data_4YMK
#
_model_server_result.job_id            qdP0NA23IYhhCylgaD0rOA 
_model_server_result.datetime_utc      '2024-11-24 15:02:55' 
_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          4ymk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":404}' 
#
_entry.id    4YMK 
#
_exptl.entry_id    4YMK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              356.54 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate' 
_entity.pdbx_number_of_molecules    2 
_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            4YMK 
_cell.length_a            77.061 
_cell.length_b            113.766 
_cell.length_c            141.698 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YMK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,K 1 1 
B,G,H,I,J,L 2 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
? 4 F N N 
? 4 J 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 NE2 HIS 94 A HIS 116 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc2 A NE2 HIS 99 A HIS 121 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc3 A NE2 HIS 131 A HIS 153 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc4 A NE2 HIS 134 A HIS 156 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc5 A NE2 HIS 135 A HIS 157 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc6 A NE2 HIS 243 A HIS 265 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc7 A NE2 HIS 272 A HIS 294 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? 
metalc ? metalc8 A NE2 HIS 275 A HIS 297 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc9 A NE2 HIS 276 A HIS 298 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc10 D ZN ZN . A ZN 402 1_555 K O HOH . A HOH 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? 
metalc ? metalc11 B NE2 HIS 94 D HIS 116 1_555 G ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc12 B NE2 HIS 99 D HIS 121 1_555 G ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc13 B NE2 HIS 131 D HIS 153 1_555 G ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc14 B NE2 HIS 134 D HIS 156 1_555 H ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc15 B NE2 HIS 135 D HIS 157 1_555 G ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? 
metalc ? metalc16 B NE2 HIS 243 D HIS 265 1_555 H ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? 
metalc ? metalc17 B NE2 HIS 272 D HIS 294 1_555 H ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc18 B NE2 HIS 275 D HIS 297 1_555 G ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
metalc ? metalc19 B NE2 HIS 276 D HIS 298 1_555 H ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc20 H ZN ZN . D ZN 402 1_555 L O HOH . D HOH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? 
#
_chem_comp.formula           'C21 H40 O4' 
_chem_comp.formula_weight    356.54 
_chem_comp.id                MPG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate' 
_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
C2 C3 MPG sing 237 n n 
C2 C1 MPG sing 238 n n 
C3 C4 MPG sing 239 n n 
C4 C5 MPG sing 240 n n 
C5 C6 MPG sing 241 n n 
C6 C7 MPG sing 242 n n 
C7 C8 MPG sing 243 n n 
C8 C9 MPG sing 244 n n 
C9 C10 MPG doub 245 z n 
C10 C11 MPG sing 246 n n 
C11 C12 MPG sing 247 n n 
C12 C13 MPG sing 248 n n 
C13 C14 MPG sing 249 n n 
C14 C15 MPG sing 250 n n 
C15 C16 MPG sing 251 n n 
C16 C17 MPG sing 252 n n 
C17 C18 MPG sing 253 n n 
O1 C1 MPG sing 254 n n 
O1 CX3 MPG sing 255 n n 
CXD O2 MPG sing 256 n n 
CXD C21 MPG sing 257 n n 
CXD CX3 MPG sing 258 n n 
C21 O3 MPG sing 259 n n 
C2 H21C MPG sing 260 n n 
C2 H22C MPG sing 261 n n 
C3 H31C MPG sing 262 n n 
C3 H32C MPG sing 263 n n 
CX3 O4 MPG doub 264 n n 
C4 H41C MPG sing 265 n n 
C4 H42C MPG sing 266 n n 
C5 H51C MPG sing 267 n n 
C5 H52C MPG sing 268 n n 
C6 H61C MPG sing 269 n n 
C6 H62C MPG sing 270 n n 
C7 H71C MPG sing 271 n n 
C7 H72C MPG sing 272 n n 
C8 H81C MPG sing 273 n n 
C8 H82C MPG sing 274 n n 
C9 H9 MPG sing 275 n n 
C10 H10 MPG sing 276 n n 
C11 H111 MPG sing 277 n n 
C11 H112 MPG sing 278 n n 
C12 H121 MPG sing 279 n n 
C12 H122 MPG sing 280 n n 
C13 H131 MPG sing 281 n n 
C13 H132 MPG sing 282 n n 
C14 H141 MPG sing 283 n n 
C14 H142 MPG sing 284 n n 
C15 H151 MPG sing 285 n n 
C15 H152 MPG sing 286 n n 
C16 H161 MPG sing 287 n n 
C16 H162 MPG sing 288 n n 
C17 H171 MPG sing 289 n n 
C17 H172 MPG sing 290 n n 
C18 H181 MPG sing 291 n n 
C18 H182 MPG sing 292 n n 
C18 H183 MPG sing 293 n n 
C1 HX31 MPG sing 294 n n 
C1 HX32 MPG sing 295 n n 
CXD HXD MPG sing 296 n n 
O2 H2 MPG sing 297 n n 
C21 H211 MPG sing 298 n n 
C21 H212 MPG sing 299 n n 
O3 H3 MPG sing 300 n n 
#
_atom_sites.entry_id                     4YMK 
_atom_sites.fract_transf_matrix[1][1]    0.012977 
_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]    0.00879 
_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]    0.007057 
_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
C 2 ZN A 1 401 1 ZN ZN . 
D 2 ZN A 1 402 2 ZN ZN . 
E 3 ST9 A 1 403 901 ST9 ST9 . 
F 4 MPG A 1 404 1 MPG MPG . 
G 2 ZN D 1 401 1 ZN ZN . 
H 2 ZN D 1 402 2 ZN ZN . 
I 3 ST9 D 1 403 901 ST9 ST9 . 
J 4 MPG D 1 404 1 MPG MPG . 
K 5 HOH A 1 501 21 HOH HOH . 
K 5 HOH A 2 502 1 HOH HOH . 
K 5 HOH A 3 503 20 HOH HOH . 
K 5 HOH A 4 504 67 HOH HOH . 
K 5 HOH A 5 505 69 HOH HOH . 
K 5 HOH A 6 506 57 HOH HOH . 
K 5 HOH A 7 507 2 HOH HOH . 
K 5 HOH A 8 508 3 HOH HOH . 
K 5 HOH A 9 509 4 HOH HOH . 
K 5 HOH A 10 510 5 HOH HOH . 
K 5 HOH A 11 511 6 HOH HOH . 
K 5 HOH A 12 512 7 HOH HOH . 
K 5 HOH A 13 513 8 HOH HOH . 
K 5 HOH A 14 514 9 HOH HOH . 
K 5 HOH A 15 515 10 HOH HOH . 
K 5 HOH A 16 516 11 HOH HOH . 
K 5 HOH A 17 517 19 HOH HOH . 
K 5 HOH A 18 518 22 HOH HOH . 
K 5 HOH A 19 519 23 HOH HOH . 
K 5 HOH A 20 520 24 HOH HOH . 
K 5 HOH A 21 521 25 HOH HOH . 
K 5 HOH A 22 522 26 HOH HOH . 
K 5 HOH A 23 523 27 HOH HOH . 
K 5 HOH A 24 524 28 HOH HOH . 
K 5 HOH A 25 525 37 HOH HOH . 
K 5 HOH A 26 526 38 HOH HOH . 
K 5 HOH A 27 527 39 HOH HOH . 
K 5 HOH A 28 528 40 HOH HOH . 
K 5 HOH A 29 529 41 HOH HOH . 
K 5 HOH A 30 530 42 HOH HOH . 
K 5 HOH A 31 531 43 HOH HOH . 
K 5 HOH A 32 532 44 HOH HOH . 
K 5 HOH A 33 533 45 HOH HOH . 
K 5 HOH A 34 534 46 HOH HOH . 
K 5 HOH A 35 535 47 HOH HOH . 
K 5 HOH A 36 536 58 HOH HOH . 
K 5 HOH A 37 537 65 HOH HOH . 
K 5 HOH A 38 538 66 HOH HOH . 
K 5 HOH A 39 539 68 HOH HOH . 
K 5 HOH A 40 540 70 HOH HOH . 
K 5 HOH A 41 541 73 HOH HOH . 
K 5 HOH A 42 542 75 HOH HOH . 
K 5 HOH A 43 543 77 HOH HOH . 
K 5 HOH A 44 544 78 HOH HOH . 
K 5 HOH A 45 545 79 HOH HOH . 
K 5 HOH A 46 546 92 HOH HOH . 
K 5 HOH A 47 547 93 HOH HOH . 
L 5 HOH D 1 501 62 HOH HOH . 
L 5 HOH D 2 502 49 HOH HOH . 
L 5 HOH D 3 503 12 HOH HOH . 
L 5 HOH D 4 504 13 HOH HOH . 
L 5 HOH D 5 505 14 HOH HOH . 
L 5 HOH D 6 506 15 HOH HOH . 
L 5 HOH D 7 507 16 HOH HOH . 
L 5 HOH D 8 508 17 HOH HOH . 
L 5 HOH D 9 509 18 HOH HOH . 
L 5 HOH D 10 510 30 HOH HOH . 
L 5 HOH D 11 511 31 HOH HOH . 
L 5 HOH D 12 512 32 HOH HOH . 
L 5 HOH D 13 513 34 HOH HOH . 
L 5 HOH D 14 514 36 HOH HOH . 
L 5 HOH D 15 515 48 HOH HOH . 
L 5 HOH D 16 516 50 HOH HOH . 
L 5 HOH D 17 517 51 HOH HOH . 
L 5 HOH D 18 518 52 HOH HOH . 
L 5 HOH D 19 519 53 HOH HOH . 
L 5 HOH D 20 520 54 HOH HOH . 
L 5 HOH D 21 521 55 HOH HOH . 
L 5 HOH D 22 522 59 HOH HOH . 
L 5 HOH D 23 523 60 HOH HOH . 
L 5 HOH D 24 524 61 HOH HOH . 
L 5 HOH D 25 525 63 HOH HOH . 
L 5 HOH D 26 526 64 HOH HOH . 
L 5 HOH D 27 527 71 HOH HOH . 
L 5 HOH D 28 528 72 HOH HOH . 
L 5 HOH D 29 529 74 HOH HOH . 
L 5 HOH D 30 530 76 HOH HOH . 
L 5 HOH D 31 531 80 HOH HOH . 
L 5 HOH D 32 532 81 HOH HOH . 
L 5 HOH D 33 533 82 HOH HOH . 
L 5 HOH D 34 534 87 HOH HOH . 
L 5 HOH D 35 535 88 HOH HOH . 
L 5 HOH D 36 536 89 HOH HOH . 
L 5 HOH D 37 537 90 HOH HOH . 
L 5 HOH D 38 538 91 HOH HOH . 
L 5 HOH D 39 539 94 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 C2 MPG . . . J 4 2.732 4.795 19.583 1 66.37 ? C2 MPG 404 D 1 
HETATM 2 C C3 MPG . . . J 4 3.443 5.868 20.411 1 63.32 ? C3 MPG 404 D 1 
HETATM 3 C C4 MPG . . . J 4 2.839 6.076 21.804 1 56.92 ? C4 MPG 404 D 1 
HETATM 4 C C5 MPG . . . J 4 3.693 6.926 22.753 1 56.5 ? C5 MPG 404 D 1 
HETATM 5 C C6 MPG . . . J 4 3.058 7.159 24.127 1 55.02 ? C6 MPG 404 D 1 
HETATM 6 C C7 MPG . . . J 4 3.993 7.871 25.117 1 51.55 ? C7 MPG 404 D 1 
HETATM 7 C C8 MPG . . . J 4 3.305 8.472 26.35 1 50.13 ? C8 MPG 404 D 1 
HETATM 8 C C9 MPG . . . J 4 4.22 9.303 27.205 1 54.35 ? C9 MPG 404 D 1 
HETATM 9 C C10 MPG . . . J 4 4.396 9.141 28.529 1 56.93 ? C10 MPG 404 D 1 
HETATM 10 C C11 MPG . . . J 4 3.697 8.092 29.353 1 53.57 ? C11 MPG 404 D 1 
HETATM 11 C C12 MPG . . . J 4 4.461 6.766 29.44 1 49.51 ? C12 MPG 404 D 1 
HETATM 12 C C13 MPG . . . J 4 3.654 5.545 29.899 1 50.05 ? C13 MPG 404 D 1 
HETATM 13 C C14 MPG . . . J 4 4.393 4.215 29.725 1 61.22 ? C14 MPG 404 D 1 
HETATM 14 C C15 MPG . . . J 4 3.625 2.999 30.259 1 70.11 ? C15 MPG 404 D 1 
HETATM 15 C C16 MPG . . . J 4 2.244 2.81 29.625 1 74.28 ? C16 MPG 404 D 1 
HETATM 16 C C17 MPG . . . J 4 1.413 1.712 30.295 1 75.42 ? C17 MPG 404 D 1 
HETATM 17 C C18 MPG . . . J 4 0.029 1.54 29.687 1 74.54 ? C18 MPG 404 D 1 
HETATM 18 O O1 MPG . . . J 4 1.19 4.528 17.753 1 76.11 ? O1 MPG 404 D 1 
HETATM 19 C C1 MPG . . . J 4 1.501 5.343 18.873 1 67.73 ? C1 MPG 404 D 1 
HETATM 20 C CXD MPG . . . J 4 -0.291 3.868 16.031 1 84.52 ? CXD MPG 404 D 1 
HETATM 21 O O2 MPG . . . J 4 0.357 2.606 16.071 1 86.73 ? O2 MPG 404 D 1 
HETATM 22 C C21 MPG . . . J 4 0.382 4.7 14.949 1 86.98 ? C21 MPG 404 D 1 
HETATM 23 O O3 MPG . . . J 4 0.019 4.226 13.662 1 89.89 ? O3 MPG 404 D 1 
HETATM 24 O O4 MPG . . . J 4 -1.062 4.908 18.085 1 87.11 ? O4 MPG 404 D 1 
HETATM 25 C CX3 MPG . . . J 4 -0.132 4.495 17.402 1 82.91 ? CX3 MPG 404 D 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           342 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#