data_8H9Y # _model_server_result.job_id V9_CMASpP2PvX-5RQelbOg _model_server_result.datetime_utc '2024-11-28 16:03:26' _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 8h9y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1311}' # _entry.id 8H9Y # _exptl.entry_id 8H9Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 678.94 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE _entity.pdbx_number_of_molecules 8 _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 8H9Y _cell.length_a 127.94 _cell.length_b 127.94 _cell.length_c 201.92 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8H9Y _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,M,N,O _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 ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L 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 O THR 179 A THR 1175 1_555 M CA CA . A CA 1312 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc2 A OE1 GLN 180 A GLN 1176 1_555 M CA CA . A CA 1312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.987 ? metalc ? metalc3 B O6' LMT . A LMT 1301 1_555 M CA CA . A CA 1312 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? # _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 8H9Y _atom_sites.fract_transf_matrix[1][1] 0.007816 _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] 0.007816 _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] 0.004952 _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 LMT A 1 1301 1301 LMT LMT . C 2 LMT A 1 1302 1302 LMT LMT . D 3 1N7 A 1 1303 1303 1N7 1N7 . E 4 PX4 A 1 1304 1304 PX4 PX4 . F 4 PX4 A 1 1305 1305 PX4 PX4 . G 4 PX4 A 1 1306 1306 PX4 PX4 . H 4 PX4 A 1 1307 1307 PX4 PX4 . I 4 PX4 A 1 1308 1308 PX4 PX4 . J 4 PX4 A 1 1309 1309 PX4 PX4 . K 4 PX4 A 1 1310 1310 PX4 PX4 . L 4 PX4 A 1 1311 1311 PX4 PX4 . M 5 CA A 1 1312 1312 CA CA . N 5 CA A 1 1313 1313 CA CA . O 6 HOH A 1 1401 1401 HOH HOH . O 6 HOH A 2 1402 1402 HOH HOH . O 6 HOH A 3 1403 1403 HOH HOH . O 6 HOH A 4 1404 1404 HOH HOH . O 6 HOH A 5 1405 1405 HOH HOH . O 6 HOH A 6 1406 1406 HOH HOH . O 6 HOH A 7 1407 1407 HOH HOH . O 6 HOH A 8 1408 1408 HOH HOH . O 6 HOH A 9 1409 1409 HOH HOH . O 6 HOH A 10 1410 1410 HOH HOH . O 6 HOH A 11 1411 1411 HOH HOH . O 6 HOH A 12 1412 1412 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 . . . L 4 33.187 -2.942 6.46 1 122.63 ? O1 PX4 1311 A 1 HETATM 2 O O2 PX4 . . . L 4 30.615 -2.56 6.071 1 117.56 ? O2 PX4 1311 A 1 HETATM 3 P P1 PX4 . . . L 4 32.056 -2.167 5.818 1 142.78 ? P1 PX4 1311 A 1 HETATM 4 O O3 PX4 . . . L 4 32.314 -2.148 4.22 1 127.79 ? O3 PX4 1311 A 1 HETATM 5 C C1 PX4 . . . L 4 32.944 -3.232 3.519 1 120.66 ? C1 PX4 1311 A 1 HETATM 6 C C2 PX4 . . . L 4 33.207 -2.822 2.069 1 122.37 ? C2 PX4 1311 A 1 HETATM 7 N N1 PX4 . . . L 4 34.223 -3.666 1.424 1 118.74 ? N1 PX4 1311 A 1 HETATM 8 C C3 PX4 . . . L 4 33.768 -5.06 1.402 1 112.66 ? C3 PX4 1311 A 1 HETATM 9 C C4 PX4 . . . L 4 34.409 -3.199 0.044 1 113.75 ? C4 PX4 1311 A 1 HETATM 10 C C5 PX4 . . . L 4 35.493 -3.572 2.159 1 112.92 ? C5 PX4 1311 A 1 HETATM 11 O O4 PX4 . . . L 4 32.219 -0.609 6.214 1 125.94 ? O4 PX4 1311 A 1 HETATM 12 C C6 PX4 . . . L 4 32.392 -0.188 7.57 1 115.58 ? C6 PX4 1311 A 1 HETATM 13 C C7 PX4 . . . L 4 33.166 1.131 7.6 1 116.95 ? C7 PX4 1311 A 1 HETATM 14 C C8 PX4 . . . L 4 32.204 2.27 7.95 1 111.84 ? C8 PX4 1311 A 1 HETATM 15 O O5 PX4 . . . L 4 31.129 1.841 8.798 1 112.46 ? O5 PX4 1311 A 1 HETATM 16 C C9 PX4 . . . L 4 30.102 2.815 9.152 1 110.17 ? C9 PX4 1311 A 1 HETATM 17 O O6 PX4 . . . L 4 30.295 3.978 8.831 1 106.5 ? O6 PX4 1311 A 1 HETATM 18 C C10 PX4 . . . L 4 28.832 2.418 9.886 1 99.28 ? C10 PX4 1311 A 1 HETATM 19 C C11 PX4 . . . L 4 29.049 2.377 11.4 1 89.87 ? C11 PX4 1311 A 1 HETATM 20 C C12 PX4 . . . L 4 27.766 2.616 12.205 1 82.1 ? C12 PX4 1311 A 1 HETATM 21 C C13 PX4 . . . L 4 27.961 2.22 13.673 1 85.1 ? C13 PX4 1311 A 1 HETATM 22 C C14 PX4 . . . L 4 26.773 2.521 14.599 1 77.03 ? C14 PX4 1311 A 1 HETATM 23 C C15 PX4 . . . L 4 27.04 1.952 16 1 75.96 ? C15 PX4 1311 A 1 HETATM 24 C C16 PX4 . . . L 4 26.154 2.525 17.109 1 73.74 ? C16 PX4 1311 A 1 HETATM 25 C C17 PX4 . . . L 4 26.634 2.099 18.504 1 76.67 ? C17 PX4 1311 A 1 HETATM 26 C C18 PX4 . . . L 4 28.058 2.588 18.8 1 83.03 ? C18 PX4 1311 A 1 HETATM 27 C C19 PX4 . . . L 4 28.467 2.41 20.264 1 84.16 ? C19 PX4 1311 A 1 HETATM 28 C C20 PX4 . . . L 4 29.974 2.591 20.436 1 83.94 ? C20 PX4 1311 A 1 HETATM 29 C C21 PX4 . . . L 4 30.448 2.219 21.841 1 83.78 ? C21 PX4 1311 A 1 HETATM 30 C C22 PX4 . . . L 4 31.962 2.092 21.91 1 71.65 ? C22 PX4 1311 A 1 HETATM 31 O O7 PX4 . . . L 4 34.216 1.055 8.575 1 120.85 ? O7 PX4 1311 A 1 HETATM 32 C C23 PX4 . . . L 4 35.498 0.534 8.1 1 114.7 ? C23 PX4 1311 A 1 HETATM 33 O O8 PX4 . . . L 4 36.113 1.112 7.214 1 109.97 ? O8 PX4 1311 A 1 HETATM 34 C C24 PX4 . . . L 4 36.065 -0.731 8.71 1 108.78 ? C24 PX4 1311 A 1 HETATM 35 C C25 PX4 . . . L 4 35.656 -0.875 10.177 1 105.67 ? C25 PX4 1311 A 1 HETATM 36 C C26 PX4 . . . L 4 34.26 -1.48 10.35 1 108.22 ? C26 PX4 1311 A 1 HETATM 37 C C27 PX4 . . . L 4 33.48 -0.79 11.475 1 104.76 ? C27 PX4 1311 A 1 HETATM 38 C C28 PX4 . . . L 4 31.969 -1.045 11.425 1 97.04 ? C28 PX4 1311 A 1 HETATM 39 C C29 PX4 . . . L 4 31.458 -1.732 12.694 1 83.78 ? C29 PX4 1311 A 1 HETATM 40 C C30 PX4 . . . L 4 30.824 -0.783 13.713 1 80.49 ? C30 PX4 1311 A 1 HETATM 41 C C31 PX4 . . . L 4 30.679 -1.482 15.07 1 77.61 ? C31 PX4 1311 A 1 HETATM 42 C C32 PX4 . . . L 4 30.074 -0.607 16.171 1 71.47 ? C32 PX4 1311 A 1 HETATM 43 C C33 PX4 . . . L 4 30.313 -1.23 17.546 1 70.52 ? C33 PX4 1311 A 1 HETATM 44 C C34 PX4 . . . L 4 29.385 -0.68 18.629 1 69.89 ? C34 PX4 1311 A 1 HETATM 45 C C35 PX4 . . . L 4 29.604 -1.426 19.944 1 65.2 ? C35 PX4 1311 A 1 HETATM 46 C C36 PX4 . . . L 4 28.671 -0.952 21.037 1 56.56 ? C36 PX4 1311 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #