data_5MKE # _model_server_result.job_id EvrnoMqSSkRibyABfjJs2Q _model_server_result.datetime_utc '2025-03-06 09:20:45' _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 5mke # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1007}' # _entry.id 5MKE # _exptl.entry_id 5MKE _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 647.883 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE _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 90 _cell.entry_id 5MKE _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MKE _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _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,LA,MA,NA,OA,PA,QA _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 ? _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 ? 5 L N N ? 5 V N N ? 5 DA N N ? 5 NA N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n E NAG 1 E 1 NAG A 1003 NAG 2 n E NAG 2 E 2 NAG A 1004 NAG 2 n F NAG 1 F 1 NAG B 1003 NAG 2 n F NAG 2 F 2 NAG B 1004 NAG 2 n G NAG 1 G 1 NAG C 1003 NAG 2 n G NAG 2 G 2 NAG C 1004 NAG # 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 covale ? covale1 A ND2 ASN 305 A ASN 305 1_555 H C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 362 A ASN 362 1_555 I C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale3 A ND2 ASN 375 A ASN 375 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale4 B ND2 ASN 305 B ASN 305 1_555 R C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale5 B ND2 ASN 362 B ASN 362 1_555 S C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale6 B ND2 ASN 375 B ASN 375 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale7 C ND2 ASN 305 C ASN 305 1_555 Z C1 NAG . C NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 C ND2 ASN 362 C ASN 362 1_555 AA C1 NAG . C NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale9 C ND2 ASN 375 C ASN 375 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale10 D ND2 ASN 305 D ASN 305 1_555 HA C1 NAG . D NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale11 D ND2 ASN 362 D ASN 362 1_555 IA C1 NAG . D NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale12 D ND2 ASN 375 D ASN 375 1_555 JA C1 NAG . D NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale13 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.535 ? covale ? covale14 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.534 ? covale ? covale15 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.55 ? # _chem_comp.formula 'C35 H68 O8 P -1' _chem_comp.formula_weight 647.883 _chem_comp.id PX6 _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE _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 O1 P1 PX6 sing 390 n n O2 P1 PX6 doub 391 n n P1 O3 PX6 sing 392 n n P1 O4 PX6 sing 393 n n O3 H1 PX6 sing 394 n n O4 C1 PX6 sing 395 n n C1 C2 PX6 sing 396 n n C1 H2 PX6 sing 397 n n C1 H3 PX6 sing 398 n n C2 C3 PX6 sing 399 n n C2 O7 PX6 sing 400 n n C2 H4 PX6 sing 401 n n C3 O5 PX6 sing 402 n n C3 H5 PX6 sing 403 n n C3 H6 PX6 sing 404 n n O5 C4 PX6 sing 405 n n C4 O6 PX6 doub 406 n n C4 C5 PX6 sing 407 n n C5 C6 PX6 sing 408 n n C5 H7 PX6 sing 409 n n C5 H8 PX6 sing 410 n n C6 C7 PX6 sing 411 n n C6 H9 PX6 sing 412 n n C6 H10 PX6 sing 413 n n C7 C8 PX6 sing 414 n n C7 H11 PX6 sing 415 n n C7 H12 PX6 sing 416 n n C8 C9 PX6 sing 417 n n C8 H13 PX6 sing 418 n n C8 H14 PX6 sing 419 n n C9 C10 PX6 sing 420 n n C9 H15 PX6 sing 421 n n C9 H16 PX6 sing 422 n n C10 C11 PX6 sing 423 n n C10 H17 PX6 sing 424 n n C10 H18 PX6 sing 425 n n C11 C12 PX6 sing 426 n n C11 H19 PX6 sing 427 n n C11 H20 PX6 sing 428 n n C12 C13 PX6 sing 429 n n C12 H21 PX6 sing 430 n n C12 H22 PX6 sing 431 n n C13 C14 PX6 sing 432 n n C13 H23 PX6 sing 433 n n C13 H24 PX6 sing 434 n n C14 C15 PX6 sing 435 n n C14 H25 PX6 sing 436 n n C14 H26 PX6 sing 437 n n C15 C16 PX6 sing 438 n n C15 H27 PX6 sing 439 n n C15 H28 PX6 sing 440 n n C16 C17 PX6 sing 441 n n C16 H29 PX6 sing 442 n n C16 H30 PX6 sing 443 n n C17 C18 PX6 sing 444 n n C17 H31 PX6 sing 445 n n C17 H32 PX6 sing 446 n n C18 C19 PX6 sing 447 n n C18 H33 PX6 sing 448 n n C18 H34 PX6 sing 449 n n C19 H35 PX6 sing 450 n n C19 H36 PX6 sing 451 n n C19 H37 PX6 sing 452 n n O7 C20 PX6 sing 453 n n C20 O8 PX6 doub 454 n n C20 C21 PX6 sing 455 n n C21 C22 PX6 sing 456 n n C21 H38 PX6 sing 457 n n C21 H39 PX6 sing 458 n n C22 C23 PX6 sing 459 n n C22 H40 PX6 sing 460 n n C22 H41 PX6 sing 461 n n C23 C24 PX6 sing 462 n n C23 H42 PX6 sing 463 n n C23 H43 PX6 sing 464 n n C24 C25 PX6 sing 465 n n C24 H44 PX6 sing 466 n n C24 H45 PX6 sing 467 n n C25 C26 PX6 sing 468 n n C25 H46 PX6 sing 469 n n C25 H47 PX6 sing 470 n n C26 C27 PX6 sing 471 n n C26 H48 PX6 sing 472 n n C26 H49 PX6 sing 473 n n C27 C28 PX6 sing 474 n n C27 H50 PX6 sing 475 n n C27 H51 PX6 sing 476 n n C28 C29 PX6 sing 477 n n C28 H52 PX6 sing 478 n n C28 H53 PX6 sing 479 n n C29 C30 PX6 sing 480 n n C29 H54 PX6 sing 481 n n C29 H55 PX6 sing 482 n n C30 C31 PX6 sing 483 n n C30 H56 PX6 sing 484 n n C30 H57 PX6 sing 485 n n C31 C32 PX6 sing 486 n n C31 H58 PX6 sing 487 n n C31 H59 PX6 sing 488 n n C32 C33 PX6 sing 489 n n C32 H60 PX6 sing 490 n n C32 H61 PX6 sing 491 n n C33 C34 PX6 sing 492 n n C33 H62 PX6 sing 493 n n C33 H63 PX6 sing 494 n n C34 C35 PX6 sing 495 n n C34 H64 PX6 sing 496 n n C34 H65 PX6 sing 497 n n C35 H66 PX6 sing 498 n n C35 H67 PX6 sing 499 n n C35 H68 PX6 sing 500 n n # _atom_sites.entry_id 5MKE _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 H 3 NAG A 1 1001 1001 NAG NAG . I 3 NAG A 1 1002 1002 NAG NAG . J 4 CHS A 1 1005 1005 CHS CHS . K 4 CHS A 1 1006 1006 CHS CHS . L 5 PX6 A 1 1007 1007 PX6 PX6 . M 6 PLM A 1 1008 1008 PLM PLM . N 6 PLM A 1 1009 1009 PLM PLM . O 6 PLM A 1 1010 1010 PLM PLM . P 7 CA A 1 1011 1011 CA CA . Q 7 CA A 1 1012 1012 CA CA . R 3 NAG B 1 1001 1001 NAG NAG . S 3 NAG B 1 1002 1002 NAG NAG . T 4 CHS B 1 1005 1005 CHS CHS . U 4 CHS B 1 1006 1006 CHS CHS . V 5 PX6 B 1 1007 1007 PX6 PX6 . W 6 PLM B 1 1008 1008 PLM PLM . X 6 PLM B 1 1009 1009 PLM PLM . Y 6 PLM B 1 1010 1010 PLM PLM . Z 3 NAG C 1 1001 1001 NAG NAG . AA 3 NAG C 1 1002 1002 NAG NAG . BA 4 CHS C 1 1005 1005 CHS CHS . CA 4 CHS C 1 1006 1006 CHS CHS . DA 5 PX6 C 1 1007 1007 PX6 PX6 . EA 6 PLM C 1 1008 1008 PLM PLM . FA 6 PLM C 1 1009 1009 PLM PLM . GA 6 PLM C 1 1010 1010 PLM PLM . HA 3 NAG D 1 1001 1001 NAG NAG . IA 3 NAG D 1 1002 1002 NAG NAG . JA 3 NAG D 1 1003 1003 NAG NAG . KA 3 NAG D 1 1004 1004 NAG NAG . LA 4 CHS D 1 1005 1005 CHS CHS . MA 4 CHS D 1 1006 1006 CHS CHS . NA 5 PX6 D 1 1007 1007 PX6 PX6 . OA 6 PLM D 1 1008 1008 PLM PLM . PA 6 PLM D 1 1009 1009 PLM PLM . QA 6 PLM D 1 1010 1010 PLM PLM . # 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 O O1 PX6 . . . L 5 91.867 67.891 103.745 1 20 ? O1 PX6 1007 A 1 HETATM 2 O O2 PX6 . . . L 5 92.012 65.439 104.565 1 20 ? O2 PX6 1007 A 1 HETATM 3 P P1 PX6 . . . L 5 91.783 66.499 103.322 1 20 ? P1 PX6 1007 A 1 HETATM 4 O O3 PX6 . . . L 5 90.415 66.459 102.834 1 20 ? O3 PX6 1007 A 1 HETATM 5 O O4 PX6 . . . L 5 92.814 66.17 102.091 1 20 ? O4 PX6 1007 A 1 HETATM 6 C C1 PX6 . . . L 5 92.614 64.975 101.381 1 20 ? C1 PX6 1007 A 1 HETATM 7 C C2 PX6 . . . L 5 92.216 65.395 99.979 1 20 ? C2 PX6 1007 A 1 HETATM 8 C C3 PX6 . . . L 5 92.369 64.222 98.991 1 20 ? C3 PX6 1007 A 1 HETATM 9 O O5 PX6 . . . L 5 91.943 64.093 97.641 1 20 ? O5 PX6 1007 A 1 HETATM 10 C C4 PX6 . . . L 5 92.562 63.055 96.903 1 20 ? C4 PX6 1007 A 1 HETATM 11 O O6 PX6 . . . L 5 93.261 62.266 97.45 1 20 ? O6 PX6 1007 A 1 HETATM 12 C C5 PX6 . . . L 5 92.347 62.938 95.38 1 20 ? C5 PX6 1007 A 1 HETATM 13 C C6 PX6 . . . L 5 93.621 63.361 94.613 1 20 ? C6 PX6 1007 A 1 HETATM 14 C C7 PX6 . . . L 5 94.118 64.759 95.056 1 20 ? C7 PX6 1007 A 1 HETATM 15 C C8 PX6 . . . L 5 95.653 64.934 94.897 1 20 ? C8 PX6 1007 A 1 HETATM 16 C C9 PX6 . . . L 5 96.026 65.957 93.791 1 20 ? C9 PX6 1007 A 1 HETATM 17 C C10 PX6 . . . L 5 95.065 65.871 92.565 1 20 ? C10 PX6 1007 A 1 HETATM 18 C C11 PX6 . . . L 5 95.647 66.538 91.285 1 20 ? C11 PX6 1007 A 1 HETATM 19 C C12 PX6 . . . L 5 94.842 66.139 90.012 1 20 ? C12 PX6 1007 A 1 HETATM 20 C C13 PX6 . . . L 5 95.512 66.647 88.706 1 20 ? C13 PX6 1007 A 1 HETATM 21 C C14 PX6 . . . L 5 95.837 68.155 88.767 1 20 ? C14 PX6 1007 A 1 HETATM 22 C C15 PX6 . . . L 5 95.457 68.881 87.458 1 20 ? C15 PX6 1007 A 1 HETATM 23 O O7 PX6 . . . L 5 90.884 65.755 100.08 1 20 ? O7 PX6 1007 A 1 HETATM 24 C C20 PX6 . . . L 5 90.641 67.119 99.847 1 20 ? C20 PX6 1007 A 1 HETATM 25 O O8 PX6 . . . L 5 91.156 67.944 100.524 1 20 ? O8 PX6 1007 A 1 HETATM 26 C C21 PX6 . . . L 5 89.691 67.48 98.684 1 20 ? C21 PX6 1007 A 1 HETATM 27 C C22 PX6 . . . L 5 90.024 66.569 97.472 1 20 ? C22 PX6 1007 A 1 HETATM 28 C C23 PX6 . . . L 5 89.435 66.998 96.106 1 20 ? C23 PX6 1007 A 1 HETATM 29 C C24 PX6 . . . L 5 89.181 65.736 95.245 1 20 ? C24 PX6 1007 A 1 HETATM 30 C C25 PX6 . . . L 5 89.78 65.872 93.831 1 20 ? C25 PX6 1007 A 1 HETATM 31 C C26 PX6 . . . L 5 89.22 67.135 93.138 1 20 ? C26 PX6 1007 A 1 HETATM 32 C C27 PX6 . . . L 5 88.001 66.766 92.26 1 20 ? C27 PX6 1007 A 1 HETATM 33 C C28 PX6 . . . L 5 88.28 65.498 91.419 1 20 ? C28 PX6 1007 A 1 HETATM 34 C C29 PX6 . . . L 5 88.585 65.856 89.945 1 20 ? C29 PX6 1007 A 1 HETATM 35 C C30 PX6 . . . L 5 89.922 66.623 89.784 1 20 ? C30 PX6 1007 A 1 HETATM 36 C C31 PX6 . . . L 5 89.674 68.114 89.454 1 20 ? C31 PX6 1007 A 1 HETATM 37 C C32 PX6 . . . L 5 88.78 68.236 88.199 1 20 ? C32 PX6 1007 A 1 HETATM 38 C C33 PX6 . . . L 5 89.39 67.476 86.997 1 20 ? C33 PX6 1007 A 1 HETATM 39 C C34 PX6 . . . L 5 88.581 67.704 85.7 1 20 ? C34 PX6 1007 A 1 HETATM 40 C C35 PX6 . . . L 5 89.321 68.616 84.7 1 20 ? C35 PX6 1007 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #