data_5YUA # _model_server_result.job_id YMswWTdAgySqce4p4MjwBA _model_server_result.datetime_utc '2024-10-27 16:17:05' _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 5yua # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1308}' # _entry.id 5YUA # _exptl.entry_id 5YUA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 678.94 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE _entity.pdbx_number_of_molecules 6 _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 5YUA _cell.length_a 126.45 _cell.length_b 126.45 _cell.length_c 201.658 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YUA _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall 'I 4 2' _symmetry.space_group_name_H-M 'I 4 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 F N N ? 5 G N N ? 5 H N N ? 5 I N N ? 5 J N N ? 5 K 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 covale ? covale1 C C12 LMT . A LMT 1302 1_555 H C34 PX4 . A PX4 1307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.495 ? covale ? covale2 J C21 PX4 . A PX4 1309 1_555 K C36 PX4 . A PX4 1310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.494 ? # _chem_comp.formula 'C36 H73 N O8 P 1' _chem_comp.formula_weight 678.94 _chem_comp.id PX4 _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIMYRISTOYL-SN-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 O1 P1 PX4 sing 451 n n O1 H1P PX4 sing 452 n n O2 P1 PX4 doub 453 n n P1 O3 PX4 sing 454 n n P1 O4 PX4 sing 455 n n O3 C1 PX4 sing 456 n n C1 C2 PX4 sing 457 n n C1 H1 PX4 sing 458 n n C1 H2 PX4 sing 459 n n C2 N1 PX4 sing 460 n n C2 H3 PX4 sing 461 n n C2 H4 PX4 sing 462 n n N1 C3 PX4 sing 463 n n N1 C4 PX4 sing 464 n n N1 C5 PX4 sing 465 n n C3 H5 PX4 sing 466 n n C3 H6 PX4 sing 467 n n C3 H7 PX4 sing 468 n n C4 H8 PX4 sing 469 n n C4 H9 PX4 sing 470 n n C4 H10 PX4 sing 471 n n C5 H11 PX4 sing 472 n n C5 H12 PX4 sing 473 n n C5 H13 PX4 sing 474 n n O4 C6 PX4 sing 475 n n C6 C7 PX4 sing 476 n n C6 H14 PX4 sing 477 n n C6 H15 PX4 sing 478 n n C7 C8 PX4 sing 479 n n C7 O7 PX4 sing 480 n n C7 H16 PX4 sing 481 n n C8 O5 PX4 sing 482 n n C8 H17 PX4 sing 483 n n C8 H18 PX4 sing 484 n n O5 C9 PX4 sing 485 n n C9 O6 PX4 doub 486 n n C9 C10 PX4 sing 487 n n C10 C11 PX4 sing 488 n n C10 H19 PX4 sing 489 n n C10 H20 PX4 sing 490 n n C11 C12 PX4 sing 491 n n C11 H21 PX4 sing 492 n n C11 H22 PX4 sing 493 n n C12 C13 PX4 sing 494 n n C12 H23 PX4 sing 495 n n C12 H24 PX4 sing 496 n n C13 C14 PX4 sing 497 n n C13 H25 PX4 sing 498 n n C13 H26 PX4 sing 499 n n C14 C15 PX4 sing 500 n n C14 H27 PX4 sing 501 n n C14 H28 PX4 sing 502 n n C15 C16 PX4 sing 503 n n C15 H29 PX4 sing 504 n n C15 H30 PX4 sing 505 n n C16 C17 PX4 sing 506 n n C16 H31 PX4 sing 507 n n C16 H32 PX4 sing 508 n n C17 C18 PX4 sing 509 n n C17 H33 PX4 sing 510 n n C17 H34 PX4 sing 511 n n C18 C19 PX4 sing 512 n n C18 H35 PX4 sing 513 n n C18 H36 PX4 sing 514 n n C19 C20 PX4 sing 515 n n C19 H37 PX4 sing 516 n n C19 H38 PX4 sing 517 n n C20 C21 PX4 sing 518 n n C20 H39 PX4 sing 519 n n C20 H40 PX4 sing 520 n n C21 C22 PX4 sing 521 n n C21 H41 PX4 sing 522 n n C21 H42 PX4 sing 523 n n C22 H43 PX4 sing 524 n n C22 H44 PX4 sing 525 n n C22 H45 PX4 sing 526 n n O7 C23 PX4 sing 527 n n C23 O8 PX4 doub 528 n n C23 C24 PX4 sing 529 n n C24 C25 PX4 sing 530 n n C24 H46 PX4 sing 531 n n C24 H47 PX4 sing 532 n n C25 C26 PX4 sing 533 n n C25 H48 PX4 sing 534 n n C25 H49 PX4 sing 535 n n C26 C27 PX4 sing 536 n n C26 H50 PX4 sing 537 n n C26 H51 PX4 sing 538 n n C27 C28 PX4 sing 539 n n C27 H52 PX4 sing 540 n n C27 H53 PX4 sing 541 n n C28 C29 PX4 sing 542 n n C28 H54 PX4 sing 543 n n C28 H55 PX4 sing 544 n n C29 C30 PX4 sing 545 n n C29 H56 PX4 sing 546 n n C29 H57 PX4 sing 547 n n C30 C31 PX4 sing 548 n n C30 H58 PX4 sing 549 n n C30 H59 PX4 sing 550 n n C31 C32 PX4 sing 551 n n C31 H60 PX4 sing 552 n n C31 H61 PX4 sing 553 n n C32 C33 PX4 sing 554 n n C32 H62 PX4 sing 555 n n C32 H63 PX4 sing 556 n n C33 C34 PX4 sing 557 n n C33 H64 PX4 sing 558 n n C33 H65 PX4 sing 559 n n C34 C35 PX4 sing 560 n n C34 H66 PX4 sing 561 n n C34 H67 PX4 sing 562 n n C35 C36 PX4 sing 563 n n C35 H68 PX4 sing 564 n n C35 H69 PX4 sing 565 n n C36 H70 PX4 sing 566 n n C36 H71 PX4 sing 567 n n C36 H72 PX4 sing 568 n n # _atom_sites.entry_id 5YUA _atom_sites.fract_transf_matrix[1][1] 0.007908 _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] 0.007908 _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] 0.004959 _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 1301 1301 CA CA . C 3 LMT A 1 1302 1302 LMT LMT . D 3 LMT A 1 1303 1303 LMT LMT . E 4 1N7 A 1 1304 1304 1N7 1N7 . F 5 PX4 A 1 1305 1305 PX4 PX4 . G 5 PX4 A 1 1306 1306 PX4 PX4 . H 5 PX4 A 1 1307 1307 PX4 PX4 . I 5 PX4 A 1 1308 1308 PX4 PX4 . J 5 PX4 A 1 1309 1309 PX4 PX4 . K 5 PX4 A 1 1310 1310 PX4 PX4 . L 6 HOH A 1 1401 1401 HOH HOH . L 6 HOH A 2 1402 1402 HOH HOH . L 6 HOH A 3 1403 1403 HOH HOH . L 6 HOH A 4 1404 1404 HOH HOH . L 6 HOH A 5 1405 1405 HOH HOH . L 6 HOH A 6 1406 1407 HOH HOH . L 6 HOH A 7 1407 1408 HOH HOH . L 6 HOH A 8 1408 1409 HOH HOH . L 6 HOH A 9 1409 1410 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 O O1 PX4 . . . I 5 13.851 -23.637 44.84 1 190.79 ? O1 PX4 1308 A 1 HETATM 2 O O2 PX4 . . . I 5 15.544 -25.573 44.275 1 195.1 ? O2 PX4 1308 A 1 HETATM 3 P P1 PX4 . . . I 5 14.699 -24.395 43.839 1 193.33 ? P1 PX4 1308 A 1 HETATM 4 O O3 PX4 . . . I 5 15.669 -23.311 43.128 1 180.19 ? O3 PX4 1308 A 1 HETATM 5 C C1 PX4 . . . I 5 16.764 -22.696 43.812 1 164.04 ? C1 PX4 1308 A 1 HETATM 6 C C2 PX4 . . . I 5 17.321 -21.543 42.976 1 147.13 ? C2 PX4 1308 A 1 HETATM 7 N N1 PX4 . . . I 5 17.376 -20.317 43.786 1 138.62 ? N1 PX4 1308 A 1 HETATM 8 C C3 PX4 . . . I 5 18.315 -20.511 44.9 1 138.51 ? C3 PX4 1308 A 1 HETATM 9 C C4 PX4 . . . I 5 17.818 -19.17 42.981 1 127.21 ? C4 PX4 1308 A 1 HETATM 10 C C5 PX4 . . . I 5 16.035 -20.042 44.31 1 142.53 ? C5 PX4 1308 A 1 HETATM 11 O O4 PX4 . . . I 5 13.747 -24.886 42.618 1 191.57 ? O4 PX4 1308 A 1 HETATM 12 C C6 PX4 . . . I 5 12.525 -25.629 42.765 1 180.25 ? C6 PX4 1308 A 1 HETATM 13 C C7 PX4 . . . I 5 11.754 -25.608 41.436 1 168.83 ? C7 PX4 1308 A 1 HETATM 14 C C8 PX4 . . . I 5 10.546 -26.549 41.43 1 164.05 ? C8 PX4 1308 A 1 HETATM 15 O O5 PX4 . . . I 5 10.077 -26.65 40.076 1 159.31 ? O5 PX4 1308 A 1 HETATM 16 C C9 PX4 . . . I 5 8.67 -26.848 39.718 1 146.91 ? C9 PX4 1308 A 1 HETATM 17 O O6 PX4 . . . I 5 7.828 -26.812 40.61 1 146.17 ? O6 PX4 1308 A 1 HETATM 18 C C10 PX4 . . . I 5 8.254 -27.103 38.271 1 129.53 ? C10 PX4 1308 A 1 HETATM 19 C C11 PX4 . . . I 5 8.852 -26.115 37.255 1 112.96 ? C11 PX4 1308 A 1 HETATM 20 C C12 PX4 . . . I 5 8.496 -26.474 35.804 1 97.4 ? C12 PX4 1308 A 1 HETATM 21 C C13 PX4 . . . I 5 9.209 -25.61 34.757 1 89.88 ? C13 PX4 1308 A 1 HETATM 22 C C14 PX4 . . . I 5 8.871 -26.045 33.326 1 92.07 ? C14 PX4 1308 A 1 HETATM 23 C C15 PX4 . . . I 5 9.408 -25.095 32.251 1 98.78 ? C15 PX4 1308 A 1 HETATM 24 C C16 PX4 . . . I 5 9.456 -25.758 30.87 1 120.24 ? C16 PX4 1308 A 1 HETATM 25 C C17 PX4 . . . I 5 8.153 -25.635 30.072 1 141.11 ? C17 PX4 1308 A 1 HETATM 26 C C18 PX4 . . . I 5 8.102 -26.578 28.86 1 150.85 ? C18 PX4 1308 A 1 HETATM 27 C C19 PX4 . . . I 5 7.503 -25.905 27.619 1 147.58 ? C19 PX4 1308 A 1 HETATM 28 C C20 PX4 . . . I 5 7.446 -26.835 26.403 1 138.99 ? C20 PX4 1308 A 1 HETATM 29 C C21 PX4 . . . I 5 7.311 -26.038 25.103 1 130.56 ? C21 PX4 1308 A 1 HETATM 30 C C22 PX4 . . . I 5 6.669 -26.834 23.983 1 122.86 ? C22 PX4 1308 A 1 HETATM 31 O O7 PX4 . . . I 5 11.263 -24.294 41.136 1 158.32 ? O7 PX4 1308 A 1 HETATM 32 C C23 PX4 . . . I 5 11.967 -23.649 40.033 1 137.2 ? C23 PX4 1308 A 1 HETATM 33 O O8 PX4 . . . I 5 13.154 -23.393 40.138 1 137.38 ? O8 PX4 1308 A 1 HETATM 34 C C24 PX4 . . . I 5 11.241 -23.328 38.75 1 115.46 ? C24 PX4 1308 A 1 HETATM 35 C C25 PX4 . . . I 5 12.213 -23.491 37.592 1 101.16 ? C25 PX4 1308 A 1 HETATM 36 C C26 PX4 . . . I 5 11.673 -22.871 36.31 1 97.63 ? C26 PX4 1308 A 1 HETATM 37 C C27 PX4 . . . I 5 12.747 -22.855 35.229 1 100.47 ? C27 PX4 1308 A 1 HETATM 38 C C28 PX4 . . . I 5 12.216 -22.313 33.907 1 102.47 ? C28 PX4 1308 A 1 HETATM 39 C C29 PX4 . . . I 5 13.354 -22.019 32.928 1 104.41 ? C29 PX4 1308 A 1 HETATM 40 C C30 PX4 . . . I 5 12.866 -21.934 31.483 1 108.06 ? C30 PX4 1308 A 1 HETATM 41 C C31 PX4 . . . I 5 14.022 -21.732 30.509 1 109.2 ? C31 PX4 1308 A 1 HETATM 42 C C32 PX4 . . . I 5 13.851 -20.413 29.766 1 117.64 ? C32 PX4 1308 A 1 HETATM 43 C C33 PX4 . . . I 5 14.88 -20.272 28.652 1 119.96 ? C33 PX4 1308 A 1 HETATM 44 C C34 PX4 . . . I 5 14.605 -19.031 27.811 1 114.94 ? C34 PX4 1308 A 1 HETATM 45 C C35 PX4 . . . I 5 15.678 -18.895 26.738 1 105.71 ? C35 PX4 1308 A 1 HETATM 46 C C36 PX4 . . . I 5 15.489 -17.631 25.933 1 103.17 ? C36 PX4 1308 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 46 #