data_3IF7 # _model_server_result.job_id X3RmgEcTheuISnCiVSlPfw _model_server_result.datetime_utc '2024-12-26 12:49:40' _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 3if7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":153}' # _entry.id 3IF7 # _exptl.entry_id 3IF7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 465.627 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium _entity.pdbx_number_of_molecules 4 _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 120 _cell.entry_id 3IF7 _cell.length_a 39.669 _cell.length_b 39.669 _cell.length_c 170.34 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IF7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N 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 metalc ? metalc1 A OD1 ASP 20 A ASP 20 1_555 B CA CA . A CA 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc2 A OD1 ASP 22 A ASP 22 1_555 B CA CA . A CA 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc3 A OD1 ASP 24 A ASP 24 1_555 B CA CA . A CA 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc4 A O THR 26 A THR 26 1_555 B CA CA . A CA 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc5 A OE1 GLU 31 A GLU 31 1_555 B CA CA . A CA 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc6 A OE2 GLU 31 A GLU 31 1_555 B CA CA . A CA 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc7 A OD1 ASP 56 A ASP 56 1_555 C CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc8 A OD1 ASP 58 A ASP 58 1_555 C CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc9 A OD1 ASN 60 A ASN 60 1_555 C CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc10 A O THR 62 A THR 62 1_555 C CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc11 A OE1 GLU 67 A GLU 67 1_555 C CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc12 A OE2 GLU 67 A GLU 67 1_555 C CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc13 A OD1 ASP 93 A ASP 93 1_555 D CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc14 A OD1 ASP 95 A ASP 95 1_555 D CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc15 A OD1 ASN 97 A ASN 97 1_555 D CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc16 A O TYR 99 A TYR 99 1_555 D CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc17 A OE1 GLU 104 A GLU 104 1_555 D CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc18 A OE2 GLU 104 A GLU 104 1_555 D CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc19 A OD1 ASP 129 A ASP 129 1_555 E CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc20 A OD1 ASP 131 A ASP 131 1_555 E CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc21 A OD1 ASP 133 A ASP 133 1_555 E CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc22 A O GLN 135 A GLN 135 1_555 E CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc23 A OE1 GLU 140 A GLU 140 1_555 E CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc24 A OE2 GLU 140 A GLU 140 1_555 E CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc25 B CA CA . A CA 149 1_555 J O HOH . A HOH 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc26 C CA CA . A CA 150 1_555 J O HOH . A HOH 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc27 D CA CA . A CA 151 1_555 J O HOH . A HOH 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc28 E CA CA . A CA 152 1_555 J O HOH . A HOH 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? # _chem_comp.formula 'C23 H50 N2 O5 P 1' _chem_comp.formula_weight 465.627 _chem_comp.id SPU _chem_comp.mon_nstd_flag . _chem_comp.name 2-{[(R)-{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}(hydroxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'sphingosylphosphorylcholine, sphingosine phosphorylcholine' # 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 C11 C14 SPU sing 277 n n C11 C21 SPU sing 278 n n C14 C17 SPU sing 279 n n C17 C20 SPU sing 280 n n C20 C23 SPU sing 281 n n C23 C26 SPU sing 282 n n C26 C29 SPU sing 283 n n C29 C32 SPU sing 284 n n C32 C35 SPU sing 285 n n C35 C38 SPU sing 286 n n C38 C41 SPU sing 287 n n C41 C43 SPU doub 288 n n C43 C45 SPU sing 289 n n C45 O47 SPU sing 290 n n C45 C49 SPU sing 291 n n C49 N51 SPU sing 292 n n C49 C54 SPU sing 293 n n C54 O57 SPU sing 294 n n O57 P58 SPU sing 295 n n P58 O59 SPU sing 296 n n P58 O60 SPU doub 297 n n P58 O61 SPU sing 298 n n O61 C62 SPU sing 299 n n C62 C65 SPU sing 300 n n C65 N68 SPU sing 301 n n N68 C70 SPU sing 302 n n N68 C74 SPU sing 303 n n N68 C78 SPU sing 304 n n C21 C22 SPU sing 305 n n C22 C231 SPU sing 306 n n C11 H11 SPU sing 307 n n C11 H11A SPU sing 308 e n C14 H14 SPU sing 309 n n C14 H14A SPU sing 310 n n C17 H17 SPU sing 311 n n C17 H17A SPU sing 312 n n C20 H20 SPU sing 313 n n C20 H20A SPU sing 314 n n C23 H23 SPU sing 315 n n C23 H23A SPU sing 316 n n C26 H26 SPU sing 317 n n C26 H26A SPU sing 318 n n C29 H29 SPU sing 319 n n C29 H29A SPU sing 320 n n C32 H32 SPU sing 321 n n C32 H32A SPU sing 322 n n C35 H35 SPU sing 323 n n C35 H35A SPU sing 324 n n C38 H38 SPU sing 325 n n C38 H38A SPU sing 326 n n C41 H41 SPU sing 327 n n C43 H43 SPU sing 328 n n C45 H45 SPU sing 329 n n O47 HO47 SPU sing 330 n n C49 H49 SPU sing 331 n n N51 HN51 SPU sing 332 n n N51 HN5A SPU sing 333 n n C54 H54 SPU sing 334 n n C54 H54A SPU sing 335 n n O59 H59 SPU sing 336 n n C62 H62 SPU sing 337 n n C62 H62A SPU sing 338 n n C65 H65 SPU sing 339 n n C65 H65A SPU sing 340 n n C70 H70 SPU sing 341 n n C70 H70A SPU sing 342 n n C70 H70B SPU sing 343 n n C74 H74 SPU sing 344 n n C74 H74A SPU sing 345 n n C74 H74B SPU sing 346 n n C78 H78 SPU sing 347 n n C78 H78A SPU sing 348 n n C78 H78B SPU sing 349 n n C21 H44 SPU sing 350 n n C21 H451 SPU sing 351 n n C22 H46 SPU sing 352 n n C22 H47 SPU sing 353 n n C231 H48 SPU sing 354 n n C231 H491 SPU sing 355 n n C231 H50 SPU sing 356 n n # _atom_sites.entry_id 3IF7 _atom_sites.fract_transf_matrix[1][1] 0.025209 _atom_sites.fract_transf_matrix[1][2] 0.014554 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.029108 _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] 0.005871 _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 CA A 1 149 149 CA CA . C 2 CA A 1 150 150 CA CA . D 2 CA A 1 151 151 CA CA . E 2 CA A 1 152 152 CA CA . F 3 SPU A 1 153 1 SPU SPU . G 3 SPU A 1 154 2 SPU SPU . H 3 SPU A 1 155 3 SPU SPU . I 3 SPU A 1 156 4 SPU SPU . J 4 HOH A 1 157 1 HOH HOH . J 4 HOH A 2 158 2 HOH HOH . J 4 HOH A 3 159 3 HOH HOH . J 4 HOH A 4 160 4 HOH HOH . J 4 HOH A 5 161 5 HOH HOH . J 4 HOH A 6 162 6 HOH HOH . J 4 HOH A 7 163 7 HOH HOH . J 4 HOH A 8 164 8 HOH HOH . J 4 HOH A 9 165 9 HOH HOH . J 4 HOH A 10 166 10 HOH HOH . J 4 HOH A 11 167 11 HOH HOH . J 4 HOH A 12 168 12 HOH HOH . J 4 HOH A 13 169 13 HOH HOH . J 4 HOH A 14 170 14 HOH HOH . J 4 HOH A 15 171 15 HOH HOH . J 4 HOH A 16 172 16 HOH HOH . J 4 HOH A 17 173 17 HOH HOH . J 4 HOH A 18 174 18 HOH HOH . J 4 HOH A 19 175 19 HOH HOH . J 4 HOH A 20 176 20 HOH HOH . J 4 HOH A 21 177 21 HOH HOH . J 4 HOH A 22 178 22 HOH HOH . J 4 HOH A 23 179 23 HOH HOH . J 4 HOH A 24 180 24 HOH HOH . J 4 HOH A 25 181 25 HOH HOH . J 4 HOH A 26 182 26 HOH HOH . J 4 HOH A 27 183 27 HOH HOH . J 4 HOH A 28 184 28 HOH HOH . J 4 HOH A 29 185 29 HOH HOH . J 4 HOH A 30 186 30 HOH HOH . J 4 HOH A 31 187 31 HOH HOH . J 4 HOH A 32 188 32 HOH HOH . J 4 HOH A 33 189 33 HOH HOH . J 4 HOH A 34 190 34 HOH HOH . J 4 HOH A 35 191 35 HOH HOH . J 4 HOH A 36 192 36 HOH HOH . J 4 HOH A 37 193 37 HOH HOH . J 4 HOH A 38 194 38 HOH HOH . J 4 HOH A 39 195 39 HOH HOH . J 4 HOH A 40 196 40 HOH HOH . J 4 HOH A 41 197 41 HOH HOH . J 4 HOH A 42 198 42 HOH HOH . J 4 HOH A 43 199 43 HOH HOH . J 4 HOH A 44 200 44 HOH HOH . J 4 HOH A 45 201 45 HOH HOH . J 4 HOH A 46 202 46 HOH HOH . J 4 HOH A 47 203 47 HOH HOH . J 4 HOH A 48 204 48 HOH HOH . J 4 HOH A 49 205 49 HOH HOH . J 4 HOH A 50 206 50 HOH HOH . J 4 HOH A 51 207 51 HOH HOH . J 4 HOH A 52 208 52 HOH HOH . J 4 HOH A 53 209 53 HOH HOH . J 4 HOH A 54 210 54 HOH HOH . J 4 HOH A 55 211 55 HOH HOH . J 4 HOH A 56 212 56 HOH HOH . J 4 HOH A 57 213 57 HOH HOH . J 4 HOH A 58 214 58 HOH HOH . J 4 HOH A 59 215 59 HOH HOH . J 4 HOH A 60 216 60 HOH HOH . J 4 HOH A 61 217 61 HOH HOH . J 4 HOH A 62 218 62 HOH HOH . J 4 HOH A 63 219 63 HOH HOH . J 4 HOH A 64 220 64 HOH HOH . J 4 HOH A 65 221 65 HOH HOH . J 4 HOH A 66 222 66 HOH HOH . J 4 HOH A 67 223 67 HOH HOH . J 4 HOH A 68 224 68 HOH HOH . J 4 HOH A 69 225 69 HOH HOH . J 4 HOH A 70 226 70 HOH HOH . J 4 HOH A 71 227 71 HOH HOH . J 4 HOH A 72 228 72 HOH HOH . J 4 HOH A 73 229 73 HOH HOH . J 4 HOH A 74 230 74 HOH HOH . J 4 HOH A 75 231 75 HOH HOH . J 4 HOH A 76 232 76 HOH HOH . J 4 HOH A 77 233 77 HOH HOH . J 4 HOH A 78 234 78 HOH HOH . J 4 HOH A 79 235 79 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 C11 SPU . . . F 3 -28.718 7.487 -17.41 1 59.8 ? C11 SPU 153 A 1 HETATM 2 C C14 SPU . . . F 3 -27.911 8.466 -18.257 1 58.65 ? C14 SPU 153 A 1 HETATM 3 C C17 SPU . . . F 3 -28.363 9.91 -18.07 1 56.88 ? C17 SPU 153 A 1 HETATM 4 C C20 SPU . . . F 3 -27.333 10.669 -17.262 1 56.35 ? C20 SPU 153 A 1 HETATM 5 C C23 SPU . . . F 3 -26.988 12.047 -17.815 1 54.27 ? C23 SPU 153 A 1 HETATM 6 C C26 SPU . . . F 3 -26.338 12.897 -16.737 1 54.82 ? C26 SPU 153 A 1 HETATM 7 C C29 SPU . . . F 3 -26.272 14.349 -17.119 1 53.15 ? C29 SPU 153 A 1 HETATM 8 C C32 SPU . . . F 3 -25.278 15.108 -16.254 1 58.47 ? C32 SPU 153 A 1 HETATM 9 C C35 SPU . . . F 3 -24.714 16.282 -17.017 1 61.31 ? C35 SPU 153 A 1 HETATM 10 C C38 SPU . . . F 3 -23.893 15.744 -18.19 1 64.92 ? C38 SPU 153 A 1 HETATM 11 C C41 SPU . . . F 3 -22.538 16.37 -18.142 1 66.16 ? C41 SPU 153 A 1 HETATM 12 C C43 SPU . . . F 3 -21.926 16.816 -19.233 1 66.41 ? C43 SPU 153 A 1 HETATM 13 C C45 SPU . . . F 3 -20.567 17.446 -19.07 1 67.38 ? C45 SPU 153 A 1 HETATM 14 O O47 SPU . . . F 3 -20.236 18.008 -20.321 1 64.52 ? O47 SPU 153 A 1 HETATM 15 C C49 SPU . . . F 3 -20.632 18.579 -18.05 1 67.01 ? C49 SPU 153 A 1 HETATM 16 N N51 SPU . . . F 3 -22.017 19.006 -17.877 1 68.08 ? N51 SPU 153 A 1 HETATM 17 C C54 SPU . . . F 3 -20.118 18.244 -16.664 1 68.77 ? C54 SPU 153 A 1 HETATM 18 O O57 SPU . . . F 3 -20.933 19.008 -15.79 1 69.36 ? O57 SPU 153 A 1 HETATM 19 P P58 SPU . . . F 3 -20.797 18.817 -14.223 1 76.61 ? P58 SPU 153 A 1 HETATM 20 O O59 SPU . . . F 3 -21.683 17.632 -13.852 1 76.18 ? O59 SPU 153 A 1 HETATM 21 O O60 SPU . . . F 3 -19.297 18.833 -13.963 1 79.77 ? O60 SPU 153 A 1 HETATM 22 O O61 SPU . . . F 3 -21.453 20.131 -13.541 1 75.57 ? O61 SPU 153 A 1 HETATM 23 C C62 SPU . . . F 3 -21.363 20.319 -12.121 1 73.48 ? C62 SPU 153 A 1 HETATM 24 C C65 SPU . . . F 3 -21.298 21.815 -11.776 1 73.34 ? C65 SPU 153 A 1 HETATM 25 N N68 SPU . . . F 3 -19.929 22.352 -11.745 1 72.16 ? N68 SPU 153 A 1 HETATM 26 C C70 SPU . . . F 3 -19.186 21.843 -12.893 1 74.15 ? C70 SPU 153 A 1 HETATM 27 C C74 SPU . . . F 3 -19.938 23.834 -11.792 1 73.58 ? C74 SPU 153 A 1 HETATM 28 C C78 SPU . . . F 3 -19.216 21.876 -10.554 1 75.45 ? C78 SPU 153 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 592 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 28 #