data_5K2D
#
_model_server_result.job_id            0Scx7tVjgFgdUXb7VZ2wuA 
_model_server_result.datetime_utc      '2024-12-03 19:01:51' 
_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          5k2d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":1208}' 
#
_entry.id    5K2D 
#
_exptl.entry_id    5K2D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              356.54 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate' 
_entity.pdbx_number_of_molecules    8 
_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            5K2D 
_cell.length_a            40.36 
_cell.length_b            180.74 
_cell.length_c            142.8 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5K2D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,S,T,U,V,W,X,Y,Z,AA,BA,CA 
_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
? 6 H N N 
? 6 I N N 
? 6 J N N 
? 6 L N N 
? 6 M N N 
? 6 U N N 
? 6 V N N 
? 6 W 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
disulf ? disulf1 A SG CYS 96 A CYS 71 1_555 A SG CYS 184 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf2 A SG CYS 99 A CYS 74 1_555 A SG CYS 171 A CYS 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? 
disulf ? disulf3 A SG CYS 102 A CYS 77 1_555 A SG CYS 191 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
disulf ? disulf4 A SG CYS 380 A CYS 259 1_555 A SG CYS 383 A CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc1 A OD1 ASP 77 A ASP 52 1_555 C NA NA . A NA 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc2 A OG SER 116 A SER 91 1_555 C NA NA . A NA 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? 
metalc ? metalc3 C NA NA . A NA 1202 1_555 CA O HOH . A HOH 1315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc4 C NA NA . A NA 1202 1_555 CA O HOH . A HOH 1339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? 
metalc ? metalc5 C NA NA . A NA 1202 1_555 CA O HOH . A HOH 1375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
#
_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 431 n n 
C10 C9 OLC doub 432 n n 
C10 C11 OLC sing 433 n n 
C9 C8 OLC sing 434 n n 
C17 C16 OLC sing 435 z n 
C11 C12 OLC sing 436 n n 
C8 C7 OLC sing 437 n n 
C24 C22 OLC sing 438 n n 
C24 O25 OLC sing 439 n n 
C16 C15 OLC sing 440 n n 
C12 C13 OLC sing 441 n n 
C7 C6 OLC sing 442 n n 
C15 C14 OLC sing 443 n n 
C13 C14 OLC sing 444 n n 
C6 C5 OLC sing 445 n n 
C5 C4 OLC sing 446 n n 
C4 C3 OLC sing 447 n n 
C3 C2 OLC sing 448 n n 
C2 C1 OLC sing 449 n n 
C21 C22 OLC sing 450 n n 
C21 O20 OLC sing 451 n n 
C1 O19 OLC doub 452 n n 
C1 O20 OLC sing 453 n n 
C22 O23 OLC sing 454 n n 
C18 H18 OLC sing 455 n n 
C18 H18A OLC sing 456 n n 
C18 H18B OLC sing 457 n n 
C10 H10 OLC sing 458 n n 
C9 H9 OLC sing 459 n n 
C17 H17 OLC sing 460 n n 
C17 H17A OLC sing 461 n n 
C11 H11 OLC sing 462 n n 
C11 H11A OLC sing 463 n n 
C8 H8 OLC sing 464 n n 
C8 H8A OLC sing 465 n n 
C24 H24 OLC sing 466 n n 
C24 H24A OLC sing 467 n n 
C16 H16 OLC sing 468 n n 
C16 H16A OLC sing 469 n n 
C12 H12 OLC sing 470 n n 
C12 H12A OLC sing 471 n n 
C7 H7 OLC sing 472 n n 
C7 H7A OLC sing 473 n n 
C15 H15 OLC sing 474 n n 
C15 H15A OLC sing 475 n n 
C13 H13 OLC sing 476 n n 
C13 H13A OLC sing 477 n n 
C6 H6 OLC sing 478 n n 
C6 H6A OLC sing 479 n n 
C14 H14 OLC sing 480 n n 
C14 H14A OLC sing 481 n n 
C5 H5 OLC sing 482 n n 
C5 H5A OLC sing 483 n n 
C4 H4 OLC sing 484 n n 
C4 H4A OLC sing 485 n n 
C3 H3 OLC sing 486 n n 
C3 H3A OLC sing 487 n n 
C2 H2 OLC sing 488 n n 
C2 H2A OLC sing 489 n n 
C21 H21 OLC sing 490 n n 
C21 H21A OLC sing 491 n n 
C22 H22 OLC sing 492 n n 
O25 HO25 OLC sing 493 n n 
O23 HO23 OLC sing 494 n n 
#
_atom_sites.entry_id                     5K2D 
_atom_sites.fract_transf_matrix[1][1]    0.024777 
_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]    0.005533 
_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]    0.007003 
_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 ZMA A 1 1201 1201 ZMA ZMA . 
C 3 NA A 1 1202 1202 NA NA . 
D 4 CLR A 1 1203 1203 CLR CLR . 
E 4 CLR A 1 1204 1204 CLR CLR . 
F 4 CLR A 1 1205 1205 CLR CLR . 
G 5 OLB A 1 1206 1206 OLB OLB . 
H 6 OLC A 1 1207 1207 OLC OLC . 
I 6 OLC A 1 1208 1208 OLC OLC . 
J 6 OLC A 1 1209 1209 OLC OLC . 
K 5 OLB A 1 1210 1210 OLB OLB . 
L 6 OLC A 1 1211 1211 OLC OLC . 
M 6 OLC A 1 1212 1212 OLC OLC . 
N 7 OLA A 1 1213 1213 OLA OLA . 
O 7 OLA A 1 1214 1214 OLA OLA . 
P 7 OLA A 1 1215 1215 OLA OLA . 
Q 7 OLA A 1 1216 1216 OLA OLA . 
R 7 OLA A 1 1217 1217 OLA OLA . 
S 7 OLA A 1 1218 1218 OLA OLA . 
T 7 OLA A 1 1219 1219 OLA OLA . 
U 6 OLC A 1 1220 1220 OLC OLC . 
V 6 OLC A 1 1221 1221 OLC OLC . 
W 6 OLC A 1 1222 1222 OLC OLC . 
X 7 OLA A 1 1223 1223 OLA OLA . 
Y 7 OLA A 1 1224 1224 OLA OLA . 
Z 8 PEG A 1 1225 1225 PEG PEG . 
AA 7 OLA A 1 1226 1226 OLA OLA . 
BA 7 OLA A 1 1227 1227 OLA OLA . 
CA 9 HOH A 1 1301 1301 HOH HOH . 
CA 9 HOH A 2 1302 1302 HOH HOH . 
CA 9 HOH A 3 1303 1303 HOH HOH . 
CA 9 HOH A 4 1304 1304 HOH HOH . 
CA 9 HOH A 5 1305 1305 HOH HOH . 
CA 9 HOH A 6 1306 1306 HOH HOH . 
CA 9 HOH A 7 1307 1307 HOH HOH . 
CA 9 HOH A 8 1308 1308 HOH HOH . 
CA 9 HOH A 9 1309 1309 HOH HOH . 
CA 9 HOH A 10 1310 1310 HOH HOH . 
CA 9 HOH A 11 1311 1311 HOH HOH . 
CA 9 HOH A 12 1312 1312 HOH HOH . 
CA 9 HOH A 13 1313 1313 HOH HOH . 
CA 9 HOH A 14 1314 1314 HOH HOH . 
CA 9 HOH A 15 1315 1315 HOH HOH . 
CA 9 HOH A 16 1316 1316 HOH HOH . 
CA 9 HOH A 17 1317 1317 HOH HOH . 
CA 9 HOH A 18 1318 1318 HOH HOH . 
CA 9 HOH A 19 1319 1319 HOH HOH . 
CA 9 HOH A 20 1320 1320 HOH HOH . 
CA 9 HOH A 21 1321 1321 HOH HOH . 
CA 9 HOH A 22 1322 1322 HOH HOH . 
CA 9 HOH A 23 1323 1323 HOH HOH . 
CA 9 HOH A 24 1324 1324 HOH HOH . 
CA 9 HOH A 25 1325 1325 HOH HOH . 
CA 9 HOH A 26 1326 1326 HOH HOH . 
CA 9 HOH A 27 1327 1327 HOH HOH . 
CA 9 HOH A 28 1328 1328 HOH HOH . 
CA 9 HOH A 29 1329 1329 HOH HOH . 
CA 9 HOH A 30 1330 1330 HOH HOH . 
CA 9 HOH A 31 1331 1331 HOH HOH . 
CA 9 HOH A 32 1332 1332 HOH HOH . 
CA 9 HOH A 33 1333 1333 HOH HOH . 
CA 9 HOH A 34 1334 1334 HOH HOH . 
CA 9 HOH A 35 1335 1335 HOH HOH . 
CA 9 HOH A 36 1336 1336 HOH HOH . 
CA 9 HOH A 37 1337 1337 HOH HOH . 
CA 9 HOH A 38 1338 1338 HOH HOH . 
CA 9 HOH A 39 1339 1339 HOH HOH . 
CA 9 HOH A 40 1340 1340 HOH HOH . 
CA 9 HOH A 41 1341 1341 HOH HOH . 
CA 9 HOH A 42 1342 1342 HOH HOH . 
CA 9 HOH A 43 1343 1343 HOH HOH . 
CA 9 HOH A 44 1344 1344 HOH HOH . 
CA 9 HOH A 45 1345 1345 HOH HOH . 
CA 9 HOH A 46 1346 1346 HOH HOH . 
CA 9 HOH A 47 1347 1347 HOH HOH . 
CA 9 HOH A 48 1348 1348 HOH HOH . 
CA 9 HOH A 49 1349 1349 HOH HOH . 
CA 9 HOH A 50 1350 1350 HOH HOH . 
CA 9 HOH A 51 1351 1351 HOH HOH . 
CA 9 HOH A 52 1352 1352 HOH HOH . 
CA 9 HOH A 53 1353 1353 HOH HOH . 
CA 9 HOH A 54 1354 1354 HOH HOH . 
CA 9 HOH A 55 1355 1355 HOH HOH . 
CA 9 HOH A 56 1356 1356 HOH HOH . 
CA 9 HOH A 57 1357 1357 HOH HOH . 
CA 9 HOH A 58 1358 1358 HOH HOH . 
CA 9 HOH A 59 1359 1359 HOH HOH . 
CA 9 HOH A 60 1360 1360 HOH HOH . 
CA 9 HOH A 61 1361 1361 HOH HOH . 
CA 9 HOH A 62 1362 1362 HOH HOH . 
CA 9 HOH A 63 1363 1363 HOH HOH . 
CA 9 HOH A 64 1364 1364 HOH HOH . 
CA 9 HOH A 65 1365 1365 HOH HOH . 
CA 9 HOH A 66 1366 1366 HOH HOH . 
CA 9 HOH A 67 1367 1367 HOH HOH . 
CA 9 HOH A 68 1368 1368 HOH HOH . 
CA 9 HOH A 69 1369 1369 HOH HOH . 
CA 9 HOH A 70 1370 1370 HOH HOH . 
CA 9 HOH A 71 1371 1371 HOH HOH . 
CA 9 HOH A 72 1372 1372 HOH HOH . 
CA 9 HOH A 73 1373 1373 HOH HOH . 
CA 9 HOH A 74 1374 1374 HOH HOH . 
CA 9 HOH A 75 1375 1375 HOH HOH . 
CA 9 HOH A 76 1376 1376 HOH HOH . 
CA 9 HOH A 77 1377 1377 HOH HOH . 
CA 9 HOH A 78 1378 1378 HOH HOH . 
CA 9 HOH A 79 1379 1379 HOH HOH . 
CA 9 HOH A 80 1380 1380 HOH HOH . 
CA 9 HOH A 81 1381 1381 HOH HOH . 
CA 9 HOH A 82 1382 1382 HOH HOH . 
CA 9 HOH A 83 1383 1383 HOH HOH . 
CA 9 HOH A 84 1384 1384 HOH HOH . 
CA 9 HOH A 85 1385 1385 HOH HOH . 
CA 9 HOH A 86 1386 1386 HOH HOH . 
CA 9 HOH A 87 1387 1387 HOH HOH . 
CA 9 HOH A 88 1388 1388 HOH HOH . 
CA 9 HOH A 89 1389 1389 HOH HOH . 
CA 9 HOH A 90 1390 1390 HOH HOH . 
CA 9 HOH A 91 1391 1391 HOH HOH . 
CA 9 HOH A 92 1392 1392 HOH HOH . 
CA 9 HOH A 93 1393 1393 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 C10 OLC . . . I 6 37.253 187.96 18.578 1 70.55 ? C10 OLC 1208 A 1 
HETATM 2 C C9 OLC . . . I 6 36.671 188.881 17.812 1 70.88 ? C9 OLC 1208 A 1 
HETATM 3 C C8 OLC . . . I 6 35.913 190.032 18.433 1 70.78 ? C8 OLC 1208 A 1 
HETATM 4 C C24 OLC . . . I 6 35.608 203.718 18.832 1 90.58 ? C24 OLC 1208 A 1 
HETATM 5 C C7 OLC . . . I 6 36.213 191.307 17.655 1 69.4 ? C7 OLC 1208 A 1 
HETATM 6 C C6 OLC . . . I 6 35.912 192.544 18.488 1 69.13 ? C6 OLC 1208 A 1 
HETATM 7 C C5 OLC . . . I 6 36.226 193.825 17.732 1 71.03 ? C5 OLC 1208 A 1 
HETATM 8 C C4 OLC . . . I 6 35.783 195.005 18.581 1 74.88 ? C4 OLC 1208 A 1 
HETATM 9 C C3 OLC . . . I 6 36.259 196.327 18 1 77.64 ? C3 OLC 1208 A 1 
HETATM 10 C C2 OLC . . . I 6 35.655 197.483 18.787 1 82.63 ? C2 OLC 1208 A 1 
HETATM 11 C C21 OLC . . . I 6 36.106 201.297 18.374 1 92.59 ? C21 OLC 1208 A 1 
HETATM 12 C C1 OLC . . . I 6 36.057 198.8 18.154 1 89.47 ? C1 OLC 1208 A 1 
HETATM 13 C C22 OLC . . . I 6 35.034 202.375 18.382 1 90.67 ? C22 OLC 1208 A 1 
HETATM 14 O O19 OLC . . . I 6 36.877 198.845 17.248 1 91.22 ? O19 OLC 1208 A 1 
HETATM 15 O O25 OLC . . . I 6 34.578 204.544 19.396 1 90.51 ? O25 OLC 1208 A 1 
HETATM 16 O O23 OLC . . . I 6 34.567 202.47 17.039 1 89.08 ? O23 OLC 1208 A 1 
HETATM 17 O O20 OLC . . . I 6 35.466 200.045 18.621 1 92.75 ? O20 OLC 1208 A 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           118 
_model_server_stats.create_model_time_ms    60 
_model_server_stats.query_time_ms           492 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           17 
#