data_5KLB # _model_server_result.job_id Sv3IAGmENoheaw7TyZV9Cw _model_server_result.datetime_utc '2024-11-16 10:41:31' _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 5klb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1305}' # _entry.id 5KLB # _exptl.entry_id 5KLB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 677.933 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE _entity.pdbx_number_of_molecules 20 _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 5KLB _cell.length_a 124.9 _cell.length_b 125.7 _cell.length_c 191.485 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KLB _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA _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 ? 2 E N N ? 2 G N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 V N N ? 2 W N N ? 2 X N N ? 2 Y N N ? 2 AA N N ? 2 BA N N ? 2 CA N N ? 2 DA N N ? 2 EA N N ? 2 FA 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 HA O HOH . A HOH 1401 1_555 Z CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc2 B OD1 ASN 243 B ASN 1225 1_555 K CA CA . B CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.033 ? metalc ? metalc3 K CA CA . B CA 1301 1_555 C OE1 GLU 246 C GLU 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.097 ? metalc ? metalc4 K CA CA . B CA 1301 1_555 D OD1 ASN 243 D ASN 1225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc5 K CA CA . B CA 1301 1_555 D OE1 GLU 246 D GLU 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.052 ? metalc ? metalc6 IA O HOH . B HOH 1401 1_555 Z CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.69 ? metalc ? metalc7 IA O HOH . B HOH 1404 1_555 Z CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.09 ? metalc ? metalc8 JA O HOH . C HOH 1401 1_555 Z CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.009 ? metalc ? metalc9 JA O HOH . C HOH 1402 1_555 Z CA CA . D CA 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.147 ? metalc ? metalc10 Z CA CA . D CA 1301 1_555 KA O HOH . D HOH 1401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc11 Z CA CA . D CA 1301 1_555 KA O HOH . D HOH 1403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? # _chem_comp.formula 'C36 H72 N O8 P' _chem_comp.formula_weight 677.933 _chem_comp.id MC3 _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE _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 C2 MC3 sing 308 n n C1 O3P MC3 sing 309 n n C1 H11 MC3 sing 310 n n C1 H12 MC3 sing 311 n n C2 C3 MC3 sing 312 n n C2 O2 MC3 sing 313 n n C2 H2 MC3 sing 314 n n C3 O3 MC3 sing 315 n n C3 H31 MC3 sing 316 n n C3 H32 MC3 sing 317 n n C4 C5 MC3 sing 318 n n C4 O4P MC3 sing 319 n n C4 H41 MC3 sing 320 n n C4 H42 MC3 sing 321 n n C5 N MC3 sing 322 n n C5 H51 MC3 sing 323 n n C5 H52 MC3 sing 324 n n C6 N MC3 sing 325 n n C6 H61 MC3 sing 326 n n C6 H62 MC3 sing 327 n n C6 H63 MC3 sing 328 n n C7 N MC3 sing 329 n n C7 H71 MC3 sing 330 n n C7 H72 MC3 sing 331 n n C7 H73 MC3 sing 332 n n C8 N MC3 sing 333 n n C8 H81 MC3 sing 334 n n C8 H82 MC3 sing 335 n n C8 H83 MC3 sing 336 n n C11 C12 MC3 sing 337 n n C11 O3 MC3 sing 338 n n C11 O11 MC3 doub 339 n n C12 C13 MC3 sing 340 n n C12 H121 MC3 sing 341 n n C12 H122 MC3 sing 342 n n C13 C14 MC3 sing 343 n n C13 H131 MC3 sing 344 n n C13 H132 MC3 sing 345 n n C14 C15 MC3 sing 346 n n C14 H141 MC3 sing 347 n n C14 H142 MC3 sing 348 n n C15 C16 MC3 sing 349 n n C15 H151 MC3 sing 350 n n C15 H152 MC3 sing 351 n n C16 C17 MC3 sing 352 n n C16 H161 MC3 sing 353 n n C16 H162 MC3 sing 354 n n C17 C18 MC3 sing 355 n n C17 H171 MC3 sing 356 n n C17 H172 MC3 sing 357 n n C18 C19 MC3 sing 358 n n C18 H181 MC3 sing 359 n n C18 H182 MC3 sing 360 n n C19 C20 MC3 sing 361 n n C19 H191 MC3 sing 362 n n C19 H192 MC3 sing 363 n n C20 C21 MC3 sing 364 n n C20 H201 MC3 sing 365 n n C20 H202 MC3 sing 366 n n C21 C22 MC3 sing 367 n n C21 H211 MC3 sing 368 n n C21 H212 MC3 sing 369 n n C22 C23 MC3 sing 370 n n C22 H221 MC3 sing 371 n n C22 H222 MC3 sing 372 n n C23 C24 MC3 sing 373 n n C23 H231 MC3 sing 374 n n C23 H232 MC3 sing 375 n n C24 H241 MC3 sing 376 n n C24 H242 MC3 sing 377 n n C24 H243 MC3 sing 378 n n C31 C32 MC3 sing 379 n n C31 O2 MC3 sing 380 n n C31 O31 MC3 doub 381 n n C32 C33 MC3 sing 382 n n C32 H321 MC3 sing 383 n n C32 H322 MC3 sing 384 n n C33 C34 MC3 sing 385 n n C33 H331 MC3 sing 386 n n C33 H332 MC3 sing 387 n n C34 C35 MC3 sing 388 n n C34 H341 MC3 sing 389 n n C34 H342 MC3 sing 390 n n C35 C36 MC3 sing 391 n n C35 H351 MC3 sing 392 n n C35 H352 MC3 sing 393 n n C36 C37 MC3 sing 394 n n C36 H361 MC3 sing 395 n n C36 H362 MC3 sing 396 n n C37 C38 MC3 sing 397 n n C37 H371 MC3 sing 398 n n C37 H372 MC3 sing 399 n n C38 C39 MC3 sing 400 n n C38 H381 MC3 sing 401 n n C38 H382 MC3 sing 402 n n C39 C40 MC3 sing 403 n n C39 H391 MC3 sing 404 n n C39 H392 MC3 sing 405 n n C40 C41 MC3 sing 406 n n C40 H401 MC3 sing 407 n n C40 H402 MC3 sing 408 n n C41 C42 MC3 sing 409 n n C41 H411 MC3 sing 410 n n C41 H412 MC3 sing 411 n n C42 C43 MC3 sing 412 n n C42 H421 MC3 sing 413 n n C42 H422 MC3 sing 414 n n C43 C44 MC3 sing 415 n n C43 H431 MC3 sing 416 n n C43 H432 MC3 sing 417 n n C44 H441 MC3 sing 418 n n C44 H442 MC3 sing 419 n n C44 H443 MC3 sing 420 n n O1P P MC3 doub 421 n n O2P P MC3 sing 422 n n O3P P MC3 sing 423 n n O4P P MC3 sing 424 n n # _atom_sites.entry_id 5KLB _atom_sites.fract_transf_matrix[1][1] 0.008006 _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] 0.007955 _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] 0.005222 _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 MC3 A 1 1301 1301 MC3 PX4 . F 3 CA A 1 1302 1302 CA CA . G 2 MC3 A 1 1303 1305 MC3 PX4 . H 4 CPS A 1 1304 402 CPS CPS . I 4 CPS A 1 1305 403 CPS CPS . J 4 CPS A 1 1306 404 CPS CPS . K 3 CA B 1 1301 1 CA CA . L 2 MC3 B 1 1302 1301 MC3 PX4 . M 2 MC3 B 1 1303 1305 MC3 PX4 . N 2 MC3 B 1 1304 1306 MC3 PX4 . O 2 MC3 B 1 1305 1307 MC3 PX4 . P 2 MC3 B 1 1306 1306 MC3 PX4 . Q 4 CPS B 1 1307 406 CPS CPS . R 4 CPS B 1 1308 407 CPS CPS . S 2 MC3 C 1 1301 1301 MC3 PX4 . T 2 MC3 C 1 1302 1302 MC3 PX4 . U 2 MC3 C 1 1303 1303 MC3 PX4 . V 2 MC3 C 1 1304 1304 MC3 PX4 . W 2 MC3 C 1 1305 1305 MC3 PX4 . X 2 MC3 C 1 1306 1306 MC3 PX4 . Y 2 MC3 C 1 1307 1304 MC3 PX4 . Z 3 CA D 1 1301 1302 CA CA . AA 2 MC3 D 1 1302 1301 MC3 PX4 . BA 2 MC3 D 1 1303 1302 MC3 PX4 . CA 2 MC3 D 1 1304 1303 MC3 PX4 . DA 2 MC3 D 1 1305 1304 MC3 PX4 . EA 2 MC3 D 1 1306 1305 MC3 PX4 . FA 2 MC3 D 1 1307 1306 MC3 PX4 . GA 4 CPS D 1 1308 405 CPS CPS . HA 5 HOH A 1 1401 5 HOH HOH . HA 5 HOH A 2 1402 7 HOH HOH . HA 5 HOH A 3 1403 1 HOH HOH . IA 5 HOH B 1 1401 12 HOH HOH . IA 5 HOH B 2 1402 4 HOH HOH . IA 5 HOH B 3 1403 1407 HOH HOH . IA 5 HOH B 4 1404 10 HOH HOH . IA 5 HOH B 5 1405 1408 HOH HOH . IA 5 HOH B 6 1406 1407 HOH HOH . JA 5 HOH C 1 1401 9 HOH HOH . JA 5 HOH C 2 1402 8 HOH HOH . JA 5 HOH C 3 1403 2 HOH HOH . KA 5 HOH D 1 1401 6 HOH HOH . KA 5 HOH D 2 1402 1408 HOH HOH . KA 5 HOH D 3 1403 11 HOH HOH . KA 5 HOH D 4 1404 3 HOH HOH . KA 5 HOH D 5 1405 1408 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 C1 MC3 . . . O 2 36.192 22.888 196.988 1 69.46 ? C1 MC3 1305 B 1 HETATM 2 C C2 MC3 . . . O 2 36.535 23.179 198.436 1 66.19 ? C2 MC3 1305 B 1 HETATM 3 C C3 MC3 . . . O 2 38.054 23.334 198.53 1 58.1 ? C3 MC3 1305 B 1 HETATM 4 C C4 MC3 . . . O 2 36.383 25.876 192.803 1 84.42 ? C4 MC3 1305 B 1 HETATM 5 C C5 MC3 . . . O 2 34.881 25.918 192.373 1 97.52 ? C5 MC3 1305 B 1 HETATM 6 C C6 MC3 . . . O 2 34.43 27.087 190.326 1 89.62 ? C6 MC3 1305 B 1 HETATM 7 C C7 MC3 . . . O 2 35.364 28.342 192.19 1 84.04 ? C7 MC3 1305 B 1 HETATM 8 C C8 MC3 . . . O 2 33.124 27.538 192.493 1 87.49 ? C8 MC3 1305 B 1 HETATM 9 C C11 MC3 . . . O 2 39.034 24.813 200.075 1 58.5 ? C11 MC3 1305 B 1 HETATM 10 C C12 MC3 . . . O 2 38.749 25.377 201.476 1 51.32 ? C12 MC3 1305 B 1 HETATM 11 C C13 MC3 . . . O 2 37.977 24.393 202.368 1 53.83 ? C13 MC3 1305 B 1 HETATM 12 C C14 MC3 . . . O 2 37.833 24.898 203.83 1 60.54 ? C14 MC3 1305 B 1 HETATM 13 C C15 MC3 . . . O 2 37.211 23.849 204.794 1 64.25 ? C15 MC3 1305 B 1 HETATM 14 C C16 MC3 . . . O 2 37.35 24.223 206.293 1 60.87 ? C16 MC3 1305 B 1 HETATM 15 C C17 MC3 . . . O 2 37.881 23.036 207.132 1 59.17 ? C17 MC3 1305 B 1 HETATM 16 C C18 MC3 . . . O 2 37.46 23.132 208.626 1 68.42 ? C18 MC3 1305 B 1 HETATM 17 C C19 MC3 . . . O 2 38.581 23.723 209.537 1 64.33 ? C19 MC3 1305 B 1 HETATM 18 C C20 MC3 . . . O 2 38.466 23.166 210.994 1 69.47 ? C20 MC3 1305 B 1 HETATM 19 C C21 MC3 . . . O 2 39.056 24.124 212.083 1 70.6 ? C21 MC3 1305 B 1 HETATM 20 C C22 MC3 . . . O 2 39.234 23.406 213.467 1 73.03 ? C22 MC3 1305 B 1 HETATM 21 C C23 MC3 . . . O 2 39.986 24.248 214.544 1 70.97 ? C23 MC3 1305 B 1 HETATM 22 C C24 MC3 . . . O 2 39.145 25.397 215.164 1 66.72 ? C24 MC3 1305 B 1 HETATM 23 C C31 MC3 . . . O 2 34.686 24.254 199.422 1 70.23 ? C31 MC3 1305 B 1 HETATM 24 C C32 MC3 . . . O 2 34.658 25.141 200.669 1 70.53 ? C32 MC3 1305 B 1 HETATM 25 C C33 MC3 . . . O 2 34.059 26.525 200.356 1 66.3 ? C33 MC3 1305 B 1 HETATM 26 C C34 MC3 . . . O 2 33.813 27.329 201.657 1 67.25 ? C34 MC3 1305 B 1 HETATM 27 C C35 MC3 . . . O 2 33.381 26.432 202.823 1 70.5 ? C35 MC3 1305 B 1 HETATM 28 C C36 MC3 . . . O 2 34.129 26.739 204.141 1 75.55 ? C36 MC3 1305 B 1 HETATM 29 C C37 MC3 . . . O 2 33.311 26.385 205.42 1 74.81 ? C37 MC3 1305 B 1 HETATM 30 C C38 MC3 . . . O 2 34.172 25.707 206.519 1 70.61 ? C38 MC3 1305 B 1 HETATM 31 C C39 MC3 . . . O 2 33.703 26.061 207.963 1 70.18 ? C39 MC3 1305 B 1 HETATM 32 C C40 MC3 . . . O 2 34.479 25.24 209.036 1 73.75 ? C40 MC3 1305 B 1 HETATM 33 C C41 MC3 . . . O 2 33.843 23.847 209.351 1 77.84 ? C41 MC3 1305 B 1 HETATM 34 C C42 MC3 . . . O 2 32.827 23.831 210.549 1 76.09 ? C42 MC3 1305 B 1 HETATM 35 C C43 MC3 . . . O 2 33.423 24.182 211.952 1 70.61 ? C43 MC3 1305 B 1 HETATM 36 C C44 MC3 . . . O 2 34.427 23.133 212.481 1 65.66 ? C44 MC3 1305 B 1 HETATM 37 N N MC3 . . . O 2 34.423 27.237 191.82 1 99.09 ? N MC3 1305 B 1 HETATM 38 O O2 MC3 . . . O 2 35.938 24.382 198.808 1 66.46 ? O2 MC3 1305 B 1 HETATM 39 O O3 MC3 . . . O 2 38.327 23.624 199.888 1 61.31 ? O3 MC3 1305 B 1 HETATM 40 O O11 MC3 . . . O 2 38.657 25.711 199.067 1 61.43 ? O11 MC3 1305 B 1 HETATM 41 O O31 MC3 . . . O 2 33.719 24.753 198.558 1 75.5 ? O31 MC3 1305 B 1 HETATM 42 O O1P MC3 . . . O 2 35.45 26.231 195.639 1 68.54 ? O1P MC3 1305 B 1 HETATM 43 O O2P MC3 . . . O 2 34.437 23.983 195.088 1 88.73 ? O2P MC3 1305 B 1 HETATM 44 O O3P MC3 . . . O 2 36.66 24.044 196.327 1 77.23 ? O3P MC3 1305 B 1 HETATM 45 O O4P MC3 . . . O 2 36.549 24.818 193.736 1 81.91 ? O4P MC3 1305 B 1 HETATM 46 P P MC3 . . . O 2 35.718 24.806 195.19 1 82.22 ? P MC3 1305 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 46 #