data_8D2X
#
_model_server_result.job_id            oIzUzoeYWB0EdfNl90EovQ 
_model_server_result.datetime_utc      '2024-11-23 09:45:27' 
_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          8d2x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":601}' 
#
_entry.id    8D2X 
#
_exptl.entry_id    8D2X 
_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                     ? 
#
_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,N,O,P,Q,R 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
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 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
disulf ? disulf4 C SG CYS 139 C CYS 139 1_555 C SG CYS 186 C CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_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 458 n n 
C03 C02 ZGS sing 459 n n 
C03 C04 ZGS doub 460 z n 
C04 C05 ZGS sing 461 n n 
C05 C06 ZGS sing 462 n n 
C06 C07 ZGS doub 463 z n 
C08 C07 ZGS sing 464 n n 
C08 C09 ZGS sing 465 n n 
C09 C10 ZGS doub 466 z n 
C10 C11 ZGS sing 467 n n 
C11 C12 ZGS sing 468 n n 
C12 C13 ZGS sing 469 n n 
C13 C14 ZGS sing 470 n n 
C14 C15 ZGS sing 471 n n 
O19 C18 ZGS doub 472 n n 
C16 C17 ZGS sing 473 n n 
C16 C15 ZGS sing 474 n n 
C17 C18 ZGS sing 475 n n 
C18 O20 ZGS sing 476 n n 
O20 C21 ZGS sing 477 n n 
O35 C22 ZGS sing 478 n n 
C21 C22 ZGS sing 479 n n 
O26 P25 ZGS doub 480 n n 
C22 C23 ZGS sing 481 n n 
O27 P25 ZGS sing 482 n n 
P25 O24 ZGS sing 483 n n 
P25 O28 ZGS sing 484 n n 
C23 O24 ZGS sing 485 n n 
O28 C29 ZGS sing 486 n n 
C29 C30 ZGS sing 487 n n 
C30 N31 ZGS sing 488 n n 
C32 N31 ZGS sing 489 n n 
N31 C33 ZGS sing 490 n n 
N31 C34 ZGS sing 491 n n 
C01 H1 ZGS sing 492 n n 
C01 H2 ZGS sing 493 n n 
C01 H3 ZGS sing 494 n n 
C02 H4 ZGS sing 495 n n 
C02 H5 ZGS sing 496 n n 
C03 H6 ZGS sing 497 n n 
C04 H7 ZGS sing 498 n n 
C05 H8 ZGS sing 499 n n 
C05 H9 ZGS sing 500 n n 
C06 H10 ZGS sing 501 n n 
C07 H11 ZGS sing 502 n n 
C08 H12 ZGS sing 503 n n 
C08 H13 ZGS sing 504 n n 
C09 H14 ZGS sing 505 n n 
C10 H15 ZGS sing 506 n n 
C11 H16 ZGS sing 507 n n 
C11 H17 ZGS sing 508 n n 
C12 H18 ZGS sing 509 n n 
C12 H19 ZGS sing 510 n n 
C13 H20 ZGS sing 511 n n 
C13 H21 ZGS sing 512 n n 
C14 H22 ZGS sing 513 n n 
C14 H23 ZGS sing 514 n n 
C15 H24 ZGS sing 515 n n 
C15 H25 ZGS sing 516 n n 
C16 H26 ZGS sing 517 n n 
C16 H27 ZGS sing 518 n n 
C17 H28 ZGS sing 519 n n 
C17 H29 ZGS sing 520 n n 
C21 H30 ZGS sing 521 n n 
C21 H31 ZGS sing 522 n n 
C22 H32 ZGS sing 523 n n 
C23 H33 ZGS sing 524 n n 
C23 H34 ZGS sing 525 n n 
C29 H35 ZGS sing 526 n n 
C29 H36 ZGS sing 527 n n 
C30 H37 ZGS sing 528 n n 
C30 H38 ZGS sing 529 n n 
C32 H39 ZGS sing 530 n n 
C32 H40 ZGS sing 531 n n 
C32 H41 ZGS sing 532 n n 
C33 H42 ZGS sing 533 n n 
C33 H43 ZGS sing 534 n n 
C33 H44 ZGS sing 535 n n 
C34 H45 ZGS sing 536 n n 
C34 H46 ZGS sing 537 n n 
C34 H47 ZGS sing 538 n n 
O27 H48 ZGS sing 539 n n 
O35 H49 ZGS sing 540 n n 
#
_atom_sites.entry_id                     8D2X 
_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 3 LMT LMT . 
G 5 LMT A 1 604 4 LMT LMT . 
H 5 LMT A 1 605 5 LMT LMT . 
I 5 LMT A 1 606 6 LMT LMT . 
J 5 LMT A 1 607 7 LMT LMT . 
K 5 LMT A 1 608 8 LMT LMT . 
L 5 LMT A 1 609 9 LMT LMT . 
M 5 LMT A 1 610 10 LMT LMT . 
N 5 LMT A 1 611 11 LMT LMT . 
O 5 LMT A 1 612 12 LMT LMT . 
P 5 LMT A 1 613 13 LMT LMT . 
Q 5 LMT A 1 614 15 LMT LMT . 
R 6 HOH A 1 701 4 HOH HOH . 
R 6 HOH A 2 702 1 HOH HOH . 
R 6 HOH A 3 703 3 HOH HOH . 
R 6 HOH A 4 704 2 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 C C01 ZGS . . . D 4 155.212 165.238 190.059 1 28.1 ? C01 ZGS 601 A 1 
HETATM 2 C C02 ZGS . . . D 4 156.453 164.401 189.691 1 28.1 ? C02 ZGS 601 A 1 
HETATM 3 C C03 ZGS . . . D 4 156.722 163.392 190.826 1 28.1 ? C03 ZGS 601 A 1 
HETATM 4 C C04 ZGS . . . D 4 158.021 163.308 191.075 1 28.1 ? C04 ZGS 601 A 1 
HETATM 5 C C05 ZGS . . . D 4 159.483 163.722 190.805 1 28.1 ? C05 ZGS 601 A 1 
HETATM 6 C C06 ZGS . . . D 4 160.5 164.44 191.708 1 28.1 ? C06 ZGS 601 A 1 
HETATM 7 C C07 ZGS . . . D 4 161.386 163.585 192.195 1 28.1 ? C07 ZGS 601 A 1 
HETATM 8 C C08 ZGS . . . D 4 162.62 163.243 193.042 1 28.1 ? C08 ZGS 601 A 1 
HETATM 9 C C09 ZGS . . . D 4 163.305 162.017 192.431 1 28.1 ? C09 ZGS 601 A 1 
HETATM 10 C C10 ZGS . . . D 4 164.505 161.832 192.941 1 28.1 ? C10 ZGS 601 A 1 
HETATM 11 C C11 ZGS . . . D 4 165.654 162.223 193.877 1 28.1 ? C11 ZGS 601 A 1 
HETATM 12 C C12 ZGS . . . D 4 166.347 160.969 194.411 1 28.1 ? C12 ZGS 601 A 1 
HETATM 13 C C13 ZGS . . . D 4 167.841 161.05 194.092 1 28.1 ? C13 ZGS 601 A 1 
HETATM 14 C C14 ZGS . . . D 4 168.536 161.989 195.089 1 28.1 ? C14 ZGS 601 A 1 
HETATM 15 C C15 ZGS . . . D 4 170.025 162.048 194.73 1 28.1 ? C15 ZGS 601 A 1 
HETATM 16 C C16 ZGS . . . D 4 170.784 162.856 195.798 1 28.1 ? C16 ZGS 601 A 1 
HETATM 17 C C17 ZGS . . . D 4 172.278 162.484 195.747 1 28.1 ? C17 ZGS 601 A 1 
HETATM 18 C C18 ZGS . . . D 4 173.031 163.135 196.922 1 28.1 ? C18 ZGS 601 A 1 
HETATM 19 C C21 ZGS . . . D 4 174.937 163.979 195.835 1 28.1 ? C21 ZGS 601 A 1 
HETATM 20 C C22 ZGS . . . D 4 175.907 163.003 196.513 1 28.1 ? C22 ZGS 601 A 1 
HETATM 21 O O19 ZGS . . . D 4 172.912 162.7 198.019 1 28.1 ? O19 ZGS 601 A 1 
HETATM 22 O O20 ZGS . . . D 4 173.864 164.246 196.697 1 28.1 ? O20 ZGS 601 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           22 
#