data_8D2V # _model_server_result.job_id 4QkbllCPUWMUN-4TN0U2SA _model_server_result.datetime_utc '2024-11-23 09:55:10' _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 8d2v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 8D2V # _exptl.entry_id 8D2V _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 518.644 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (9~{Z},12~{Z},15~{Z})-octadeca-9,12,15-trienoate' _entity.pdbx_number_of_molecules 1 _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 8D2V _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8D2V _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 ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 22 B CYS 22 1_555 B SG CYS 86 B CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 130 B CYS 130 1_555 B SG CYS 186 B CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 C SG CYS 22 C CYS 22 1_555 C SG CYS 93 C CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 C SG CYS 139 C CYS 139 1_555 C SG CYS 186 C CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A OE1 GLN 50 A GLN 51 1_555 M NA NA . A NA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc2 A OE2 GLU 183 A GLU 184 1_555 M NA NA . A NA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc3 A OH TYR 424 A TYR 425 1_555 M NA NA . A NA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc4 D O26 ZGS . A ZGS 601 1_555 M NA NA . A NA 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? # _chem_comp.formula 'C26 H49 N O7 P 1' _chem_comp.formula_weight 518.644 _chem_comp.id ZGS _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] (9~{Z},12~{Z},15~{Z})-octadeca-9,12,15-trienoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms LysoPC(18:3(9Z,12Z,15Z)) # 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 C01 C02 ZGS sing 456 n n C03 C02 ZGS sing 457 n n C03 C04 ZGS doub 458 z n C04 C05 ZGS sing 459 n n C05 C06 ZGS sing 460 n n C06 C07 ZGS doub 461 z n C08 C07 ZGS sing 462 n n C08 C09 ZGS sing 463 n n C09 C10 ZGS doub 464 z n C10 C11 ZGS sing 465 n n C11 C12 ZGS sing 466 n n C12 C13 ZGS sing 467 n n C13 C14 ZGS sing 468 n n C14 C15 ZGS sing 469 n n O19 C18 ZGS doub 470 n n C16 C17 ZGS sing 471 n n C16 C15 ZGS sing 472 n n C17 C18 ZGS sing 473 n n C18 O20 ZGS sing 474 n n O20 C21 ZGS sing 475 n n O35 C22 ZGS sing 476 n n C21 C22 ZGS sing 477 n n O26 P25 ZGS doub 478 n n C22 C23 ZGS sing 479 n n O27 P25 ZGS sing 480 n n P25 O24 ZGS sing 481 n n P25 O28 ZGS sing 482 n n C23 O24 ZGS sing 483 n n O28 C29 ZGS sing 484 n n C29 C30 ZGS sing 485 n n C30 N31 ZGS sing 486 n n C32 N31 ZGS sing 487 n n N31 C33 ZGS sing 488 n n N31 C34 ZGS sing 489 n n C01 H1 ZGS sing 490 n n C01 H2 ZGS sing 491 n n C01 H3 ZGS sing 492 n n C02 H4 ZGS sing 493 n n C02 H5 ZGS sing 494 n n C03 H6 ZGS sing 495 n n C04 H7 ZGS sing 496 n n C05 H8 ZGS sing 497 n n C05 H9 ZGS sing 498 n n C06 H10 ZGS sing 499 n n C07 H11 ZGS sing 500 n n C08 H12 ZGS sing 501 n n C08 H13 ZGS sing 502 n n C09 H14 ZGS sing 503 n n C10 H15 ZGS sing 504 n n C11 H16 ZGS sing 505 n n C11 H17 ZGS sing 506 n n C12 H18 ZGS sing 507 n n C12 H19 ZGS sing 508 n n C13 H20 ZGS sing 509 n n C13 H21 ZGS sing 510 n n C14 H22 ZGS sing 511 n n C14 H23 ZGS sing 512 n n C15 H24 ZGS sing 513 n n C15 H25 ZGS sing 514 n n C16 H26 ZGS sing 515 n n C16 H27 ZGS sing 516 n n C17 H28 ZGS sing 517 n n C17 H29 ZGS sing 518 n n C21 H30 ZGS sing 519 n n C21 H31 ZGS sing 520 n n C22 H32 ZGS sing 521 n n C23 H33 ZGS sing 522 n n C23 H34 ZGS sing 523 n n C29 H35 ZGS sing 524 n n C29 H36 ZGS sing 525 n n C30 H37 ZGS sing 526 n n C30 H38 ZGS sing 527 n n C32 H39 ZGS sing 528 n n C32 H40 ZGS sing 529 n n C32 H41 ZGS sing 530 n n C33 H42 ZGS sing 531 n n C33 H43 ZGS sing 532 n n C33 H44 ZGS sing 533 n n C34 H45 ZGS sing 534 n n C34 H46 ZGS sing 535 n n C34 H47 ZGS sing 536 n n O27 H48 ZGS sing 537 n n O35 H49 ZGS sing 538 n n # _atom_sites.entry_id 8D2V _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 D 4 ZGS A 1 601 600 ZGS ZGS . E 5 LMT A 1 602 1 LMT LMT . F 5 LMT A 1 603 2 LMT LMT . G 5 LMT A 1 604 3 LMT LMT . H 5 LMT A 1 605 4 LMT LMT . I 5 LMT A 1 606 5 LMT LMT . J 5 LMT A 1 607 6 LMT LMT . K 5 LMT A 1 608 7 LMT LMT . L 5 LMT A 1 609 8 LMT LMT . M 6 NA A 1 610 1 NA NA . # 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 C C01 ZGS . . . D 4 167.525 173.653 173.248 1 75.88 ? C01 ZGS 601 A 1 HETATM 2 C C02 ZGS . . . D 4 167.23 172.254 173.825 1 75.88 ? C02 ZGS 601 A 1 HETATM 3 C C03 ZGS . . . D 4 165.969 171.662 173.157 1 75.88 ? C03 ZGS 601 A 1 HETATM 4 C C04 ZGS . . . D 4 165.452 170.673 173.878 1 75.88 ? C04 ZGS 601 A 1 HETATM 5 C C05 ZGS . . . D 4 164.404 169.569 174.133 1 75.88 ? C05 ZGS 601 A 1 HETATM 6 C C06 ZGS . . . D 4 163.503 169.309 175.356 1 75.88 ? C06 ZGS 601 A 1 HETATM 7 C C07 ZGS . . . D 4 163.5 168.027 175.704 1 75.88 ? C07 ZGS 601 A 1 HETATM 8 C C08 ZGS . . . D 4 163.054 166.861 176.603 1 75.88 ? C08 ZGS 601 A 1 HETATM 9 C C09 ZGS . . . D 4 162.527 165.731 175.711 1 75.88 ? C09 ZGS 601 A 1 HETATM 10 C C10 ZGS . . . D 4 161.812 164.864 176.393 1 75.88 ? C10 ZGS 601 A 1 HETATM 11 C C11 ZGS . . . D 4 160.959 163.605 176.497 1 75.88 ? C11 ZGS 601 A 1 HETATM 12 C C12 ZGS . . . D 4 159.5 164.029 176.62 1 75.88 ? C12 ZGS 601 A 1 HETATM 13 C C13 ZGS . . . D 4 159.072 163.746 178.058 1 75.88 ? C13 ZGS 601 A 1 HETATM 14 C C14 ZGS . . . D 4 157.572 163.424 178.068 1 75.88 ? C14 ZGS 601 A 1 HETATM 15 C C15 ZGS . . . D 4 157.294 162.398 179.171 1 75.88 ? C15 ZGS 601 A 1 HETATM 16 C C16 ZGS . . . D 4 156.905 163.013 180.417 1 75.88 ? C16 ZGS 601 A 1 HETATM 17 C C17 ZGS . . . D 4 156.568 162.181 181.67 1 75.88 ? C17 ZGS 601 A 1 HETATM 18 C C18 ZGS . . . D 4 157.833 162.04 182.531 1 75.88 ? C18 ZGS 601 A 1 HETATM 19 C C21 ZGS . . . D 4 158.603 161.559 184.853 1 75.88 ? C21 ZGS 601 A 1 HETATM 20 C C22 ZGS . . . D 4 157.76 161.254 186.093 1 75.88 ? C22 ZGS 601 A 1 HETATM 21 C C23 ZGS . . . D 4 156.295 160.925 185.767 1 75.88 ? C23 ZGS 601 A 1 HETATM 22 C C29 ZGS . . . D 4 152.289 158.286 187.017 1 75.88 ? C29 ZGS 601 A 1 HETATM 23 C C30 ZGS . . . D 4 151.275 157.046 187.168 1 75.88 ? C30 ZGS 601 A 1 HETATM 24 C C32 ZGS . . . D 4 149.318 155.873 188.097 1 75.88 ? C32 ZGS 601 A 1 HETATM 25 C C33 ZGS . . . D 4 150.318 157.675 189.338 1 75.88 ? C33 ZGS 601 A 1 HETATM 26 C C34 ZGS . . . D 4 149.07 158.144 187.349 1 75.88 ? C34 ZGS 601 A 1 HETATM 27 N N31 ZGS . . . D 4 149.975 157.189 187.991 1 75.88 ? N31 ZGS 601 A 1 HETATM 28 O O19 ZGS . . . D 4 158.843 161.804 181.959 1 75.88 ? O19 ZGS 601 A 1 HETATM 29 O O20 ZGS . . . D 4 157.748 162.229 183.943 1 75.88 ? O20 ZGS 601 A 1 HETATM 30 O O24 ZGS . . . D 4 155.733 159.831 186.497 1 75.88 ? O24 ZGS 601 A 1 HETATM 31 O O26 ZGS . . . D 4 155.419 158.501 184.397 1 75.88 ? O26 ZGS 601 A 1 HETATM 32 O O27 ZGS . . . D 4 153.678 160.125 185.094 1 75.88 ? O27 ZGS 601 A 1 HETATM 33 O O28 ZGS . . . D 4 153.597 157.943 186.445 1 75.88 ? O28 ZGS 601 A 1 HETATM 34 O O35 ZGS . . . D 4 157.749 162.436 186.784 1 75.88 ? O35 ZGS 601 A 1 HETATM 35 P P25 ZGS . . . D 4 154.589 159.041 185.586 1 75.88 ? P25 ZGS 601 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 35 #