data_6Y9B
#
_model_server_result.job_id            oV4-UgF1m_yfTQDUVW9nLw 
_model_server_result.datetime_utc      '2024-11-05 05:35:50' 
_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":"K","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 . . . K 5 141.457 151.312 117.577 1 106.61 ? O1 XP4 402 C 1 
HETATM 2 O O2 XP4 . . . K 5 142.042 152.797 115.617 1 106.61 ? O2 XP4 402 C 1 
HETATM 3 P P1 XP4 . . . K 5 142.562 151.986 116.788 1 106.61 ? P1 XP4 402 C 1 
HETATM 4 O O3 XP4 . . . K 5 143.673 151.031 116.396 1 106.61 ? O3 XP4 402 C 1 
HETATM 5 O O4 XP4 . . . K 5 143.235 153.049 117.799 1 106.61 ? O4 XP4 402 C 1 
HETATM 6 C C1 XP4 . . . K 5 143.852 152.556 119.018 1 106.61 ? C1 XP4 402 C 1 
HETATM 7 C C2 XP4 . . . K 5 144.39 153.723 119.814 1 106.61 ? C2 XP4 402 C 1 
HETATM 8 C C3 XP4 . . . K 5 143.318 154.702 120.234 1 106.61 ? C3 XP4 402 C 1 
HETATM 9 O O5 XP4 . . . K 5 143.79 155.371 121.423 1 106.61 ? O5 XP4 402 C 1 
HETATM 10 C C4 XP4 . . . K 5 142.937 156.185 122.033 1 106.61 ? C4 XP4 402 C 1 
HETATM 11 O O6 XP4 . . . K 5 141.96 156.64 121.5 1 106.61 ? O6 XP4 402 C 1 
HETATM 12 C C5 XP4 . . . K 5 143.365 156.445 123.449 1 106.61 ? C5 XP4 402 C 1 
HETATM 13 C C6 XP4 . . . K 5 144.631 155.732 123.81 1 106.61 ? C6 XP4 402 C 1 
HETATM 14 C C7 XP4 . . . K 5 144.934 155.772 125.302 1 106.61 ? C7 XP4 402 C 1 
HETATM 15 C C8 XP4 . . . K 5 143.942 155.03 126.163 1 106.61 ? C8 XP4 402 C 1 
HETATM 16 C C9 XP4 . . . K 5 144.324 154.974 127.62 1 106.61 ? C9 XP4 402 C 1 
HETATM 17 C C10 XP4 . . . K 5 145.568 154.169 127.905 1 106.61 ? C10 XP4 402 C 1 
HETATM 18 C C11 XP4 . . . K 5 146.251 154.53 129.2 1 106.61 ? C11 XP4 402 C 1 
HETATM 19 C C12 XP4 . . . K 5 147.411 153.639 129.567 1 106.61 ? C12 XP4 402 C 1 
HETATM 20 C C13 XP4 . . . K 5 148.319 154.218 130.623 1 106.61 ? C13 XP4 402 C 1 
HETATM 21 C C14 XP4 . . . K 5 147.6 154.748 131.838 1 106.61 ? C14 XP4 402 C 1 
HETATM 22 C C15 XP4 . . . K 5 148.499 155.411 132.851 1 106.61 ? C15 XP4 402 C 1 
HETATM 23 C C16 XP4 . . . K 5 147.765 156.06 133.996 1 106.61 ? C16 XP4 402 C 1 
HETATM 24 C C17 XP4 . . . K 5 148.669 156.71 135.015 1 106.61 ? C17 XP4 402 C 1 
HETATM 25 O O7 XP4 . . . K 5 145.054 153.315 121.044 1 106.61 ? O7 XP4 402 C 1 
HETATM 26 C C18 XP4 . . . K 5 146.251 152.712 120.976 1 106.61 ? C18 XP4 402 C 1 
HETATM 27 O O8 XP4 . . . K 5 146.541 151.876 120.162 1 106.61 ? O8 XP4 402 C 1 
HETATM 28 C C19 XP4 . . . K 5 147.204 153.295 121.981 1 106.61 ? C19 XP4 402 C 1 
HETATM 29 C C20 XP4 . . . K 5 147.589 152.357 123.081 1 106.61 ? C20 XP4 402 C 1 
HETATM 30 C C21 XP4 . . . K 5 148.638 152.966 123.994 1 106.61 ? C21 XP4 402 C 1 
HETATM 31 C C22 XP4 . . . K 5 149.019 152.127 125.187 1 106.61 ? C22 XP4 402 C 1 
HETATM 32 C C23 XP4 . . . K 5 150.166 152.703 125.98 1 106.61 ? C23 XP4 402 C 1 
HETATM 33 C C24 XP4 . . . K 5 150.532 151.934 127.224 1 106.61 ? C24 XP4 402 C 1 
HETATM 34 C C25 XP4 . . . K 5 151.784 152.437 127.899 1 106.61 ? C25 XP4 402 C 1 
HETATM 35 C C26 XP4 . . . K 5 152.147 151.719 129.175 1 106.61 ? C26 XP4 402 C 1 
HETATM 36 C C27 XP4 . . . K 5 153.498 152.107 129.723 1 106.61 ? C27 XP4 402 C 1 
HETATM 37 C C28 XP4 . . . K 5 153.86 151.458 131.036 1 106.61 ? C28 XP4 402 C 1 
HETATM 38 C C29 XP4 . . . K 5 153.039 151.924 132.212 1 106.61 ? C29 XP4 402 C 1 
HETATM 39 C C30 XP4 . . . K 5 153.496 151.359 133.533 1 106.61 ? C30 XP4 402 C 1 
HETATM 40 C C31 XP4 . . . K 5 152.721 151.87 134.723 1 106.61 ? C31 XP4 402 C 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    37 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           40 
#