data_6Y9B # _model_server_result.job_id zAvgDm12sg_KvfStENGwXQ _model_server_result.datetime_utc '2024-11-05 05:45:07' _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 6y9b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":402}' # _entry.id 6Y9B # _exptl.entry_id 6Y9B _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 591.777 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE _entity.pdbx_number_of_molecules 3 _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 6Y9B _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y9B _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 nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 # _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 K N N ? 5 M N N ? 5 O 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 B SG CYS 23 L CYS 23 1_555 B SG CYS 94 L CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 D SG CYS 22 I CYS 22 1_555 D SG CYS 96 I CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 E SG CYS 22 J CYS 22 1_555 E SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 F SG CYS 23 M CYS 23 1_555 F SG CYS 94 M CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 G SG CYS 23 N CYS 23 1_555 G SG CYS 94 N CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A NE2 HIS 177 C HIS 175 1_555 J FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc2 A NE2 HIS 270 C HIS 268 1_555 J FE HEM . C HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc3 H NE2 HIS 177 A HIS 175 1_555 L FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc4 H NE2 HIS 270 A HIS 268 1_555 L FE HEM . A HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc5 I NE2 HIS 177 B HIS 175 1_555 N FE HEM . B HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc6 I NE2 HIS 270 B HIS 268 1_555 N FE HEM . B HEM 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? # _chem_comp.formula 'C31 H60 O8 P -1' _chem_comp.formula_weight 591.777 _chem_comp.id XP4 _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-DIMYRISTOYL-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 XP4 sing 456 n n O2 P1 XP4 doub 457 n n P1 O3 XP4 sing 458 n n P1 O4 XP4 sing 459 n n O3 H1 XP4 sing 460 n n O4 C1 XP4 sing 461 n n C1 C2 XP4 sing 462 n n C1 H2 XP4 sing 463 n n C1 H3 XP4 sing 464 n n C2 C3 XP4 sing 465 n n C2 O7 XP4 sing 466 n n C2 H4 XP4 sing 467 n n C3 O5 XP4 sing 468 n n C3 H5 XP4 sing 469 n n C3 H6 XP4 sing 470 n n O5 C4 XP4 sing 471 n n C4 O6 XP4 doub 472 n n C4 C5 XP4 sing 473 n n C5 C6 XP4 sing 474 n n C5 H7 XP4 sing 475 n n C5 H8 XP4 sing 476 n n C6 C7 XP4 sing 477 n n C6 H9 XP4 sing 478 n n C6 H10 XP4 sing 479 n n C7 C8 XP4 sing 480 n n C7 H11 XP4 sing 481 n n C7 H12 XP4 sing 482 n n C8 C9 XP4 sing 483 n n C8 H13 XP4 sing 484 n n C8 H14 XP4 sing 485 n n C9 C10 XP4 sing 486 n n C9 H15 XP4 sing 487 n n C9 H16 XP4 sing 488 n n C10 C11 XP4 sing 489 n n C10 H17 XP4 sing 490 n n C10 H18 XP4 sing 491 n n C11 C12 XP4 sing 492 n n C11 H19 XP4 sing 493 n n C11 H20 XP4 sing 494 n n C12 C13 XP4 sing 495 n n C12 H21 XP4 sing 496 n n C12 H22 XP4 sing 497 n n C13 C14 XP4 sing 498 n n C13 H23 XP4 sing 499 n n C13 H24 XP4 sing 500 n n C14 C15 XP4 sing 501 n n C14 H25 XP4 sing 502 n n C14 H26 XP4 sing 503 n n C15 C16 XP4 sing 504 n n C15 H27 XP4 sing 505 n n C15 H28 XP4 sing 506 n n C16 C17 XP4 sing 507 n n C16 H29 XP4 sing 508 n n C16 H30 XP4 sing 509 n n C17 H31 XP4 sing 510 n n C17 H32 XP4 sing 511 n n C17 H33 XP4 sing 512 n n O7 C18 XP4 sing 513 n n C18 O8 XP4 doub 514 n n C18 C19 XP4 sing 515 n n C19 C20 XP4 sing 516 n n C19 H34 XP4 sing 517 n n C19 H35 XP4 sing 518 n n C20 C21 XP4 sing 519 n n C20 H36 XP4 sing 520 n n C20 H37 XP4 sing 521 n n C21 C22 XP4 sing 522 n n C21 H38 XP4 sing 523 n n C21 H39 XP4 sing 524 n n C22 C23 XP4 sing 525 n n C22 H40 XP4 sing 526 n n C22 H41 XP4 sing 527 n n C23 C24 XP4 sing 528 n n C23 H42 XP4 sing 529 n n C23 H43 XP4 sing 530 n n C24 C25 XP4 sing 531 n n C24 H44 XP4 sing 532 n n C24 H45 XP4 sing 533 n n C25 C26 XP4 sing 534 n n C25 H46 XP4 sing 535 n n C25 H47 XP4 sing 536 n n C26 C27 XP4 sing 537 n n C26 H48 XP4 sing 538 n n C26 H49 XP4 sing 539 n n C27 C28 XP4 sing 540 n n C27 H50 XP4 sing 541 n n C27 H51 XP4 sing 542 n n C28 C29 XP4 sing 543 n n C28 H52 XP4 sing 544 n n C28 H53 XP4 sing 545 n n C29 C30 XP4 sing 546 n n C29 H54 XP4 sing 547 n n C29 H55 XP4 sing 548 n n C30 C31 XP4 sing 549 n n C30 H56 XP4 sing 550 n n C30 H57 XP4 sing 551 n n C31 H58 XP4 sing 552 n n C31 H59 XP4 sing 553 n n C31 H60 XP4 sing 554 n n # _atom_sites.entry_id 6Y9B _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 J 4 HEM C 1 401 1073 HEM HEM . K 5 XP4 C 1 402 1101 XP4 UI9 . L 4 HEM A 1 401 1073 HEM HEM . M 5 XP4 A 1 402 1101 XP4 UI9 . N 4 HEM B 1 401 1073 HEM HEM . O 5 XP4 B 1 402 1101 XP4 UI9 . # 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 XP4 . . . O 5 163.401 144.448 117.577 1 106.31 ? O1 XP4 402 B 1 HETATM 2 O O2 XP4 . . . O 5 161.829 144.184 115.614 1 106.31 ? O2 XP4 402 B 1 HETATM 3 P P1 XP4 . . . O 5 162.258 145.051 116.783 1 106.31 ? P1 XP4 402 B 1 HETATM 4 O O3 XP4 . . . O 5 162.513 146.492 116.385 1 106.31 ? O3 XP4 402 B 1 HETATM 5 O O4 XP4 . . . O 5 160.998 145.09 117.79 1 106.31 ? O4 XP4 402 B 1 HETATM 6 C C1 XP4 . . . O 5 161.105 145.878 119.006 1 106.31 ? C1 XP4 402 B 1 HETATM 7 C C2 XP4 . . . O 5 159.824 145.748 119.8 1 106.31 ? C2 XP4 402 B 1 HETATM 8 C C3 XP4 . . . O 5 159.529 144.328 120.225 1 106.31 ? C3 XP4 402 B 1 HETATM 9 O O5 XP4 . . . O 5 158.71 144.397 121.411 1 106.31 ? O5 XP4 402 B 1 HETATM 10 C C4 XP4 . . . O 5 158.445 143.25 122.026 1 106.31 ? C4 XP4 402 B 1 HETATM 11 O O6 XP4 . . . O 5 158.554 142.176 121.497 1 106.31 ? O6 XP4 402 B 1 HETATM 12 C C5 XP4 . . . O 5 157.998 143.492 123.44 1 106.31 ? C5 XP4 402 B 1 HETATM 13 C C6 XP4 . . . O 5 157.964 144.945 123.795 1 106.31 ? C6 XP4 402 B 1 HETATM 14 C C7 XP4 . . . O 5 157.771 145.192 125.285 1 106.31 ? C7 XP4 402 B 1 HETATM 15 C C8 XP4 . . . O 5 158.914 144.721 126.15 1 106.31 ? C8 XP4 402 B 1 HETATM 16 C C9 XP4 . . . O 5 158.764 145.084 127.606 1 106.31 ? C9 XP4 402 B 1 HETATM 17 C C10 XP4 . . . O 5 158.82 146.566 127.885 1 106.31 ? C10 XP4 402 B 1 HETATM 18 C C11 XP4 . . . O 5 158.158 146.974 129.177 1 106.31 ? C11 XP4 402 B 1 HETATM 19 C C12 XP4 . . . O 5 158.331 148.428 129.538 1 106.31 ? C12 XP4 402 B 1 HETATM 20 C C13 XP4 . . . O 5 157.367 148.918 130.59 1 106.31 ? C13 XP4 402 B 1 HETATM 21 C C14 XP4 . . . O 5 157.276 148.034 131.808 1 106.31 ? C14 XP4 402 B 1 HETATM 22 C C15 XP4 . . . O 5 156.244 148.473 132.817 1 106.31 ? C15 XP4 402 B 1 HETATM 23 C C16 XP4 . . . O 5 156.058 147.515 133.965 1 106.31 ? C16 XP4 402 B 1 HETATM 24 C C17 XP4 . . . O 5 155.035 147.965 134.98 1 106.31 ? C17 XP4 402 B 1 HETATM 25 O O7 XP4 . . . O 5 159.833 146.532 121.026 1 106.31 ? O7 XP4 402 B 1 HETATM 26 C C18 XP4 . . . O 5 159.74 147.869 120.953 1 106.31 ? C18 XP4 402 B 1 HETATM 27 O O8 XP4 . . . O 5 160.314 148.542 120.137 1 106.31 ? O8 XP4 402 B 1 HETATM 28 C C19 XP4 . . . O 5 158.751 148.395 121.953 1 106.31 ? C19 XP4 402 B 1 HETATM 29 C C20 XP4 . . . O 5 159.358 149.209 123.051 1 106.31 ? C20 XP4 402 B 1 HETATM 30 C C21 XP4 . . . O 5 158.296 149.804 123.96 1 106.31 ? C21 XP4 402 B 1 HETATM 31 C C22 XP4 . . . O 5 158.82 150.565 125.15 1 106.31 ? C22 XP4 402 B 1 HETATM 32 C C23 XP4 . . . O 5 157.738 151.26 125.938 1 106.31 ? C23 XP4 402 B 1 HETATM 33 C C24 XP4 . . . O 5 158.209 151.973 127.18 1 106.31 ? C24 XP4 402 B 1 HETATM 34 C C25 XP4 . . . O 5 157.136 152.795 127.849 1 106.31 ? C25 XP4 402 B 1 HETATM 35 C C26 XP4 . . . O 5 157.564 153.479 129.123 1 106.31 ? C26 XP4 402 B 1 HETATM 36 C C27 XP4 . . . O 5 156.54 154.444 129.665 1 106.31 ? C27 XP4 402 B 1 HETATM 37 C C28 XP4 . . . O 5 156.91 155.093 130.976 1 106.31 ? C28 XP4 402 B 1 HETATM 38 C C29 XP4 . . . O 5 156.926 154.154 132.156 1 106.31 ? C29 XP4 402 B 1 HETATM 39 C C30 XP4 . . . O 5 157.174 154.841 133.474 1 106.31 ? C30 XP4 402 B 1 HETATM 40 C C31 XP4 . . . O 5 157.128 153.918 134.668 1 106.31 ? C31 XP4 402 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #