data_3RIC # _model_server_result.job_id Jw-5iDTbLbJD-aQs1V6Chw _model_server_result.datetime_utc '2024-10-19 21:46:00' _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 3ric # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3RIC # _exptl.entry_id 3RIC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 890.301 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE _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 123.82 _cell.angle_gamma 90 _cell.entry_id 3RIC _cell.length_a 76.871 _cell.length_b 48.128 _cell.length_c 69.086 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RIC _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_454 -x-1,y,-z-1 -1 0 0 0 1 0 0 0 -1 -38.418724 0 -57.395974 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C48 H91 N O11 S' _chem_comp.formula_weight 890.301 _chem_comp.id CIS _chem_comp.mon_nstd_flag . _chem_comp.name (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '(2S,3R,4E)-N-NERVONIC-1-[BETA-D-(3-SULFATE)-GALACTOPYRANOSYL]-2-AMINO-OCTADECENE-3-OL;CIS-TETRACOSENOYL SULFATIDE' # 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 C17 C16 CIS sing 70 n n C17 H171 CIS sing 71 n n C17 H172 CIS sing 72 n n C17 H173 CIS sing 73 n n C16 C15 CIS sing 74 n n C16 H161 CIS sing 75 n n C16 H162 CIS sing 76 n n C15 C14 CIS sing 77 n n C15 H151 CIS sing 78 n n C15 H152 CIS sing 79 n n C14 C13 CIS sing 80 n n C14 H141 CIS sing 81 n n C14 H142 CIS sing 82 n n C13 C12 CIS sing 83 n n C13 H131 CIS sing 84 n n C13 H132 CIS sing 85 n n C12 C11 CIS sing 86 n n C12 H121 CIS sing 87 n n C12 H122 CIS sing 88 n n C11 C10 CIS sing 89 n n C11 H111 CIS sing 90 n n C11 H112 CIS sing 91 n n C10 C9 CIS sing 92 n n C10 H101 CIS sing 93 n n C10 H102 CIS sing 94 n n C9 C8 CIS sing 95 n n C9 H91 CIS sing 96 n n C9 H92 CIS sing 97 n n C8 C7 CIS sing 98 n n C8 H81 CIS sing 99 n n C8 H82 CIS sing 100 n n C7 C6 CIS sing 101 n n C7 H71 CIS sing 102 n n C7 H72 CIS sing 103 n n C6 C5 CIS sing 104 n n C6 H61 CIS sing 105 n n C6 H62 CIS sing 106 n n C5 C4 CIS sing 107 n n C5 H51 CIS sing 108 n n C5 H52 CIS sing 109 n n C4 C3 CIS doub 110 e n C4 H4 CIS sing 111 n n C3 C2 CIS sing 112 n n C3 H3 CIS sing 113 n n C2 O1 CIS sing 114 n n C2 C1 CIS sing 115 n n C2 H2 CIS sing 116 n n O1 HO1 CIS sing 117 n n C1 C CIS sing 118 n n C1 N CIS sing 119 n n C1 H1 CIS sing 120 n n C O CIS sing 121 n n C H1A CIS sing 122 n n C H2A CIS sing 123 n n O C43 CIS sing 124 n n C43 C44 CIS sing 125 n n C43 O6 CIS sing 126 n n C43 H43 CIS sing 127 n n C44 O3 CIS sing 128 n n C44 C45 CIS sing 129 n n C44 H44 CIS sing 130 n n O3 HO3 CIS sing 131 n n O6 C47 CIS sing 132 n n C47 C48 CIS sing 133 n n C47 C46 CIS sing 134 n n C47 H47 CIS sing 135 n n C48 O7 CIS sing 136 n n C48 H481 CIS sing 137 n n C48 H482 CIS sing 138 n n O7 HO7 CIS sing 139 n n C46 O5 CIS sing 140 n n C46 C45 CIS sing 141 n n C46 H46 CIS sing 142 n n O5 HO5 CIS sing 143 n n C45 O4 CIS sing 144 n n C45 H45 CIS sing 145 n n O4 S CIS sing 146 n n S O10 CIS sing 147 n n S O9 CIS doub 148 n n S O8 CIS doub 149 n n O10 H10 CIS sing 150 n n N C18 CIS sing 151 n n N HN CIS sing 152 n n C18 O2 CIS doub 153 n n C18 C19 CIS sing 154 n n C19 C20 CIS sing 155 n n C19 H191 CIS sing 156 n n C19 H192 CIS sing 157 n n C20 C21 CIS sing 158 n n C20 H201 CIS sing 159 n n C20 H202 CIS sing 160 n n C21 C22 CIS sing 161 n n C21 H211 CIS sing 162 n n C21 H212 CIS sing 163 n n C22 C23 CIS sing 164 n n C22 H221 CIS sing 165 n n C22 H222 CIS sing 166 n n C23 C24 CIS sing 167 n n C23 H231 CIS sing 168 n n C23 H232 CIS sing 169 n n C24 C25 CIS sing 170 n n C24 H241 CIS sing 171 n n C24 H242 CIS sing 172 n n C25 C26 CIS sing 173 n n C25 H251 CIS sing 174 n n C25 H252 CIS sing 175 n n C26 C27 CIS sing 176 n n C26 H261 CIS sing 177 n n C26 H262 CIS sing 178 n n C27 C28 CIS sing 179 n n C27 H271 CIS sing 180 n n C27 H272 CIS sing 181 n n C28 C29 CIS sing 182 n n C28 H281 CIS sing 183 n n C28 H282 CIS sing 184 n n C29 C30 CIS sing 185 n n C29 H291 CIS sing 186 n n C29 H292 CIS sing 187 n n C30 C31 CIS sing 188 n n C30 H301 CIS sing 189 n n C30 H302 CIS sing 190 n n C31 C32 CIS sing 191 n n C31 H311 CIS sing 192 n n C31 H312 CIS sing 193 n n C32 C33 CIS doub 194 z n C32 H32 CIS sing 195 n n C33 C34 CIS sing 196 n n C33 H33 CIS sing 197 n n C34 C35 CIS sing 198 n n C34 H341 CIS sing 199 n n C34 H342 CIS sing 200 n n C35 C36 CIS sing 201 n n C35 H351 CIS sing 202 n n C35 H352 CIS sing 203 n n C36 C37 CIS sing 204 n n C36 H361 CIS sing 205 n n C36 H362 CIS sing 206 n n C37 C38 CIS sing 207 n n C37 H371 CIS sing 208 n n C37 H372 CIS sing 209 n n C38 C39 CIS sing 210 n n C38 H381 CIS sing 211 n n C38 H382 CIS sing 212 n n C39 C40 CIS sing 213 n n C39 H391 CIS sing 214 n n C39 H392 CIS sing 215 n n C40 C41 CIS sing 216 n n C40 H401 CIS sing 217 n n C40 H402 CIS sing 218 n n C41 H411 CIS sing 219 n n C41 H412 CIS sing 220 n n C41 H413 CIS sing 221 n n # _atom_sites.entry_id 3RIC _atom_sites.fract_transf_matrix[1][1] 0.013009 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008715 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020778 _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] 0.017423 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 CIS A 1 301 210 CIS CIS . C 3 HOH A 1 401 211 HOH HOH . C 3 HOH A 2 402 212 HOH HOH . C 3 HOH A 3 403 213 HOH HOH . C 3 HOH A 4 404 214 HOH HOH . C 3 HOH A 5 405 215 HOH HOH . C 3 HOH A 6 406 216 HOH HOH . C 3 HOH A 7 407 217 HOH HOH . C 3 HOH A 8 408 218 HOH HOH . C 3 HOH A 9 409 219 HOH HOH . C 3 HOH A 10 410 220 HOH HOH . C 3 HOH A 11 411 221 HOH HOH . C 3 HOH A 12 412 222 HOH HOH . C 3 HOH A 13 413 223 HOH HOH . C 3 HOH A 14 414 224 HOH HOH . C 3 HOH A 15 415 225 HOH HOH . C 3 HOH A 16 416 226 HOH HOH . C 3 HOH A 17 417 227 HOH HOH . C 3 HOH A 18 418 228 HOH HOH . C 3 HOH A 19 419 229 HOH HOH . C 3 HOH A 20 420 230 HOH HOH . C 3 HOH A 21 421 231 HOH HOH . C 3 HOH A 22 422 232 HOH HOH . C 3 HOH A 23 423 233 HOH HOH . C 3 HOH A 24 424 234 HOH HOH . C 3 HOH A 25 425 235 HOH HOH . C 3 HOH A 26 426 236 HOH HOH . C 3 HOH A 27 427 237 HOH HOH . C 3 HOH A 28 428 238 HOH HOH . C 3 HOH A 29 429 239 HOH HOH . C 3 HOH A 30 430 240 HOH HOH . C 3 HOH A 31 431 241 HOH HOH . C 3 HOH A 32 432 242 HOH HOH . C 3 HOH A 33 433 243 HOH HOH . C 3 HOH A 34 434 244 HOH HOH . C 3 HOH A 35 435 245 HOH HOH . C 3 HOH A 36 436 246 HOH HOH . C 3 HOH A 37 437 247 HOH HOH . C 3 HOH A 38 438 248 HOH HOH . C 3 HOH A 39 439 249 HOH HOH . C 3 HOH A 40 440 250 HOH HOH . C 3 HOH A 41 441 251 HOH HOH . C 3 HOH A 42 442 252 HOH HOH . C 3 HOH A 43 443 253 HOH HOH . C 3 HOH A 44 444 254 HOH HOH . C 3 HOH A 45 445 255 HOH HOH . C 3 HOH A 46 446 256 HOH HOH . C 3 HOH A 47 447 257 HOH HOH . C 3 HOH A 48 448 258 HOH HOH . C 3 HOH A 49 449 259 HOH HOH . C 3 HOH A 50 450 260 HOH HOH . C 3 HOH A 51 451 261 HOH HOH . C 3 HOH A 52 452 262 HOH HOH . C 3 HOH A 53 453 263 HOH HOH . C 3 HOH A 54 454 264 HOH HOH . C 3 HOH A 55 455 265 HOH HOH . C 3 HOH A 56 456 266 HOH HOH . C 3 HOH A 57 457 267 HOH HOH . C 3 HOH A 58 458 268 HOH HOH . C 3 HOH A 59 459 269 HOH HOH . C 3 HOH A 60 460 270 HOH HOH . C 3 HOH A 61 461 271 HOH HOH . C 3 HOH A 62 462 272 HOH HOH . C 3 HOH A 63 463 273 HOH HOH . # 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 C17 CIS . . . B 2 -21.571 -8.176 -36.473 1 67.09 ? C17 CIS 301 A 1 HETATM 2 C C16 CIS . . . B 2 -21.633 -8.96 -35.179 1 66.33 ? C16 CIS 301 A 1 HETATM 3 C C15 CIS . . . B 2 -22.103 -7.999 -34.103 1 62.48 ? C15 CIS 301 A 1 HETATM 4 C C14 CIS . . . B 2 -22.238 -8.594 -32.724 1 59.75 ? C14 CIS 301 A 1 HETATM 5 C C13 CIS . . . B 2 -21.549 -7.643 -31.728 1 60.28 ? C13 CIS 301 A 1 HETATM 6 C C12 CIS . . . B 2 -22.228 -7.447 -30.376 1 58.3 ? C12 CIS 301 A 1 HETATM 7 C C11 CIS . . . B 2 -21.182 -7.358 -29.278 1 57.7 ? C11 CIS 301 A 1 HETATM 8 C C10 CIS . . . B 2 -21.843 -6.957 -27.975 1 55.49 ? C10 CIS 301 A 1 HETATM 9 C C9 CIS . . . B 2 -20.858 -6.757 -26.837 1 55.07 ? C9 CIS 301 A 1 HETATM 10 C C8 CIS . . . B 2 -21.627 -6.599 -25.537 1 54.14 ? C8 CIS 301 A 1 HETATM 11 C C7 CIS . . . B 2 -20.707 -6.629 -24.343 1 53.16 ? C7 CIS 301 A 1 HETATM 12 C C6 CIS . . . B 2 -19.806 -5.404 -24.32 1 52.61 ? C6 CIS 301 A 1 HETATM 13 C C5 CIS . . . B 2 -19.291 -5.123 -22.908 1 49.21 ? C5 CIS 301 A 1 HETATM 14 C C4 CIS . . . B 2 -20.212 -4.16 -22.208 1 48.53 ? C4 CIS 301 A 1 HETATM 15 C C3 CIS . . . B 2 -20.988 -4.529 -21.187 1 49.92 ? C3 CIS 301 A 1 HETATM 16 C C2 CIS . . . B 2 -21.917 -3.52 -20.517 1 47.5 ? C2 CIS 301 A 1 HETATM 17 O O1 CIS . . . B 2 -23.251 -3.873 -20.896 1 46.46 ? O1 CIS 301 A 1 HETATM 18 C C1 CIS . . . B 2 -21.807 -3.539 -18.989 1 46.3 ? C1 CIS 301 A 1 HETATM 19 C C CIS . . . B 2 -22.808 -2.596 -18.289 1 45.42 ? C CIS 301 A 1 HETATM 20 O O CIS . . . B 2 -22.621 -1.267 -18.777 1 42.23 ? O CIS 301 A 1 HETATM 21 C C43 CIS . . . B 2 -23.331 -0.268 -18.064 1 43.59 ? C43 CIS 301 A 1 HETATM 22 C C44 CIS . . . B 2 -23.06 1.069 -18.719 1 45.31 ? C44 CIS 301 A 1 HETATM 23 O O3 CIS . . . B 2 -21.656 1.408 -18.78 1 46.18 ? O3 CIS 301 A 1 HETATM 24 O O6 CIS . . . B 2 -24.751 -0.508 -18.055 1 46.25 ? O6 CIS 301 A 1 HETATM 25 C C47 CIS . . . B 2 -25.477 0.39 -17.205 1 45.91 ? C47 CIS 301 A 1 HETATM 26 C C48 CIS . . . B 2 -26.953 0.027 -17.093 1 45.98 ? C48 CIS 301 A 1 HETATM 27 O O7 CIS . . . B 2 -27.073 -1.221 -16.412 1 50.5 ? O7 CIS 301 A 1 HETATM 28 C C46 CIS . . . B 2 -25.321 1.766 -17.803 1 43.81 ? C46 CIS 301 A 1 HETATM 29 O O5 CIS . . . B 2 -25.933 1.708 -19.095 1 45.78 ? O5 CIS 301 A 1 HETATM 30 C C45 CIS . . . B 2 -23.835 2.119 -17.914 1 44.59 ? C45 CIS 301 A 1 HETATM 31 O O4 CIS . . . B 2 -23.682 3.353 -18.586 1 44.54 ? O4 CIS 301 A 1 HETATM 32 S S CIS . . . B 2 -23.421 4.747 -17.783 1 44.19 ? S CIS 301 A 1 HETATM 33 O O10 CIS . . . B 2 -24.155 5.718 -18.563 1 48.92 ? O10 CIS 301 A 1 HETATM 34 O O9 CIS . . . B 2 -22.001 5.146 -17.773 1 44.25 ? O9 CIS 301 A 1 HETATM 35 O O8 CIS . . . B 2 -23.856 4.622 -16.379 1 45.09 ? O8 CIS 301 A 1 HETATM 36 N N CIS . . . B 2 -20.439 -3.082 -18.662 1 46.84 ? N CIS 301 A 1 HETATM 37 C C18 CIS . . . B 2 -19.505 -3.881 -18.261 1 47.03 ? C18 CIS 301 A 1 HETATM 38 O O2 CIS . . . B 2 -19.702 -5.18 -18.109 1 43.46 ? O2 CIS 301 A 1 HETATM 39 C C19 CIS . . . B 2 -18.121 -3.323 -17.969 1 45.91 ? C19 CIS 301 A 1 HETATM 40 C C20 CIS . . . B 2 -17.104 -3.959 -18.915 1 44.95 ? C20 CIS 301 A 1 HETATM 41 C C21 CIS . . . B 2 -15.687 -3.559 -18.475 1 44.1 ? C21 CIS 301 A 1 HETATM 42 C C22 CIS . . . B 2 -14.626 -4.017 -19.494 1 44.87 ? C22 CIS 301 A 1 HETATM 43 C C23 CIS . . . B 2 -13.253 -4.254 -18.82 1 43.03 ? C23 CIS 301 A 1 HETATM 44 C C24 CIS . . . B 2 -12.247 -4.76 -19.842 1 43.69 ? C24 CIS 301 A 1 HETATM 45 C C25 CIS . . . B 2 -12.642 -6.16 -20.292 1 47.23 ? C25 CIS 301 A 1 HETATM 46 C C26 CIS . . . B 2 -11.629 -6.666 -21.303 1 49.74 ? C26 CIS 301 A 1 HETATM 47 C C27 CIS . . . B 2 -12.125 -7.899 -22.02 1 52.08 ? C27 CIS 301 A 1 HETATM 48 C C28 CIS . . . B 2 -10.911 -8.683 -22.483 1 55.73 ? C28 CIS 301 A 1 HETATM 49 C C29 CIS . . . B 2 -11.253 -9.591 -23.651 1 58.42 ? C29 CIS 301 A 1 HETATM 50 C C30 CIS . . . B 2 -10.089 -10.551 -23.859 1 59.57 ? C30 CIS 301 A 1 HETATM 51 C C31 CIS . . . B 2 -8.724 -9.901 -24.162 1 59.23 ? C31 CIS 301 A 1 HETATM 52 C C32 CIS . . . B 2 -7.735 -10.371 -23.122 1 59.84 ? C32 CIS 301 A 1 HETATM 53 C C33 CIS . . . B 2 -6.736 -9.632 -22.619 1 58.09 ? C33 CIS 301 A 1 HETATM 54 C C34 CIS . . . B 2 -6.395 -8.223 -23.019 1 55.25 ? C34 CIS 301 A 1 HETATM 55 C C35 CIS . . . B 2 -6.744 -7.335 -21.854 1 54.17 ? C35 CIS 301 A 1 HETATM 56 C C36 CIS . . . B 2 -5.854 -6.107 -21.789 1 53.89 ? C36 CIS 301 A 1 HETATM 57 C C37 CIS . . . B 2 -6.575 -5.019 -21.001 1 53.65 ? C37 CIS 301 A 1 HETATM 58 C C38 CIS . . . B 2 -5.61 -4.184 -20.171 1 53.25 ? C38 CIS 301 A 1 HETATM 59 C C39 CIS . . . B 2 -5.129 -2.94 -20.905 1 52.11 ? C39 CIS 301 A 1 HETATM 60 C C40 CIS . . . B 2 -3.875 -2.429 -20.178 1 53.04 ? C40 CIS 301 A 1 HETATM 61 C C41 CIS . . . B 2 -3.893 -0.934 -19.998 1 50.41 ? C41 CIS 301 A 1 # _model_server_stats.io_time_ms 109 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 61 #