data_3VBS # _model_server_result.job_id sbOg3GhribVpx_xibIVp0A _model_server_result.datetime_utc '2024-11-13 10:36:42' _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 3vbs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 3VBS # _exptl.entry_id 3VBS _exptl.method 'X-RAY DIFFRACTION' # _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 ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3VBS _cell.length_a 599.8 _cell.length_b 599.8 _cell.length_c 599.8 _cell.Z_PDB 480 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VBS _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # 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 ? 80-meric 80 '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)(1-20) # 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' ? ? 0.103838 -0.116036 -0.987802 -0.987802 0.103838 -0.116036 0.116036 0.987802 -0.103838 146.42811 146.42811 -146.42811 X0 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 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' ? ? 0.431262 -0.118055 0.89447 -0.402105 0.862346 0.307688 -0.807666 -0.492365 0.324426 -30.40965 33.98184 289.28404 3 'point symmetry operation' ? ? -0.488975 -0.593123 0.639616 -0.768675 0.639616 0.005484 -0.412362 -0.488975 -0.768675 211.21987 164.52289 390.96478 4 'point symmetry operation' ? ? -0.488975 -0.768675 -0.412362 -0.593123 0.639616 -0.488975 0.639616 0.005484 -0.768675 390.96478 211.21987 164.52289 5 'point symmetry operation' ? ? 0.431262 -0.402105 -0.807666 -0.118055 0.862346 -0.492365 0.89447 0.307688 0.324426 260.42372 109.53913 -77.10663 6 'point symmetry operation' ? ? -0.973071 0.229241 -0.024098 0.229241 0.951507 -0.205143 -0.024098 -0.205143 -0.978435 258.87438 3.57218 323.26587 7 'point symmetry operation' ? ? -0.492365 0.324426 -0.807666 -0.118055 0.89447 0.431262 0.862346 0.307688 -0.402105 289.28404 -30.40965 33.98184 8 'point symmetry operation' ? ? 0.309533 0.73556 -0.602611 -0.758899 0.572941 0.309533 0.572941 0.361511 0.73556 81.63635 128.33333 -98.10856 9 'point symmetry operation' ? ? 0.324426 0.89447 0.307688 -0.807666 0.431262 -0.402105 -0.492365 -0.118055 0.862346 -77.10663 260.42372 109.53913 10 'point symmetry operation' ? ? -0.468267 0.581547 0.665229 -0.196962 0.665229 -0.720192 -0.861355 -0.468267 -0.196962 32.4325 183.31709 369.96285 11 'point symmetry operation' ? ? 0.951507 -0.205143 0.229241 -0.205143 -0.978435 -0.024098 0.229241 -0.024098 -0.973071 3.57218 323.26587 258.87438 12 'point symmetry operation' ? ? 0.307688 -0.402105 0.862346 0.324426 -0.807666 -0.492365 0.89447 0.431262 -0.118055 33.98184 289.28404 -30.40965 13 'point symmetry operation' ? ? -0.402105 -0.807666 0.431262 0.862346 -0.492365 -0.118055 0.307688 0.324426 0.89447 260.42372 109.53913 -77.10663 14 'point symmetry operation' ? ? -0.196962 -0.861355 -0.468267 0.665229 -0.468267 0.581547 -0.720192 -0.196962 0.665229 369.96285 32.4325 183.31709 15 'point symmetry operation' ? ? 0.639616 -0.488975 -0.593123 0.005484 -0.768675 0.639616 -0.768675 -0.412362 -0.488975 211.21987 164.52289 390.96478 16 'point symmetry operation' ? ? -0.978435 -0.024098 -0.205143 -0.024098 -0.973071 0.229241 -0.205143 0.229241 0.951507 323.26587 258.87438 3.57218 17 'point symmetry operation' ? ? -0.246585 0.195734 -0.949149 0.195734 -0.949149 -0.246585 -0.949149 -0.246585 0.195734 292.85622 292.85622 292.85622 18 'point symmetry operation' ? ? 0.581547 0.665229 -0.468267 0.665229 -0.720192 -0.196962 -0.468267 -0.196962 -0.861355 32.4325 183.31709 369.96285 19 'point symmetry operation' ? ? 0.361511 0.73556 0.572941 0.73556 -0.602611 0.309533 0.572941 0.309533 -0.758899 -98.10856 81.63635 128.33333 20 'point symmetry operation' ? ? -0.602611 0.309533 0.73556 0.309533 -0.758899 0.572941 0.73556 0.572941 0.361511 81.63635 128.33333 -98.10856 21 'point symmetry operation' ? ? -0.205143 0.229241 0.951507 -0.978435 -0.024098 -0.205143 -0.024098 -0.973071 0.229241 3.57218 323.26587 258.87438 22 'point symmetry operation' ? ? -0.949149 -0.246585 0.195734 -0.246585 0.195734 -0.949149 0.195734 -0.949149 -0.246585 292.85622 292.85622 292.85622 23 'point symmetry operation' ? ? -0.468267 -0.196962 -0.861355 0.581547 0.665229 -0.468267 0.665229 -0.720192 -0.196962 369.96285 32.4325 183.31709 24 'point symmetry operation' ? ? 0.572941 0.309533 -0.758899 0.361511 0.73556 0.572941 0.73556 -0.602611 0.309533 128.33333 -98.10856 81.63635 25 'point symmetry operation' ? ? 0.73556 0.572941 0.361511 -0.602611 0.309533 0.73556 0.309533 -0.758899 0.572941 -98.10856 81.63635 128.33333 26 'point symmetry operation' ? ? 0.229241 -0.024098 -0.973071 0.951507 -0.205143 0.229241 -0.205143 -0.978435 -0.024098 258.87438 3.57218 323.26587 27 'point symmetry operation' ? ? 0.89447 0.431262 -0.118055 0.307688 -0.402105 0.862346 0.324426 -0.807666 -0.492365 -30.40965 33.98184 289.28404 28 'point symmetry operation' ? ? 0.307688 0.324426 0.89447 -0.402105 -0.807666 0.431262 0.862346 -0.492365 -0.118055 -77.10663 260.42372 109.53913 29 'point symmetry operation' ? ? -0.720192 -0.196962 0.665229 -0.196962 -0.861355 -0.468267 0.665229 -0.468267 0.581547 183.31709 369.96285 32.4325 30 'point symmetry operation' ? ? -0.768675 -0.412362 -0.488975 0.639616 -0.488975 -0.593123 0.005484 -0.768675 0.639616 390.96478 211.21987 164.52289 31 'point symmetry operation' ? ? -0.024098 -0.205143 -0.978435 -0.973071 0.229241 -0.024098 0.229241 0.951507 -0.205143 323.26587 258.87438 3.57218 32 'point symmetry operation' ? ? 0.862346 0.307688 -0.402105 -0.492365 0.324426 -0.807666 -0.118055 0.89447 0.431262 33.98184 289.28404 -30.40965 33 'point symmetry operation' ? ? 0.572941 0.361511 0.73556 0.309533 0.73556 -0.602611 -0.758899 0.572941 0.309533 -98.10856 81.63635 128.33333 34 'point symmetry operation' ? ? -0.492365 -0.118055 0.862346 0.324426 0.89447 0.307688 -0.807666 0.431262 -0.402105 109.53913 -77.10663 260.42372 35 'point symmetry operation' ? ? -0.861355 -0.468267 -0.196962 -0.468267 0.581547 0.665229 -0.196962 0.665229 -0.720192 369.96285 32.4325 183.31709 36 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0 0 0 37 'point symmetry operation' ? ? -0.807666 -0.492365 0.324426 0.431262 -0.118055 0.89447 -0.402105 0.862346 0.307688 289.28404 -30.40965 33.98184 38 'point symmetry operation' ? ? -0.412362 -0.488975 -0.768675 -0.488975 -0.593123 0.639616 -0.768675 0.639616 0.005484 390.96478 211.21987 164.52289 39 'point symmetry operation' ? ? 0.639616 0.005484 -0.768675 -0.488975 -0.768675 -0.412362 -0.593123 0.639616 -0.488975 164.52289 390.96478 211.21987 40 'point symmetry operation' ? ? 0.89447 0.307688 0.324426 0.431262 -0.402105 -0.807666 -0.118055 0.862346 -0.492365 -77.10663 260.42372 109.53913 41 'point symmetry operation' ? ? -0.205143 -0.978435 -0.024098 0.229241 -0.024098 -0.973071 0.951507 -0.205143 0.229241 323.26587 258.87438 3.57218 42 'point symmetry operation' ? ? 0.324426 -0.807666 -0.492365 0.89447 0.431262 -0.118055 0.307688 -0.402105 0.862346 289.28404 -30.40965 33.98184 43 'point symmetry operation' ? ? 0.862346 -0.492365 -0.118055 0.307688 0.324426 0.89447 -0.402105 -0.807666 0.431262 109.53913 -77.10663 260.42372 44 'point symmetry operation' ? ? 0.665229 -0.468267 0.581547 -0.720192 -0.196962 0.665229 -0.196962 -0.861355 -0.468267 32.4325 183.31709 369.96285 45 'point symmetry operation' ? ? 0.005484 -0.768675 0.639616 -0.768675 -0.412362 -0.488975 0.639616 -0.488975 -0.593123 164.52289 390.96478 211.21987 46 'point symmetry operation' ? ? -0.024098 -0.973071 0.229241 -0.205143 0.229241 0.951507 -0.978435 -0.024098 -0.205143 258.87438 3.57218 323.26587 47 'point symmetry operation' ? ? 0.195734 -0.949149 -0.246585 -0.949149 -0.246585 0.195734 -0.246585 0.195734 -0.949149 292.85622 292.85622 292.85622 48 'point symmetry operation' ? ? 0.665229 -0.720192 -0.196962 -0.468267 -0.196962 -0.861355 0.581547 0.665229 -0.468267 183.31709 369.96285 32.4325 49 'point symmetry operation' ? ? 0.73556 -0.602611 0.309533 0.572941 0.309533 -0.758899 0.361511 0.73556 0.572941 81.63635 128.33333 -98.10856 50 'point symmetry operation' ? ? 0.309533 -0.758899 0.572941 0.73556 0.572941 0.361511 -0.602611 0.309533 0.73556 128.33333 -98.10856 81.63635 51 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 0 0 52 'point symmetry operation' ? ? -0.402105 0.862346 0.307688 -0.807666 -0.492365 0.324426 0.431262 -0.118055 0.89447 33.98184 289.28404 -30.40965 53 'point symmetry operation' ? ? -0.768675 0.639616 0.005484 -0.412362 -0.488975 -0.768675 -0.488975 -0.593123 0.639616 164.52289 390.96478 211.21987 54 'point symmetry operation' ? ? -0.593123 0.639616 -0.488975 0.639616 0.005484 -0.768675 -0.488975 -0.768675 -0.412362 211.21987 164.52289 390.96478 55 'point symmetry operation' ? ? -0.118055 0.862346 -0.492365 0.89447 0.307688 0.324426 0.431262 -0.402105 -0.807666 109.53913 -77.10663 260.42372 56 'point symmetry operation' ? ? 0.229241 0.951507 -0.205143 -0.024098 -0.205143 -0.978435 -0.973071 0.229241 -0.024098 3.57218 323.26587 258.87438 57 'point symmetry operation' ? ? -0.118055 0.89447 0.431262 0.862346 0.307688 -0.402105 -0.492365 0.324426 -0.807666 -30.40965 33.98184 289.28404 58 'point symmetry operation' ? ? -0.758899 0.572941 0.309533 0.572941 0.361511 0.73556 0.309533 0.73556 -0.602611 128.33333 -98.10856 81.63635 59 'point symmetry operation' ? ? -0.807666 0.431262 -0.402105 -0.492365 -0.118055 0.862346 0.324426 0.89447 0.307688 260.42372 109.53913 -77.10663 60 'point symmetry operation' ? ? -0.196962 0.665229 -0.720192 -0.861355 -0.468267 -0.196962 -0.468267 0.581547 0.665229 183.31709 369.96285 32.4325 # _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 # _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 288 n n C1 C2 SPH sing 289 n n C1 H11 SPH sing 290 n n C1 H12 SPH sing 291 n n O1 HO1 SPH sing 292 n n C2 N2 SPH sing 293 n n C2 C3 SPH sing 294 n n C2 H2 SPH sing 295 n n N2 HN21 SPH sing 296 n n N2 HN22 SPH sing 297 n n C3 O3 SPH sing 298 n n C3 C4 SPH sing 299 n n C3 H3 SPH sing 300 n n O3 HO3 SPH sing 301 n n C4 C5 SPH doub 302 z n C4 H4 SPH sing 303 n n C5 C6 SPH sing 304 n n C5 H5 SPH sing 305 n n C6 C7 SPH sing 306 n n C6 H61 SPH sing 307 n n C6 H62 SPH sing 308 n n C7 C8 SPH sing 309 n n C7 H71 SPH sing 310 n n C7 H72 SPH sing 311 n n C8 C9 SPH sing 312 n n C8 H81 SPH sing 313 n n C8 H82 SPH sing 314 n n C9 C10 SPH sing 315 n n C9 H91 SPH sing 316 n n C9 H92 SPH sing 317 n n C10 C11 SPH sing 318 n n C10 H101 SPH sing 319 n n C10 H102 SPH sing 320 n n C11 C12 SPH sing 321 n n C11 H111 SPH sing 322 n n C11 H112 SPH sing 323 n n C12 C13 SPH sing 324 n n C12 H121 SPH sing 325 n n C12 H122 SPH sing 326 n n C13 C14 SPH sing 327 n n C13 H131 SPH sing 328 n n C13 H132 SPH sing 329 n n C14 C15 SPH sing 330 n n C14 H141 SPH sing 331 n n C14 H142 SPH sing 332 n n C15 C16 SPH sing 333 n n C15 H151 SPH sing 334 n n C15 H152 SPH sing 335 n n C16 C17 SPH sing 336 n n C16 H161 SPH sing 337 n n C16 H162 SPH sing 338 n n C17 C18 SPH sing 339 n n C17 H171 SPH sing 340 n n C17 H172 SPH sing 341 n n C18 H181 SPH sing 342 n n C18 H182 SPH sing 343 n n C18 H183 SPH sing 344 n n # _atom_sites.entry_id 3VBS _atom_sites.fract_transf_matrix[1][1] 0.001667 _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] 0.001667 _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] 0.001667 _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 301 _pdbx_nonpoly_scheme.auth_seq_num 1 _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 5 112.074 266.004 94.842 1 53.51 ? C1 SPH 301 A 1 HETATM 2 O O1 SPH . . . E 5 112.034 266.681 93.572 1 70.56 ? O1 SPH 301 A 1 HETATM 3 C C2 SPH . . . E 5 110.715 266.155 95.54 1 61.12 ? C2 SPH 301 A 1 HETATM 4 N N2 SPH . . . E 5 109.664 265.662 94.645 1 71.54 ? N2 SPH 301 A 1 HETATM 5 C C3 SPH . . . E 5 110.686 265.398 96.913 1 42.86 ? C3 SPH 301 A 1 HETATM 6 O O3 SPH . . . E 5 109.738 266.048 97.79 1 45.75 ? O3 SPH 301 A 1 HETATM 7 C C4 SPH . . . E 5 110.337 263.899 96.688 1 37.93 ? C4 SPH 301 A 1 HETATM 8 C C5 SPH . . . E 5 109.855 263.036 97.593 1 13.79 ? C5 SPH 301 A 1 HETATM 9 C C6 SPH . . . E 5 109.553 263.382 99.037 1 18.33 ? C6 SPH 301 A 1 HETATM 10 C C7 SPH . . . E 5 109.327 262.102 99.84 1 21.12 ? C7 SPH 301 A 1 HETATM 11 C C8 SPH . . . E 5 107.946 261.497 99.594 1 17.37 ? C8 SPH 301 A 1 HETATM 12 C C9 SPH . . . E 5 107.163 261.377 100.899 1 5 ? C9 SPH 301 A 1 HETATM 13 C C10 SPH . . . E 5 105.779 260.764 100.652 1 37.94 ? C10 SPH 301 A 1 HETATM 14 C C11 SPH . . . E 5 104.654 261.812 100.776 1 59.71 ? C11 SPH 301 A 1 HETATM 15 C C12 SPH . . . E 5 103.396 261.26 101.478 1 62.13 ? C12 SPH 301 A 1 HETATM 16 C C13 SPH . . . E 5 102.438 262.386 101.923 1 57.68 ? C13 SPH 301 A 1 HETATM 17 C C14 SPH . . . E 5 101.187 261.833 102.628 1 40.43 ? C14 SPH 301 A 1 HETATM 18 C C15 SPH . . . E 5 100.219 262.946 103.031 1 13.08 ? C15 SPH 301 A 1 HETATM 19 C C16 SPH . . . E 5 99.308 262.486 104.176 1 33.34 ? C16 SPH 301 A 1 HETATM 20 C C17 SPH . . . E 5 97.87 262.215 103.705 1 42.32 ? C17 SPH 301 A 1 HETATM 21 C C18 SPH . . . E 5 96.966 261.73 104.839 1 16.45 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 21 #