data_5JDF
#
_model_server_result.job_id            JnfV5fmNygacJxDks2VTyQ 
_model_server_result.datetime_utc      '2024-11-15 02:17:53' 
_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          5jdf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":407}' 
#
_entry.id    5JDF 
#
_exptl.entry_id    5JDF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              356.54 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate' 
_entity.pdbx_number_of_molecules    5 
_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            5JDF 
_cell.length_a            49.801 
_cell.length_b            72.258 
_cell.length_c            95.803 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5JDF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,P 
_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    x,y,z 
_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
? 3 D N N 
? 3 E N N 
? 3 F N N 
? 3 G N N 
? 3 H 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
metalc ? metalc1 A O THR 50 A THR 50 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc2 A OE1 GLU 54 A GLU 54 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc3 A OE2 GLU 54 A GLU 54 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.202 ? 
metalc ? metalc4 A OE2 GLU 54 A GLU 54 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc5 A O ILE 118 A ILE 118 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? 
metalc ? metalc6 A OD1 ASP 121 A ASP 121 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? 
metalc ? metalc7 A O GLY 122 A GLY 122 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? 
metalc ? metalc8 A OD2 ASP 127 A ASP 127 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc9 A O THR 209 A THR 209 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc10 A OE1 GLU 213 A GLU 213 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc11 A OE2 GLU 213 A GLU 213 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.104 ? 
metalc ? metalc12 A OE2 GLU 213 A GLU 213 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.348 ? 
metalc ? metalc13 A OD1 ASP 240 A ASP 240 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 3.096 ? 
metalc ? metalc14 A OD2 ASP 240 A ASP 240 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.807 ? 
metalc ? metalc15 B CA CA . A CA 401 1_555 H O25 OLC . A OLC 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? 
metalc ? metalc16 B CA CA . A CA 401 1_555 P O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
#
_chem_comp.formula           'C21 H40 O4' 
_chem_comp.formula_weight    356.54 
_chem_comp.id                OLC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     1-Oleoyl-R-glycerol 
#
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
C18 C17 OLC sing 320 n n 
C10 C9 OLC doub 321 n n 
C10 C11 OLC sing 322 n n 
C9 C8 OLC sing 323 n n 
C17 C16 OLC sing 324 z n 
C11 C12 OLC sing 325 n n 
C8 C7 OLC sing 326 n n 
C24 C22 OLC sing 327 n n 
C24 O25 OLC sing 328 n n 
C16 C15 OLC sing 329 n n 
C12 C13 OLC sing 330 n n 
C7 C6 OLC sing 331 n n 
C15 C14 OLC sing 332 n n 
C13 C14 OLC sing 333 n n 
C6 C5 OLC sing 334 n n 
C5 C4 OLC sing 335 n n 
C4 C3 OLC sing 336 n n 
C3 C2 OLC sing 337 n n 
C2 C1 OLC sing 338 n n 
C21 C22 OLC sing 339 n n 
C21 O20 OLC sing 340 n n 
C1 O19 OLC doub 341 n n 
C1 O20 OLC sing 342 n n 
C22 O23 OLC sing 343 n n 
C18 H18 OLC sing 344 n n 
C18 H18A OLC sing 345 n n 
C18 H18B OLC sing 346 n n 
C10 H10 OLC sing 347 n n 
C9 H9 OLC sing 348 n n 
C17 H17 OLC sing 349 n n 
C17 H17A OLC sing 350 n n 
C11 H11 OLC sing 351 n n 
C11 H11A OLC sing 352 n n 
C8 H8 OLC sing 353 n n 
C8 H8A OLC sing 354 n n 
C24 H24 OLC sing 355 n n 
C24 H24A OLC sing 356 n n 
C16 H16 OLC sing 357 n n 
C16 H16A OLC sing 358 n n 
C12 H12 OLC sing 359 n n 
C12 H12A OLC sing 360 n n 
C7 H7 OLC sing 361 n n 
C7 H7A OLC sing 362 n n 
C15 H15 OLC sing 363 n n 
C15 H15A OLC sing 364 n n 
C13 H13 OLC sing 365 n n 
C13 H13A OLC sing 366 n n 
C6 H6 OLC sing 367 n n 
C6 H6A OLC sing 368 n n 
C14 H14 OLC sing 369 n n 
C14 H14A OLC sing 370 n n 
C5 H5 OLC sing 371 n n 
C5 H5A OLC sing 372 n n 
C4 H4 OLC sing 373 n n 
C4 H4A OLC sing 374 n n 
C3 H3 OLC sing 375 n n 
C3 H3A OLC sing 376 n n 
C2 H2 OLC sing 377 n n 
C2 H2A OLC sing 378 n n 
C21 H21 OLC sing 379 n n 
C21 H21A OLC sing 380 n n 
C22 H22 OLC sing 381 n n 
O25 HO25 OLC sing 382 n n 
O23 HO23 OLC sing 383 n n 
#
_atom_sites.entry_id                     5JDF 
_atom_sites.fract_transf_matrix[1][1]    0.02008 
_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]    0.013839 
_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]    0.010438 
_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
B 2 CA A 1 401 1 CA CA . 
C 2 CA A 1 402 2 CA CA . 
D 3 OLC A 1 403 1 OLC MON . 
E 3 OLC A 1 404 3 OLC MON . 
F 3 OLC A 1 405 4 OLC MON . 
G 3 OLC A 1 406 5 OLC MON . 
H 3 OLC A 1 407 6 OLC MON . 
I 4 MYS A 1 408 15 MYS FAT . 
J 4 MYS A 1 409 20 MYS FAT . 
K 4 MYS A 1 410 24 MYS FAT . 
L 4 MYS A 1 411 25 MYS FAT . 
M 4 MYS A 1 412 26 MYS FAT . 
N 4 MYS A 1 413 28 MYS FAT . 
O 5 1PE A 1 414 1 1PE PEG . 
P 6 HOH A 1 501 10 HOH HOH . 
P 6 HOH A 2 502 21 HOH HOH . 
P 6 HOH A 3 503 12 HOH HOH . 
P 6 HOH A 4 504 8 HOH HOH . 
P 6 HOH A 5 505 14 HOH HOH . 
P 6 HOH A 6 506 24 HOH HOH . 
P 6 HOH A 7 507 3 HOH HOH . 
P 6 HOH A 8 508 16 HOH HOH . 
P 6 HOH A 9 509 5 HOH HOH . 
P 6 HOH A 10 510 2 HOH HOH . 
P 6 HOH A 11 511 9 HOH HOH . 
P 6 HOH A 12 512 11 HOH HOH . 
P 6 HOH A 13 513 19 HOH HOH . 
P 6 HOH A 14 514 23 HOH HOH . 
P 6 HOH A 15 515 17 HOH HOH . 
P 6 HOH A 16 516 18 HOH HOH . 
P 6 HOH A 17 517 22 HOH HOH . 
P 6 HOH A 18 518 20 HOH HOH . 
P 6 HOH A 19 519 4 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 C8 OLC . . . H 3 -14.623 6.751 21.99 1 86.22 ? C8 OLC 407 A 1 
HETATM 2 C C24 OLC . . . H 3 -11.169 5.789 32.872 1 83.47 ? C24 OLC 407 A 1 
HETATM 3 C C7 OLC . . . H 3 -14.787 6.936 23.499 1 89.35 ? C7 OLC 407 A 1 
HETATM 4 C C6 OLC . . . H 3 -14.301 5.684 24.237 1 99.42 ? C6 OLC 407 A 1 
HETATM 5 C C5 OLC . . . H 3 -14.486 5.917 25.737 1 95.07 ? C5 OLC 407 A 1 
HETATM 6 C C4 OLC . . . H 3 -14.019 4.712 26.558 1 84.72 ? C4 OLC 407 A 1 
HETATM 7 C C3 OLC . . . H 3 -14.248 5.061 28.03 1 92.41 ? C3 OLC 407 A 1 
HETATM 8 C C2 OLC . . . H 3 -13.807 3.931 28.96 1 96.16 ? C2 OLC 407 A 1 
HETATM 9 C C21 OLC . . . H 3 -13.418 4.758 32.543 1 107.34 ? C21 OLC 407 A 1 
HETATM 10 C C1 OLC . . . H 3 -14.077 4.388 30.396 1 112.87 ? C1 OLC 407 A 1 
HETATM 11 C C22 OLC . . . H 3 -12.201 4.832 33.468 1 98.63 ? C22 OLC 407 A 1 
HETATM 12 O O19 OLC . . . H 3 -15.178 4.837 30.714 1 111.37 ? O19 OLC 407 A 1 
HETATM 13 O O25 OLC . . . H 3 -10.032 5.865 33.734 1 83.41 ? O25 OLC 407 A 1 
HETATM 14 O O23 OLC . . . H 3 -12.608 5.314 34.751 1 109.31 ? O23 OLC 407 A 1 
HETATM 15 O O20 OLC . . . H 3 -13.023 4.283 31.251 1 115.06 ? O20 OLC 407 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           15 
#