data_4N53 # _model_server_result.job_id '_RLpgH-bsN9yWw9LIcf8fQ' _model_server_result.datetime_utc '2024-10-13 09:15:22' _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 4n53 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 4N53 # _exptl.entry_id 4N53 _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 4N53 _cell.length_a 591.375 _cell.length_b 591.375 _cell.length_c 591.375 _cell.Z_PDB 480 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4N53 _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' ? ? 0.268914 -0.882059 -0.386855 -0.882058 -0.386856 0.268916 -0.386857 0.268913 -0.882058 144.31319 144.31294 144.31339 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' ? ? 0.743328 0.565244 0.357718 -0.59304 0.309462 0.743328 0.309462 -0.764678 0.565244 -96.15444 77.96529 128.4346 3 'point symmetry operation' ? ? 0.328025 0.321545 0.888262 -0.394314 -0.807853 0.438053 0.858438 -0.493946 -0.138206 -77.61599 254.58507 111.65697 4 'point symmetry operation' ? ? 0.328025 -0.394314 0.858438 0.321545 -0.807853 -0.493946 0.888262 0.438053 -0.138206 29.99585 285.77681 -27.14676 5 'point symmetry operation' ? ? 0.743328 -0.59304 0.309462 0.565244 0.309462 -0.764678 0.357718 0.743328 0.565244 77.96517 128.43458 -96.15457 6 'point symmetry operation' ? ? -0.700683 -0.208062 0.682461 -0.208062 -0.855371 -0.474395 0.682461 -0.474395 0.556054 176.9691 366.2421 34.04045 7 'point symmetry operation' ? ? -0.186252 -0.982307 -0.019548 0.205803 -0.019551 -0.978398 0.960706 -0.186252 0.205804 315.77289 258.63025 2.84899 8 'point symmetry operation' ? ? 0.438052 -0.394317 -0.807852 -0.138203 0.858438 -0.493947 0.888263 0.328022 0.321544 254.58532 111.65686 -77.61599 9 'point symmetry operation' ? ? 0.309462 0.743327 -0.593042 -0.764676 0.565246 0.309463 0.565246 0.357718 0.743327 77.96553 128.43416 -96.15464 10 'point symmetry operation' ? ? -0.394315 0.858439 0.328023 -0.807852 -0.493947 0.321547 0.438054 -0.138203 0.888261 29.99607 285.77649 -27.14716 11 'point symmetry operation' ? ? 0.556053 0.682459 -0.4744 0.682459 -0.700685 -0.208064 -0.4744 -0.208064 -0.855368 34.04164 176.96987 366.24232 12 'point symmetry operation' ? ? -0.138204 0.888264 0.438049 0.858437 0.328022 -0.394318 -0.493949 0.321542 -0.807852 -27.14659 29.99675 285.77736 13 'point symmetry operation' ? ? -0.493947 -0.138202 0.858439 0.321544 0.888264 0.32802 -0.807853 0.43805 -0.394317 111.65677 -77.61558 254.58561 14 'point symmetry operation' ? ? -0.019551 -0.978398 0.205804 -0.186253 0.205804 0.960705 -0.982307 -0.019549 -0.186254 258.63019 2.84947 315.77301 15 'point symmetry operation' ? ? 0.629385 -0.471202 -0.617935 0.036804 -0.77622 0.629387 -0.776222 -0.418869 -0.471199 210.6614 160.19193 384.78065 16 'point symmetry operation' ? ? -0.85537 -0.474396 -0.208062 -0.474396 0.556056 0.682458 -0.208062 0.682458 -0.700686 366.24218 34.04096 176.96947 17 'point symmetry operation' ? ? -0.418872 -0.471201 -0.776219 -0.471201 -0.617933 0.629388 -0.776219 0.629388 0.036805 384.78106 210.66064 160.19129 18 'point symmetry operation' ? ? -0.272129 0.210974 -0.938848 0.210974 -0.938849 -0.272126 -0.938848 -0.272126 0.210979 288.62682 288.62657 288.62565 19 'point symmetry operation' ? ? -0.617935 0.629385 -0.471201 0.629385 0.036803 -0.776222 -0.471201 -0.776222 -0.418867 210.66135 160.19248 384.78063 20 'point symmetry operation' ? ? -0.978398 0.205803 -0.01955 0.205803 0.960705 -0.186256 -0.01955 -0.186256 -0.982307 258.63028 2.84992 315.77332 21 'point symmetry operation' ? ? 0.000001 1 -0.000001 0.000003 0.000001 1 1 -0.000001 -0.000003 0 -0.00039 0.00039 22 'point symmetry operation' ? ? -0.593039 0.309463 0.743328 0.309463 -0.764676 0.565246 0.743328 0.565246 0.357715 77.96501 128.43406 -96.15449 23 'point symmetry operation' ? ? -0.394315 -0.807852 0.438054 0.858439 -0.493947 -0.138203 0.328023 0.321547 0.888261 254.58483 111.65672 -77.61621 24 'point symmetry operation' ? ? 0.321544 -0.807854 -0.493945 0.888263 0.438051 -0.138204 0.328022 -0.394314 0.858439 285.77688 -27.1467 29.99595 25 'point symmetry operation' ? ? 0.565245 0.30946 -0.764678 0.35772 0.743327 0.565244 0.743327 -0.593042 0.309462 128.43481 -96.15459 77.96564 26 'point symmetry operation' ? ? -0.208064 -0.855371 -0.474395 0.682459 -0.474396 0.556055 -0.700684 -0.20806 0.682461 366.24228 34.041 176.96893 27 'point symmetry operation' ? ? 0.205802 -0.019552 -0.978398 0.960705 -0.186254 0.205802 -0.186255 -0.982307 -0.019547 258.63065 2.84976 315.77294 28 'point symmetry operation' ? ? -0.138204 0.858437 -0.493949 0.888264 0.328022 0.321542 0.438049 -0.394318 -0.807852 111.6573 -77.61558 254.58576 29 'point symmetry operation' ? ? -0.764677 0.565246 0.309461 0.565246 0.357721 0.743325 0.309461 0.743325 -0.593044 128.4344 -96.15466 77.966 30 'point symmetry operation' ? ? -0.807853 -0.493945 0.321546 0.438052 -0.138201 0.888263 -0.394315 0.85844 0.32802 285.77657 -27.1471 29.99616 31 'point symmetry operation' ? ? 0.68246 -0.700684 -0.208063 -0.474397 -0.208063 -0.85537 0.556054 0.68246 -0.474397 176.96944 366.24225 34.04085 32 'point symmetry operation' ? ? 0.858438 0.328023 -0.394317 -0.493948 0.321544 -0.807852 -0.138204 0.888262 0.438052 29.99634 285.77693 -27.14698 33 'point symmetry operation' ? ? 0.321544 0.888263 0.328022 -0.807854 0.438051 -0.394314 -0.493945 -0.138204 0.858439 -77.61577 254.5854 111.65659 34 'point symmetry operation' ? ? -0.186252 0.205803 0.960706 -0.982307 -0.019551 -0.186252 -0.019548 -0.978398 0.205804 2.84939 315.77329 258.62975 35 'point symmetry operation' ? ? 0.036806 -0.77622 0.629387 -0.77622 -0.418872 -0.4712 0.629387 -0.4712 -0.617935 160.1917 384.78102 210.66059 36 'point symmetry operation' ? ? -0.474397 0.556055 0.682459 -0.208065 0.682458 -0.700686 -0.855369 -0.474399 -0.208061 34.04119 176.97007 366.24207 37 'point symmetry operation' ? ? -0.4712 -0.617934 0.629387 -0.776221 0.629386 0.036804 -0.41887 -0.471201 -0.77622 210.66092 160.19217 384.78077 38 'point symmetry operation' ? ? 0.210975 -0.938848 -0.272127 -0.938848 -0.272127 0.210976 -0.272127 0.210976 -0.938848 288.62656 288.62639 288.6261 39 'point symmetry operation' ? ? 0.629385 0.036804 -0.776222 -0.471202 -0.77622 -0.418869 -0.617935 0.629387 -0.471199 160.19225 384.78099 210.66054 40 'point symmetry operation' ? ? 0.205802 0.960705 -0.186255 -0.019552 -0.186254 -0.982307 -0.978398 0.205802 -0.019547 2.84984 315.7736 258.62985 41 'point symmetry operation' ? ? 0.000001 0.000003 1 1 0.000001 -0.000001 -0.000001 1 -0.000003 -0.00039 0 0.00039 42 'point symmetry operation' ? ? 0.309462 -0.764676 0.565246 0.743327 0.565246 0.357718 -0.593042 0.309463 0.743327 128.43429 -96.15451 77.96548 43 'point symmetry operation' ? ? 0.858438 -0.493948 -0.138204 0.328023 0.321544 0.888262 -0.394317 -0.807852 0.438052 111.65715 -77.6158 254.58528 44 'point symmetry operation' ? ? 0.888263 0.43805 -0.138206 0.328024 -0.394316 0.858438 0.321542 -0.807853 -0.493947 -27.14637 29.99626 285.77723 45 'point symmetry operation' ? ? 0.35772 0.743329 0.565242 0.743329 -0.59304 0.309461 0.565242 0.309461 -0.76468 -96.15452 77.96545 128.43512 46 'point symmetry operation' ? ? 0.68246 -0.474397 0.556054 -0.700684 -0.208063 0.68246 -0.208063 -0.85537 -0.474397 34.04124 176.96953 366.24217 47 'point symmetry operation' ? ? 0.960706 -0.186253 0.205801 -0.186253 -0.982307 -0.01955 0.205801 -0.01955 -0.978399 2.84968 315.77322 258.63022 48 'point symmetry operation' ? ? 0.888263 0.328024 0.321542 0.43805 -0.394316 -0.807853 -0.138206 0.858438 -0.493947 -77.61577 254.58556 111.65712 49 'point symmetry operation' ? ? 0.565245 0.35772 0.743327 0.30946 0.743327 -0.593042 -0.764678 0.565244 0.309462 -96.15459 77.96581 128.4347 50 'point symmetry operation' ? ? 0.438052 -0.138203 0.888263 -0.394317 0.858438 0.328022 -0.807852 -0.493947 0.321544 -27.14677 29.99647 285.77692 51 'point symmetry operation' ? ? -0.474397 -0.208065 -0.855369 0.556055 0.682458 -0.474399 0.682459 -0.700686 -0.208061 366.24243 34.0414 176.96927 52 'point symmetry operation' ? ? -0.493947 0.321544 -0.807853 -0.138202 0.888264 0.43805 0.858439 0.32802 -0.394317 285.77701 -27.14692 29.99643 53 'point symmetry operation' ? ? -0.807853 0.438052 -0.394315 -0.493945 -0.138201 0.85844 0.321546 0.888263 0.32802 254.58516 111.65633 -77.61599 54 'point symmetry operation' ? ? -0.982308 -0.01955 -0.186251 -0.01955 -0.978398 0.205806 -0.186251 0.205806 0.960705 315.77296 258.62978 2.8487 55 'point symmetry operation' ? ? -0.776221 -0.418872 -0.471198 0.629386 -0.471202 -0.617934 0.036806 -0.776218 0.629389 384.78095 210.66112 160.19105 56 'point symmetry operation' ? ? -0.208064 0.682459 -0.700684 -0.855371 -0.474396 -0.20806 -0.474395 0.556055 0.682461 176.96964 366.242 34.04041 57 'point symmetry operation' ? ? -0.776221 0.629386 0.036806 -0.418872 -0.471202 -0.776218 -0.471198 -0.617934 0.629389 160.19194 384.78113 210.66011 58 'point symmetry operation' ? ? -0.938848 -0.272128 0.210977 -0.272128 0.210973 -0.938849 0.210977 -0.938849 -0.272125 288.62638 288.62683 288.62583 59 'point symmetry operation' ? ? -0.4712 -0.776221 -0.41887 -0.617934 0.629386 -0.471201 0.629387 0.036804 -0.77622 384.78092 210.66107 160.1916 60 'point symmetry operation' ? ? -0.019551 -0.186253 -0.982307 -0.978398 0.205804 -0.019549 0.205804 0.960705 -0.186254 315.77326 258.62988 2.84915 # _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 4N53 _atom_sites.fract_transf_matrix[1][1] 0.001691 _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] 0.001691 _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] 0.001691 _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 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 . . . E 5 62.516 126.422 39.361 1 53 ? C1 SPH 301 A 1 HETATM 2 O O1 SPH . . . E 5 62.797 125.121 38.888 1 69.43 ? O1 SPH 301 A 1 HETATM 3 C C2 SPH . . . E 5 61.316 126.385 40.301 1 56.69 ? C2 SPH 301 A 1 HETATM 4 N N2 SPH . . . E 5 61.324 125.168 41.089 1 47.13 ? N2 SPH 301 A 1 HETATM 5 C C3 SPH . . . E 5 61.301 127.619 41.199 1 51.55 ? C3 SPH 301 A 1 HETATM 6 O O3 SPH . . . E 5 59.998 128.156 41.272 1 53.06 ? O3 SPH 301 A 1 HETATM 7 C C4 SPH . . . E 5 61.781 127.342 42.593 1 48.92 ? C4 SPH 301 A 1 HETATM 8 C C5 SPH . . . E 5 60.781 127.095 43.639 1 38.18 ? C5 SPH 301 A 1 HETATM 9 C C6 SPH . . . E 5 60.66 128.048 44.804 1 23.64 ? C6 SPH 301 A 1 HETATM 10 C C7 SPH . . . E 5 61.694 127.754 45.884 1 28.83 ? C7 SPH 301 A 1 HETATM 11 C C8 SPH . . . E 5 60.98 127.446 47.196 1 36.23 ? C8 SPH 301 A 1 HETATM 12 C C9 SPH . . . E 5 60.312 128.699 47.752 1 18.94 ? C9 SPH 301 A 1 HETATM 13 C C10 SPH . . . E 5 59.82 128.486 49.179 1 16.43 ? C10 SPH 301 A 1 HETATM 14 C C11 SPH . . . E 5 58.425 127.871 49.193 1 12.29 ? C11 SPH 301 A 1 HETATM 15 C C12 SPH . . . E 5 57.644 128.321 50.422 1 7.12 ? C12 SPH 301 A 1 HETATM 16 C C13 SPH . . . E 5 56.154 128.05 50.255 1 12.86 ? C13 SPH 301 A 1 HETATM 17 C C14 SPH . . . E 5 55.396 128.188 51.571 1 2.72 ? C14 SPH 301 A 1 HETATM 18 C C15 SPH . . . E 5 53.939 128.562 51.327 1 4.3 ? C15 SPH 301 A 1 HETATM 19 C C16 SPH . . . E 5 53.299 129.132 52.588 1 6.55 ? C16 SPH 301 A 1 HETATM 20 C C17 SPH . . . E 5 51.779 129.022 52.541 1 12.33 ? C17 SPH 301 A 1 HETATM 21 C C18 SPH . . . E 5 51.161 129.348 53.896 1 8.25 ? C18 SPH 301 A 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 21 #