data_4XDJ # _model_server_result.job_id n1dhjT8p41zNRts6EvYVEQ _model_server_result.datetime_utc '2024-12-02 00:02:46' _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 4xdj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":605}' # _entry.id 4XDJ # _exptl.entry_id 4XDJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 790.145 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE _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 90.97 _cell.angle_gamma 90 _cell.entry_id 4XDJ _cell.length_a 76.745 _cell.length_b 113.871 _cell.length_c 111.782 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XDJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,K,L,M 1 1 C,D,N,O,P,Q,R 2 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 H N N ? 3 I N N ? 3 K N N ? 3 M 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 disulf ? disulf1 A SG CYS 58 A CYS 123 1_555 B SG CYS 58 B CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf2 C SG CYS 58 C CYS 123 1_555 D SG CYS 58 D CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc1 A O THR 107 A THR 172 1_555 F K K . A K 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc2 A O THR 107 A THR 172 1_555 G K K . A K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc3 A OG1 THR 107 A THR 172 1_555 G K K . A K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc4 A O ILE 108 A ILE 173 1_555 E K K . A K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? metalc ? metalc5 A O ILE 108 A ILE 173 1_555 F K K . A K 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc6 A O GLY 109 A GLY 174 1_555 E K K . A K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc7 A O THR 216 A THR 281 1_555 F K K . A K 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc8 A O THR 216 A THR 281 1_555 G K K . A K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc9 A OG1 THR 216 A THR 281 1_555 G K K . A K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.052 ? metalc ? metalc10 A O VAL 217 A VAL 282 1_555 E K K . A K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc11 A O VAL 217 A VAL 282 1_555 F K K . A K 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc12 A O GLY 218 A GLY 283 1_555 E K K . A K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc13 E K K . A K 601 1_555 B O ILE 108 B ILE 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? metalc ? metalc14 E K K . A K 601 1_555 B O GLY 109 B GLY 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc15 E K K . A K 601 1_555 B O VAL 217 B VAL 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc16 E K K . A K 601 1_555 B O GLY 218 B GLY 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc17 F K K . A K 602 1_555 B O THR 107 B THR 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc18 F K K . A K 602 1_555 B O ILE 108 B ILE 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc19 F K K . A K 602 1_555 B O THR 216 B THR 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc20 F K K . A K 602 1_555 B O VAL 217 B VAL 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? metalc ? metalc21 G K K . A K 603 1_555 B O THR 107 B THR 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc22 G K K . A K 603 1_555 B OG1 THR 107 B THR 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc23 G K K . A K 603 1_555 B O THR 216 B THR 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? metalc ? metalc24 G K K . A K 603 1_555 B OG1 THR 216 B THR 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.008 ? metalc ? metalc25 C O THR 107 C THR 172 1_555 O K K . C K 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc26 C O THR 107 C THR 172 1_555 P K K . C K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc27 C OG1 THR 107 C THR 172 1_555 P K K . C K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc28 C O ILE 108 C ILE 173 1_555 N K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc29 C O ILE 108 C ILE 173 1_555 O K K . C K 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc30 C O GLY 109 C GLY 174 1_555 N K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc31 C O THR 216 C THR 281 1_555 O K K . C K 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc32 C O THR 216 C THR 281 1_555 P K K . C K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc33 C OG1 THR 216 C THR 281 1_555 P K K . C K 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.094 ? metalc ? metalc34 C O VAL 217 C VAL 282 1_555 N K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? metalc ? metalc35 C O VAL 217 C VAL 282 1_555 O K K . C K 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc36 C O GLY 218 C GLY 283 1_555 N K K . C K 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc37 N K K . C K 601 1_555 D O ILE 108 D ILE 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc38 N K K . C K 601 1_555 D O GLY 109 D GLY 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc39 N K K . C K 601 1_555 D O VAL 217 D VAL 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc40 N K K . C K 601 1_555 D O GLY 218 D GLY 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc41 O K K . C K 602 1_555 D O THR 107 D THR 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? metalc ? metalc42 O K K . C K 602 1_555 D O ILE 108 D ILE 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc43 O K K . C K 602 1_555 D O THR 216 D THR 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc44 O K K . C K 602 1_555 D O VAL 217 D VAL 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? metalc ? metalc45 P K K . C K 603 1_555 D O THR 107 D THR 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.007 ? metalc ? metalc46 P K K . C K 603 1_555 D OG1 THR 107 D THR 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.965 ? metalc ? metalc47 P K K . C K 603 1_555 D O THR 216 D THR 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc48 P K K . C K 603 1_555 D OG1 THR 216 D THR 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.045 ? # _chem_comp.formula 'C44 H88 N O8 P' _chem_comp.formula_weight 790.145 _chem_comp.id PC1 _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 3-SN-PHOSPHATIDYLCHOLINE # 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 O12 P PC1 sing 235 n n P O14 PC1 doub 236 n n P O13 PC1 sing 237 n n P O11 PC1 sing 238 n n O13 C11 PC1 sing 239 n n C11 C12 PC1 sing 240 n n C11 H111 PC1 sing 241 n n C11 H112 PC1 sing 242 n n C12 N PC1 sing 243 n n C12 H121 PC1 sing 244 n n C12 H122 PC1 sing 245 n n N C13 PC1 sing 246 n n N C14 PC1 sing 247 n n N C15 PC1 sing 248 n n C13 H131 PC1 sing 249 n n C13 H132 PC1 sing 250 n n C13 H133 PC1 sing 251 n n C14 H141 PC1 sing 252 n n C14 H142 PC1 sing 253 n n C14 H143 PC1 sing 254 n n C15 H151 PC1 sing 255 n n C15 H152 PC1 sing 256 n n C15 H153 PC1 sing 257 n n O11 C1 PC1 sing 258 n n C1 C2 PC1 sing 259 n n C1 H11 PC1 sing 260 n n C1 H12 PC1 sing 261 n n C2 O21 PC1 sing 262 n n C2 C3 PC1 sing 263 n n C2 H2 PC1 sing 264 n n O21 C21 PC1 sing 265 n n C21 O22 PC1 doub 266 n n C21 C22 PC1 sing 267 n n C22 C23 PC1 sing 268 n n C22 H221 PC1 sing 269 n n C22 H222 PC1 sing 270 n n C23 C24 PC1 sing 271 n n C23 H231 PC1 sing 272 n n C23 H232 PC1 sing 273 n n C24 C25 PC1 sing 274 n n C24 H241 PC1 sing 275 n n C24 H242 PC1 sing 276 n n C25 C26 PC1 sing 277 n n C25 H251 PC1 sing 278 n n C25 H252 PC1 sing 279 n n C26 C27 PC1 sing 280 n n C26 H261 PC1 sing 281 n n C26 H262 PC1 sing 282 n n C27 C28 PC1 sing 283 n n C27 H271 PC1 sing 284 n n C27 H272 PC1 sing 285 n n C28 C29 PC1 sing 286 n n C28 H281 PC1 sing 287 n n C28 H282 PC1 sing 288 n n C29 C2A PC1 sing 289 n n C29 H291 PC1 sing 290 n n C29 H292 PC1 sing 291 n n C2A C2B PC1 sing 292 n n C2A H2A1 PC1 sing 293 n n C2A H2A2 PC1 sing 294 n n C2B C2C PC1 sing 295 n n C2B H2B1 PC1 sing 296 n n C2B H2B2 PC1 sing 297 n n C2C C2D PC1 sing 298 n n C2C H2C1 PC1 sing 299 n n C2C H2C2 PC1 sing 300 n n C2D C2E PC1 sing 301 n n C2D H2D1 PC1 sing 302 n n C2D H2D2 PC1 sing 303 n n C2E C2F PC1 sing 304 n n C2E H2E1 PC1 sing 305 n n C2E H2E2 PC1 sing 306 n n C2F C2G PC1 sing 307 n n C2F H2F1 PC1 sing 308 n n C2F H2F2 PC1 sing 309 n n C2G C2H PC1 sing 310 n n C2G H2G1 PC1 sing 311 n n C2G H2G2 PC1 sing 312 n n C2H C2I PC1 sing 313 n n C2H H2H1 PC1 sing 314 n n C2H H2H2 PC1 sing 315 n n C2I H2I1 PC1 sing 316 n n C2I H2I2 PC1 sing 317 n n C2I H2I3 PC1 sing 318 n n C3 O31 PC1 sing 319 n n C3 H31 PC1 sing 320 n n C3 H32 PC1 sing 321 n n O31 C31 PC1 sing 322 n n C31 O32 PC1 doub 323 n n C31 C32 PC1 sing 324 n n C32 C33 PC1 sing 325 n n C32 H321 PC1 sing 326 n n C32 H322 PC1 sing 327 n n C33 C34 PC1 sing 328 n n C33 H331 PC1 sing 329 n n C33 H332 PC1 sing 330 n n C34 C35 PC1 sing 331 n n C34 H341 PC1 sing 332 n n C34 H342 PC1 sing 333 n n C35 C36 PC1 sing 334 n n C35 H351 PC1 sing 335 n n C35 H352 PC1 sing 336 n n C36 C37 PC1 sing 337 n n C36 H361 PC1 sing 338 n n C36 H362 PC1 sing 339 n n C37 C38 PC1 sing 340 n n C37 H371 PC1 sing 341 n n C37 H372 PC1 sing 342 n n C38 C39 PC1 sing 343 n n C38 H381 PC1 sing 344 n n C38 H382 PC1 sing 345 n n C39 C3A PC1 sing 346 n n C39 H391 PC1 sing 347 n n C39 H392 PC1 sing 348 n n C3A C3B PC1 sing 349 n n C3A H3A1 PC1 sing 350 n n C3A H3A2 PC1 sing 351 n n C3B C3C PC1 sing 352 n n C3B H3B1 PC1 sing 353 n n C3B H3B2 PC1 sing 354 n n C3C C3D PC1 sing 355 n n C3C H3C1 PC1 sing 356 n n C3C H3C2 PC1 sing 357 n n C3D C3E PC1 sing 358 n n C3D H3D1 PC1 sing 359 n n C3D H3D2 PC1 sing 360 n n C3E C3F PC1 sing 361 n n C3E H3E1 PC1 sing 362 n n C3E H3E2 PC1 sing 363 n n C3F C3G PC1 sing 364 n n C3F H3F1 PC1 sing 365 n n C3F H3F2 PC1 sing 366 n n C3G C3H PC1 sing 367 n n C3G H3G1 PC1 sing 368 n n C3G H3G2 PC1 sing 369 n n C3H C3I PC1 sing 370 n n C3H H3H1 PC1 sing 371 n n C3H H3H2 PC1 sing 372 n n C3I H3I1 PC1 sing 373 n n C3I H3I2 PC1 sing 374 n n C3I H3I3 PC1 sing 375 n n # _atom_sites.entry_id 4XDJ _atom_sites.fract_transf_matrix[1][1] 0.01303 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000221 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008782 _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] 0.008947 _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 E 2 K A 1 601 601 K K . F 2 K A 1 602 602 K K . G 2 K A 1 603 603 K K . H 3 PC1 A 1 604 800 PC1 PC1 . I 3 PC1 A 1 605 801 PC1 PC1 . J 4 TRD A 1 606 802 TRD TRD . K 3 PC1 B 1 801 801 PC1 PC1 . L 4 TRD B 1 802 802 TRD TRD . M 3 PC1 B 1 803 800 PC1 PC1 . N 2 K C 1 601 601 K K . O 2 K C 1 602 602 K K . P 2 K C 1 603 603 K K . Q 4 TRD C 1 604 802 TRD TRD . R 4 TRD D 1 401 802 TRD TRD . # 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 C38 PC1 . . . I 3 25.799 43.217 58.906 1 108.48 ? C38 PC1 605 A 1 HETATM 2 C C39 PC1 . . . I 3 26.488 44.206 59.832 1 108.36 ? C39 PC1 605 A 1 HETATM 3 C C3A PC1 . . . I 3 25.564 45.27 60.399 1 108.6 ? C3A PC1 605 A 1 HETATM 4 C C3B PC1 . . . I 3 26.136 45.978 61.613 1 109.48 ? C3B PC1 605 A 1 HETATM 5 C C3C PC1 . . . I 3 25.204 46.99 62.255 1 109.94 ? C3C PC1 605 A 1 HETATM 6 C C3D PC1 . . . I 3 25.717 47.525 63.577 1 110.36 ? C3D PC1 605 A 1 HETATM 7 C C3E PC1 . . . I 3 24.866 48.626 64.178 1 111.18 ? C3E PC1 605 A 1 HETATM 8 C C3F PC1 . . . I 3 25.334 49.059 65.558 1 112.14 ? C3F PC1 605 A 1 HETATM 9 C C3G PC1 . . . I 3 24.635 50.289 66.108 1 112.96 ? C3G PC1 605 A 1 HETATM 10 C C3H PC1 . . . I 3 25.188 50.757 67.442 1 113.71 ? C3H PC1 605 A 1 HETATM 11 C C3I PC1 . . . I 3 24.704 52.125 67.87 1 113.73 ? C3I PC1 605 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 11 #