data_8K4N
#
_model_server_result.job_id            jPf73F1b-97ir7sT-15ctg 
_model_server_result.datetime_utc      '2024-10-11 00:31:36' 
_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          8k4n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":401}' 
#
_entry.id    8K4N 
#
_exptl.entry_id    8K4N 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              467.491 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R)-2-azanyl-3-[oxidanyl-[(2R)-2-oxidanyl-3-tetradec-9-enoyloxy-propoxy]phosphoryl]oxy-propanoic acid' 
_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            8K4N 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8K4N 
_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    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_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                      6 
_struct_asym.id                             F 
_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 D SG CYS 21 E CYS 22 1_555 D SG CYS 95 E CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 D SG CYS 158 E CYS 147 1_555 D SG CYS 228 E CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf3 E SG CYS 79 D CYS 127 1_555 E SG CYS 156 D CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
#
_chem_comp.formula           'C20 H38 N O9 P' 
_chem_comp.formula_weight    467.491 
_chem_comp.id                VF0 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R)-2-azanyl-3-[oxidanyl-[(2R)-2-oxidanyl-3-tetradec-9-enoyloxy-propoxy]phosphoryl]oxy-propanoic acid' 
_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
N32 C31 VF0 sing 374 n n 
C31 C30 VF0 sing 375 n n 
C31 C33 VF0 sing 376 n n 
C30 O29 VF0 sing 377 n n 
O34 C33 VF0 doub 378 n n 
C33 O35 VF0 sing 379 n n 
O27 P26 VF0 doub 380 n n 
O29 P26 VF0 sing 381 n n 
P26 O28 VF0 sing 382 n n 
P26 O25 VF0 sing 383 n n 
O25 C24 VF0 sing 384 n n 
C24 C22 VF0 sing 385 n n 
O19 C18 VF0 doub 386 n n 
C22 C21 VF0 sing 387 n n 
C22 O23 VF0 sing 388 n n 
C21 O20 VF0 sing 389 n n 
O20 C18 VF0 sing 390 n n 
C18 C17 VF0 sing 391 n n 
C17 C16 VF0 sing 392 n n 
C16 C15 VF0 sing 393 n n 
C15 C14 VF0 sing 394 n n 
C14 C13 VF0 sing 395 n n 
C13 C12 VF0 sing 396 n n 
C12 C11 VF0 sing 397 n n 
C11 C10 VF0 sing 398 n n 
C10 C09 VF0 doub 399 z n 
C06 C05 VF0 sing 400 n n 
C06 C07 VF0 sing 401 n n 
C09 C08 VF0 sing 402 n n 
C08 C07 VF0 sing 403 n n 
C10 H101 VF0 sing 404 n n 
C13 H132 VF0 sing 405 n n 
C13 H131 VF0 sing 406 n n 
C15 H152 VF0 sing 407 n n 
C15 H151 VF0 sing 408 n n 
C17 H171 VF0 sing 409 n n 
C17 H172 VF0 sing 410 n n 
C21 H212 VF0 sing 411 n n 
C21 H211 VF0 sing 412 n n 
C22 H221 VF0 sing 413 n n 
C24 H241 VF0 sing 414 n n 
C24 H242 VF0 sing 415 n n 
C05 H051 VF0 sing 416 n n 
C05 H052 VF0 sing 417 n n 
C05 H1 VF0 sing 418 n n 
C06 H062 VF0 sing 419 n n 
C06 H061 VF0 sing 420 n n 
C07 H071 VF0 sing 421 n n 
C07 H072 VF0 sing 422 n n 
C08 H081 VF0 sing 423 n n 
C08 H082 VF0 sing 424 n n 
C09 H091 VF0 sing 425 n n 
C11 H112 VF0 sing 426 n n 
C11 H111 VF0 sing 427 n n 
C12 H122 VF0 sing 428 n n 
C12 H121 VF0 sing 429 n n 
C14 H141 VF0 sing 430 n n 
C14 H142 VF0 sing 431 n n 
C16 H161 VF0 sing 432 n n 
C16 H162 VF0 sing 433 n n 
C30 H301 VF0 sing 434 n n 
C30 H302 VF0 sing 435 n n 
C31 H311 VF0 sing 436 n n 
N32 H2 VF0 sing 437 n n 
N32 H321 VF0 sing 438 n n 
O23 H231 VF0 sing 439 n n 
O28 H3 VF0 sing 440 n n 
O35 H4 VF0 sing 441 n n 
#
_atom_sites.entry_id                     8K4N 
_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 
#
_pdbx_nonpoly_scheme.asym_id          F 
_pdbx_nonpoly_scheme.entity_id        6 
_pdbx_nonpoly_scheme.mon_id           VF0 
_pdbx_nonpoly_scheme.pdb_strand_id    D 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      401 
_pdbx_nonpoly_scheme.auth_seq_num     401 
_pdbx_nonpoly_scheme.pdb_mon_id       VF0 
_pdbx_nonpoly_scheme.auth_mon_id      LIG 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 C10 VF0 . . . F 6 163.036 147.921 138.376 1 54.54 ? C10 VF0 401 D 1 
HETATM 2 C C13 VF0 . . . F 6 165.584 147.891 135.603 1 54.54 ? C13 VF0 401 D 1 
HETATM 3 C C15 VF0 . . . F 6 165.522 147.462 133.127 1 54.54 ? C15 VF0 401 D 1 
HETATM 4 C C17 VF0 . . . F 6 163.827 146.758 131.43 1 54.54 ? C17 VF0 401 D 1 
HETATM 5 C C21 VF0 . . . F 6 166.499 146.536 129.753 1 54.54 ? C21 VF0 401 D 1 
HETATM 6 C C22 VF0 . . . F 6 168.009 146.748 129.743 1 54.54 ? C22 VF0 401 D 1 
HETATM 7 C C24 VF0 . . . F 6 168.546 146.548 128.333 1 54.54 ? C24 VF0 401 D 1 
HETATM 8 C C05 VF0 . . . F 6 158.626 146.438 140.354 1 54.54 ? C05 VF0 401 D 1 
HETATM 9 C C06 VF0 . . . F 6 159.547 147.379 139.58 1 54.54 ? C06 VF0 401 D 1 
HETATM 10 C C07 VF0 . . . F 6 160.653 147.882 140.504 1 54.54 ? C07 VF0 401 D 1 
HETATM 11 C C08 VF0 . . . F 6 161.37 149.068 139.862 1 54.54 ? C08 VF0 401 D 1 
HETATM 12 C C09 VF0 . . . F 6 162.847 148.747 139.644 1 54.54 ? C09 VF0 401 D 1 
HETATM 13 C C11 VF0 . . . F 6 164.127 148.55 137.522 1 54.54 ? C11 VF0 401 D 1 
HETATM 14 C C12 VF0 . . . F 6 164.17 147.852 136.168 1 54.54 ? C12 VF0 401 D 1 
HETATM 15 C C14 VF0 . . . F 6 165.739 146.843 134.506 1 54.54 ? C14 VF0 401 D 1 
HETATM 16 C C16 VF0 . . . F 6 164.037 147.478 132.759 1 54.54 ? C16 VF0 401 D 1 
HETATM 17 C C18 VF0 . . . F 6 164.472 147.564 130.303 1 54.54 ? C18 VF0 401 D 1 
HETATM 18 C C30 VF0 . . . F 6 169.155 149.424 125.078 1 54.54 ? C30 VF0 401 D 1 
HETATM 19 C C31 VF0 . . . F 6 167.81 149.54 124.368 1 54.54 ? C31 VF0 401 D 1 
HETATM 20 C C33 VF0 . . . F 6 166.734 148.841 125.192 1 54.54 ? C33 VF0 401 D 1 
HETATM 21 N N32 VF0 . . . F 6 167.888 148.918 123.061 1 54.54 ? N32 VF0 401 D 1 
HETATM 22 O O19 VF0 . . . F 6 163.793 148.094 129.492 1 54.54 ? O19 VF0 401 D 1 
HETATM 23 O O20 VF0 . . . F 6 165.863 147.685 130.226 1 54.54 ? O20 VF0 401 D 1 
HETATM 24 O O23 VF0 . . . F 6 168.622 145.824 130.593 1 54.54 ? O23 VF0 401 D 1 
HETATM 25 O O25 VF0 . . . F 6 169.83 147.088 128.247 1 54.54 ? O25 VF0 401 D 1 
HETATM 26 O O27 VF0 . . . F 6 170.785 146.991 125.866 1 54.54 ? O27 VF0 401 D 1 
HETATM 27 O O28 VF0 . . . F 6 171.402 148.76 127.118 1 54.54 ? O28 VF0 401 D 1 
HETATM 28 O O29 VF0 . . . F 6 168.986 148.768 126.298 1 54.54 ? O29 VF0 401 D 1 
HETATM 29 O O34 VF0 . . . F 6 166.6 147.592 125.122 1 54.54 ? O34 VF0 401 D 1 
HETATM 30 O O35 VF0 . . . F 6 165.982 149.517 125.94 1 54.54 ? O35 VF0 401 D 1 
HETATM 31 P P26 VF0 . . . F 6 170.253 147.898 126.878 1 54.54 ? P26 VF0 401 D 1 
HETATM 32 H H101 VF0 . . . F 6 163.296 147.02 138.613 1 54.54 ? H101 VF0 401 D 1 
HETATM 33 H H132 VF0 . . . F 6 165.758 148.769 135.237 1 54.54 ? H132 VF0 401 D 1 
HETATM 34 H H131 VF0 . . . F 6 166.218 147.706 136.31 1 54.54 ? H131 VF0 401 D 1 
HETATM 35 H H152 VF0 . . . F 6 165.862 148.367 133.121 1 54.54 ? H152 VF0 401 D 1 
HETATM 36 H H151 VF0 . . . F 6 166.009 146.941 132.473 1 54.54 ? H151 VF0 401 D 1 
HETATM 37 H H171 VF0 . . . F 6 164.227 145.876 131.468 1 54.54 ? H171 VF0 401 D 1 
HETATM 38 H H172 VF0 . . . F 6 162.878 146.667 131.263 1 54.54 ? H172 VF0 401 D 1 
HETATM 39 H H212 VF0 . . . F 6 166.286 145.792 130.333 1 54.54 ? H212 VF0 401 D 1 
HETATM 40 H H211 VF0 . . . F 6 166.191 146.346 128.855 1 54.54 ? H211 VF0 401 D 1 
HETATM 41 H H221 VF0 . . . F 6 168.213 147.646 130.04 1 54.54 ? H221 VF0 401 D 1 
HETATM 42 H H241 VF0 . . . F 6 168.58 145.6 128.139 1 54.54 ? H241 VF0 401 D 1 
HETATM 43 H H242 VF0 . . . F 6 167.964 146.988 127.698 1 54.54 ? H242 VF0 401 D 1 
HETATM 44 H H051 VF0 . . . F 6 157.806 146.303 139.854 1 54.54 ? H051 VF0 401 D 1 
HETATM 45 H H052 VF0 . . . F 6 158.417 146.825 141.218 1 54.54 ? H052 VF0 401 D 1 
HETATM 46 H H062 VF0 . . . F 6 159.035 148.132 139.25 1 54.54 ? H062 VF0 401 D 1 
HETATM 47 H H061 VF0 . . . F 6 159.939 146.905 138.832 1 54.54 ? H061 VF0 401 D 1 
HETATM 48 H H071 VF0 . . . F 6 161.285 147.167 140.669 1 54.54 ? H071 VF0 401 D 1 
HETATM 49 H H072 VF0 . . . F 6 160.262 148.164 141.344 1 54.54 ? H072 VF0 401 D 1 
HETATM 50 H H081 VF0 . . . F 6 160.954 149.275 139.013 1 54.54 ? H081 VF0 401 D 1 
HETATM 51 H H082 VF0 . . . F 6 161.298 149.834 140.449 1 54.54 ? H082 VF0 401 D 1 
HETATM 52 H H091 VF0 . . . F 6 163.186 148.252 140.403 1 54.54 ? H091 VF0 401 D 1 
HETATM 53 H H112 VF0 . . . F 6 163.931 149.488 137.396 1 54.54 ? H112 VF0 401 D 1 
HETATM 54 H H111 VF0 . . . F 6 164.98 148.452 137.968 1 54.54 ? H111 VF0 401 D 1 
HETATM 55 H H122 VF0 . . . F 6 163.89 146.934 136.28 1 54.54 ? H122 VF0 401 D 1 
HETATM 56 H H121 VF0 . . . F 6 163.57 148.297 135.556 1 54.54 ? H121 VF0 401 D 1 
HETATM 57 H H141 VF0 . . . F 6 166.63 146.471 134.549 1 54.54 ? H141 VF0 401 D 1 
HETATM 58 H H142 VF0 . . . F 6 165.098 146.135 134.647 1 54.54 ? H142 VF0 401 D 1 
HETATM 59 H H161 VF0 . . . F 6 163.521 147.038 133.449 1 54.54 ? H161 VF0 401 D 1 
HETATM 60 H H162 VF0 . . . F 6 163.73 148.392 132.67 1 54.54 ? H162 VF0 401 D 1 
HETATM 61 H H301 VF0 . . . F 6 169.51 150.311 125.235 1 54.54 ? H301 VF0 401 D 1 
HETATM 62 H H302 VF0 . . . F 6 169.774 148.92 124.529 1 54.54 ? H302 VF0 401 D 1 
HETATM 63 H H311 VF0 . . . F 6 167.583 150.475 124.267 1 54.54 ? H311 VF0 401 D 1 
HETATM 64 H H2 VF0 . . . F 6 168.738 148.85 122.814 1 54.54 ? H2 VF0 401 D 1 
HETATM 65 H H321 VF0 . . . F 6 167.45 149.422 122.475 1 54.54 ? H321 VF0 401 D 1 
HETATM 66 H H231 VF0 . . . F 6 169.292 145.486 130.196 1 54.54 ? H231 VF0 401 D 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           66 
#