656 0.798855 0.264735 -0.82515 -0.499042 13.53208 3.58273 551.07512 11 'point symmetry operation' ? ? -0.998719 0.000225 0.05059 0.000225 -0.99996 0.008908 0.05059 0.008908 0.99868 525.85588 535.07497 -15.69511 12 'point symmetry operation' ? ? -0.808558 0.486259 0.331339 -0.516332 -0.316267 -0.79585 -0.282197 -0.814572 0.506791 268.84867 705.8826 426.94542 13 'point symmetry operation' ? ? -0.499999 0.314024 0.807087 -0.311453 0.804388 -0.505922 -0.808083 -0.50433 -0.304389 104.67427 271.88592 702.35827 14 'point symmetry operation' ? ? -0.49946 -0.278456 0.820367 0.331727 0.813298 0.478021 -0.800311 0.51089 -0.313838 260.21611 -167.14641 429.93224 15 'point symmetry operation' ? ? -0.807686 -0.472395 0.352826 0.524354 -0.301851 0.796203 -0.269621 0.828088 0.491503 520.52066 -4.48662 -13.84915 16 'point symmetry operation' ? ? -0.999773 0.021297 -0.000101 0.021297 0.999729 -0.009451 -0.000101 -0.009451 -0.999955 534.02884 -3.14815 537.23658 17 'point symmetry operation' ? ? -0.781979 0.53346 0.322381 0.53346 0.305286 0.78881 0.322381 0.78881 -0.523307 251.38409 -168.14415 108.22976 18 'point symmetry operation' ? ? -0.451742 0.321702 0.832128 0.321702 -0.811234 0.488269 0.832128 0.488269 0.262976 82.8922 269.43509 -158.77865 19 'point symmetry operation' ? ? -0.465439 -0.321335 0.824688 -0.321335 -0.806839 -0.495737 0.824688 -0.495737 0.272278 261.40324 704.86993 105.2079 20 'point symmetry operation' ? ? -0.804141 -0.506996 0.310342 -0.506996 0.312398 -0.803345 0.310342 -0.803345 -0.508257 540.22102 536.40422 535.36897 21 'point symmetry operation' ? ? -0.014918 -0.02987 -0.999442 0.99978 -0.015171 -0.01447 -0.014731 -0.999439 0.03009 549.13937 6.87575 531.88515 22 'point symmetry operation' ? ? 0.299973 0.7899 -0.534859 0.7899 -0.520035 -0.324995 -0.534859 -0.324995 -0.779938 119.6258 282.22628 707.5518 23 'point symmetry operation' ? ? 0.818697 0.509559 0.264735 0.465776 -0.319656 -0.82515 -0.335839 0.798855 -0.499042 -158.79299 449.56216 276.69188 24 'point symmetry operation' ? ? 0.824395 -0.483471 0.294328 0.475337 0.309049 -0.823738 0.307291 0.81899 0.48459 98.6483 277.63088 -165.26084 25 'point symmetry operation' ? ? 0.309192 -0.816856 -0.486976 0.80537 0.497231 -0.32271 0.505747 -0.292417 0.811611 536.17456 4.03563 -7.54273 26 'point symmetry operation' ? ? 0.036209 0.029641 0.998905 0.99933 -0.006357 -0.036035 0.005282 0.99954 -0.029851 -14.89309 10.39356 5.25493 27 'point symmetry operation' ? ? -0.283029 -0.800763 0.527895 0.801129 -0.5 -0.328927 0.52734 0.329817 0.783029 420.36945 274.86181 -172.96309 28 'point symmetry operation' ? ? -0.808558 -0.516332 -0.282197 0.486259 -0.316267 -0.814572 0.331339 -0.79585 0.506791 702.33217 440.29507 256.32405 29 'point symmetry operation' ? ? -0.814116 0.48986 -0.311853 0.48986 0.290928 -0.821826 -0.311853 -0.821826 -0.476812 441.33219 278.07019 699.85611 30 'point symmetry operation' ? ? -0.292021 0.82729 0.479912 0.806956 0.482463 -0.340664 -0.513367 0.287786 -0.808476 -1.9374 12.37644 544.68686 31 'point symmetry operation' ? ? -0.03567 0.020963 -0.999144 -0.999235 0.015267 0.035993 0.016009 0.999664 0.020402 540.99808 524.72528 -11.10799 32 'point symmetry operation' ? ? 0.309525 0.81631 -0.48768 -0.796464 0.502737 0.336007 0.519461 0.284416 0.805771 97.33644 258.77816 -164.71483 33 'point symmetry operation' ? ? 0.824395 0.475337 0.307291 -0.483471 0.309049 0.81899 0.294328 -0.823738 0.48459 -162.51013 97.23898 279.74377 34 'point symmetry operation' ? ? 0.797407 -0.530744 0.287146 -0.492802 -0.298127 0.817476 -0.348264 -0.793367 -0.49928 120.5575 263.3494 708.04113 35 'point symmetry operation' ? ? 0.265858 -0.811562 -0.520275 -0.811562 -0.479694 0.333557 -0.520275 0.333557 -0.786164 555.34949 527.55046 528.28486 36 'point symmetry operation' ? ? 0.014379 -0.020734 0.999682 -0.999875 0.006261 0.014512 -0.00656 -0.999765 -0.020641 4.32951 533.06116 543.33023 37 'point symmetry operation' ? ? -0.326469 -0.805447 0.494644 -0.794565 0.517297 0.317915 -0.511941 -0.289237 -0.808862 442.24219 259.18949 699.48844 38 'point symmetry operation' ? ? -0.834534 -0.468564 -0.289828 -0.468564 0.326874 0.820732 -0.289828 0.820732 -0.49234 698.54483 87.95953 256.60262 39 'point symmetry operation' ? ? -0.807686 0.524354 -0.269621 -0.472395 -0.301851 0.828088 0.352826 0.796203 0.491503 419.0359 256.00527 -173.27408 40 'point symmetry operation' ? ? -0.283029 0.801129 0.52734 -0.800763 -0.5 0.329817 0.527895 -0.328927 0.783029 -10.01277 531.0932 3.93333 41 'point symmetry operation' ? ? -0.014918 0.99978 -0.014731 -0.02987 -0.015171 -0.999439 -0.999442 -0.01447 0.03009 9.15312 548.09372 532.92835 42 'point symmetry operation' ? ? 0.506492 0.328564 0.79719 0.295663 0.802318 -0.518526 -0.809969 0.498328 0.309224 -168.23269 111.9552 269.34523 43 'point symmetry operation' ? ? 0.309525 -0.796464 0.519461 0.81631 0.502737 0.284416 -0.48768 0.336007 0.805771 261.54224 -162.70658 93.24012 44 'point symmetry operation' ? ? -0.333617 -0.820552 -0.464106 0.812556 -0.499904 0.299749 -0.477968 -0.27711 0.833521 704.54355 103.68162 247.98428 45 'point symmetry operation' ? ? -0.534134 0.289588 -0.794254 0.289588 -0.819989 -0.493717 -0.794254 -0.493717 0.354123 548.55849 542.98037 519.72655 46 'point symmetry operation' ? ? -0.03567 -0.999235 0.016009 0.020963 0.015267 0.999664 -0.999144 0.035993 0.020402 543.7991 -8.24779 521.87494 47 'point symmetry operation' ? ? -0.546753 -0.302752 -0.780642 -0.302751 -0.797774 0.521439 -0.780642 0.521439 0.344527 707.52465 425.48552 245.78083 48 'point symmetry operation' ? ? -0.333617 0.812556 -0.477968 -0.820552 -0.499904 -0.27711 -0.464106 0.299749 0.833521 269.32892 698.66462 89.20409 49 'point symmetry operation' ? ? 0.309192 0.80537 0.505747 -0.816856 0.497231 -0.292417 -0.486976 -0.32271 0.811611 -165.21648 433.76528 268.52844 50 'point symmetry operation' ? ? 0.493334 -0.314379 0.811041 -0.296771 0.815624 0.496673 -0.817648 -0.485719 0.309076 4.41541 -3.13061 535.93373 51 'point symmetry operation' ? ? 0.014379 -0.999875 -0.00656 -0.020734 0.006261 -0.999765 0.999682 0.014512 -0.020641 536.49677 539.9548 -0.84913 52 'point symmetry operation' ? ? -0.499999 -0.311453 -0.808083 0.314024 0.804388 -0.50433 0.807087 -0.505922 -0.304389 704.58054 102.64817 266.86218 53 'point symmetry operation' ? ? -0.292021 0.806956 -0.513367 0.82729 0.482463 0.287786 0.479912 -0.340664 -0.808476 269.07142 -161.12181 445.5121 54 'point symmetry operation' ? ? 0.350894 0.809748 0.4703 0.809748 -0.514624 0.281905 0.4703 0.281905 -0.83627 -168.17179 113.166 288.21252 55 'point symmetry operation' ? ? 0.54026 -0.306935 0.783524 0.28564 -0.808933 -0.513845 0.791536 0.501416 -0.349361 -2.89384 546.45518 12.3461 56 'point symmetry operation' ? ? 0.036209 0.99933 0.005282 0.029641 -0.006357 0.99954 0.998905 -0.036035 -0.029851 -9.8751 -4.74499 15.40817 57 'point symmetry operation' ? ? 0.54026 0.28564 0.791536 -0.306935 -0.808933 0.501416 0.783524 -0.513845 -0.349361 -164.29862 434.96686 287.37408 58 'point symmetry operation' ? ? 0.316113 -0.823048 0.471874 -0.823048 -0.485296 -0.295092 0.471874 -0.295092 -0.830816 279.6313 700.21952 441.40601 59 'point symmetry operation' ? ? -0.326469 -0.794565 -0.511941 -0.805447 0.517297 -0.289237 0.494644 0.317915 -0.808862 708.41861 424.44284 264.63708 60 'point symmetry operation' ? ? -0.49946 0.331727 -0.800311 -0.278457 0.813298 0.51089 0.820367 0.478021 -0.313838 529.49381 -11.24919 1.35593 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _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 5 E CYS 66 1_555 E SG CYS 52 E CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 E SG CYS 36 E CYS 97 1_555 E SG CYS 65 E CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 E SG CYS 70 E CYS 131 1_555 E SG CYS 111 E CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 E SG CYS 97 E CYS 158 1_555 E SG CYS 127 E CYS 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 E SG CYS 132 E CYS 193 1_555 E SG CYS 174 E CYS 235 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 E SG CYS 160 E CYS 221 1_555 E SG CYS 190 E CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? # _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 6ILJ _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 F _pdbx_nonpoly_scheme.entity_id 6 _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 301 _pdbx_nonpoly_scheme.auth_seq_num 301 _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 . . . F 6 151.576 238.857 321.539 1 46.96 ? C1 SPH 301 A 1 HETATM 2 O O1 SPH . . . F 6 152.257 238.002 320.654 1 46.96 ? O1 SPH 301 A 1 HETATM 3 C C2 SPH . . . F 6 152.311 238.866 322.87 1 46.96 ? C2 SPH 301 A 1 HETATM 4 N N2 SPH . . . F 6 152.2 237.547 323.457 1 46.96 ? N2 SPH 301 A 1 HETATM 5 C C3 SPH . . . F 6 153.779 239.201 322.655 1 46.96 ? C3 SPH 301 A 1 HETATM 6 O O3 SPH . . . F 6 153.9 240.144 321.615 1 46.96 ? O3 SPH 301 A 1 HETATM 7 C C4 SPH . . . F 6 154.379 239.77 323.907 1 46.96 ? C4 SPH 301 A 1 HETATM 8 C C5 SPH . . . F 6 153.662 240.795 324.667 1 46.96 ? C5 SPH 301 A 1 HETATM 9 C C6 SPH . . . F 6 154.398 241.912 325.36 1 46.96 ? C6 SPH 301 A 1 HETATM 10 C C7 SPH . . . F 6 155.322 241.364 326.434 1 46.96 ? C7 SPH 301 A 1 HETATM 11 C C8 SPH . . . F 6 155.423 242.345 327.592 1 46.96 ? C8 SPH 301 A 1 HETATM 12 C C9 SPH . . . F 6 156.17 241.72 328.762 1 46.96 ? C9 SPH 301 A 1 HETATM 13 C C10 SPH . . . F 6 155.304 241.732 330.013 1 46.96 ? C10 SPH 301 A 1 HETATM 14 C C11 SPH . . . F 6 155.677 242.86 330.964 1 46.96 ? C11 SPH 301 A 1 HETATM 15 C C12 SPH . . . F 6 154.79 244.086 330.784 1 46.96 ? C12 SPH 301 A 1 HETATM 16 C C13 SPH . . . F 6 154.28 244.677 332.097 1 46.96 ? C13 SPH 301 A 1 HETATM 17 C C14 SPH . . . F 6 155.228 244.512 333.278 1 46.96 ? C14 SPH 301 A 1 HETATM 18 C C15 SPH . . . F 6 155.429 245.868 333.941 1 46.96 ? C15 SPH 301 A 1 HETATM 19 C C16 SPH . . . F 6 156.644 245.912 334.858 1 46.96 ? C16 SPH 301 A 1 HETATM 20 C C17 SPH . . . F 6 156.644 247.212 335.649 1 46.96 ? C17 SPH 301 A 1 HETATM 21 C C18 SPH . . . F 6 157.22 247.003 337.039 1 46.96 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #