data_5KMG
#
_model_server_result.job_id            0xRV0KGaxdkRFGIcDa3stw 
_model_server_result.datetime_utc      '2025-07-14 06:28:07' 
_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          5kmg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":502}' 
#
_entry.id    5KMG 
#
_exptl.entry_id    5KMG 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              548.663 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'Peloruside A' 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? 42-meric 42 'representative helical assembly' 1 
? trimeric 3 'helical asymmetric unit' 2 
? trimeric 3 'helical asymmetric unit, std helical frame' 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G 1 (1-14) 
A,B,C,D,E,F,G 2 8 
A,B,C,D,E,F,G 3 H 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'helical symmetry operation' ? ? -0.898181 0.439626 0 -0.439626 -0.898181 0 0 0 1 492.99173 790.17869 -69.36 
3 'helical symmetry operation' ? ? -0.999984 0.005585 0 -0.005585 -0.999984 0 0 0 1 674.10699 677.88247 -60.69 
4 'helical symmetry operation' ? ? -0.903036 -0.429566 0 0.429566 -0.903036 0 0 0 1 788.41924 498.03284 -52.02 
5 'helical symmetry operation' ? ? -0.626604 -0.779338 0 0.779338 -0.626604 0 0 0 1 813.20832 286.37586 -43.35 
6 'helical symmetry operation' ? ? -0.225631 -0.974213 0 0.974213 -0.225631 0 0 0 1 743.54728 84.97944 -34.68 
7 'helical symmetry operation' ? ? 0.220187 -0.975458 0 0.975458 0.220187 0 0 0 1 593.28161 -66.12783 -26.01 
8 'helical symmetry operation' ? ? 0.622241 -0.782825 0 0.782825 0.622241 0 0 0 1 392.27739 -136.91259 -17.34 
9 'helical symmetry operation' ? ? 0.900622 -0.434602 0 0.434602 0.900622 0 0 0 1 180.48526 -113.306 -8.67 
10 'helical symmetry operation' ? ? 0.900622 0.434602 0 -0.434602 0.900622 0 0 0 1 -113.306 180.48526 8.67 
11 'helical symmetry operation' ? ? 0.622241 0.782825 0 -0.782825 0.622241 0 0 0 1 -136.91259 392.27739 17.34 
12 'helical symmetry operation' ? ? 0.220187 0.975458 0 -0.975458 0.220187 0 0 0 1 -66.12783 593.28161 26.01 
13 'helical symmetry operation' ? ? -0.225631 0.974213 0 -0.974213 -0.225631 0 0 0 1 84.97944 743.54728 34.68 
14 'helical symmetry operation' ? ? -0.626604 0.779338 0 -0.779338 -0.626604 0 0 0 1 286.37586 813.20832 43.35 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      7 
_struct_asym.id                             G 
_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
metalc ? metalc1 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? 
metalc ? metalc2 D O1B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? 
#
_chem_comp.formula           'C27 H48 O11' 
_chem_comp.formula_weight    548.663 
_chem_comp.id                POU 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'Peloruside A' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     (1R,3R,4S,7S,9S,11S,13R,14R,15R)-4,11,13,14-tetrahydroxy-7-[(2Z,4R)-4-(hydroxymethyl)hex-2-en-2-yl]-3,9,15-trimethoxy-12,12-dimethyl-6,17-dioxabicyclo[11.3.1]heptadecan-5-one 
#
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
C17 O7 POU sing 353 n n 
O7 C7 POU sing 354 n n 
C7 C6 POU sing 355 n n 
C7 C8 POU sing 356 n n 
O2 C2 POU sing 357 n n 
C6 C5 POU sing 358 n n 
C5 C4 POU sing 359 n n 
C5 O9 POU sing 360 n n 
C2 C1 POU sing 361 n n 
C2 C3 POU sing 362 n n 
O24 C24 POU sing 363 n n 
O91 C9 POU sing 364 n n 
O1 C1 POU doub 365 n n 
C8 C9 POU sing 366 n n 
C8 O8 POU sing 367 n n 
C4 C3 POU sing 368 n n 
C1 O15 POU sing 369 n n 
C24 C23 POU sing 370 n n 
C9 O9 POU sing 371 n n 
C9 C10 POU sing 372 n n 
C3 O3 POU sing 373 n n 
O3 C16 POU sing 374 n n 
O15 C15 POU sing 375 n n 
C23 C26 POU sing 376 n n 
C23 C22 POU sing 377 n n 
C19 C10 POU sing 378 n n 
C10 C11 POU sing 379 n n 
C10 C18 POU sing 380 n n 
O13 C20 POU sing 381 n n 
O13 C13 POU sing 382 n n 
C26 C27 POU sing 383 n n 
C11 C12 POU sing 384 n n 
C11 O11 POU sing 385 n n 
C15 C21 POU sing 386 n n 
C15 C14 POU sing 387 n n 
C22 C21 POU doub 388 z n 
C12 C13 POU sing 389 n n 
C21 C25 POU sing 390 n n 
C13 C14 POU sing 391 n n 
C27 H1 POU sing 392 n n 
C27 H2 POU sing 393 n n 
C27 H3 POU sing 394 n n 
C20 H4 POU sing 395 n n 
C20 H5 POU sing 396 n n 
C20 H6 POU sing 397 n n 
C16 H7 POU sing 398 n n 
C16 H8 POU sing 399 n n 
C16 H9 POU sing 400 n n 
C17 H10 POU sing 401 n n 
C17 H11 POU sing 402 n n 
C17 H12 POU sing 403 n n 
C25 H13 POU sing 404 n n 
C25 H14 POU sing 405 n n 
C25 H15 POU sing 406 n n 
C18 H16 POU sing 407 n n 
C18 H17 POU sing 408 n n 
C18 H18 POU sing 409 n n 
C19 H19 POU sing 410 n n 
C19 H20 POU sing 411 n n 
C19 H21 POU sing 412 n n 
C22 H22 POU sing 413 n n 
C26 H23 POU sing 414 n n 
C26 H24 POU sing 415 n n 
C24 H25 POU sing 416 n n 
C24 H26 POU sing 417 n n 
C12 H27 POU sing 418 n n 
C12 H28 POU sing 419 n n 
C14 H29 POU sing 420 n n 
C14 H30 POU sing 421 n n 
C4 H31 POU sing 422 n n 
C4 H32 POU sing 423 n n 
C6 H33 POU sing 424 n n 
C6 H34 POU sing 425 n n 
O24 H35 POU sing 426 n n 
O11 H36 POU sing 427 n n 
O2 H37 POU sing 428 n n 
O8 H38 POU sing 429 n n 
O91 H39 POU sing 430 n n 
C23 H40 POU sing 431 n n 
C11 H41 POU sing 432 n n 
C13 H42 POU sing 433 n n 
C5 H43 POU sing 434 n n 
C2 H44 POU sing 435 n n 
C8 H45 POU sing 436 n n 
C15 H46 POU sing 437 n n 
C3 H47 POU sing 438 n n 
C7 H48 POU sing 439 n n 
#
_atom_sites.entry_id                     5KMG 
_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 GTP A 1 501 1 GTP GTP . 
E 5 MG A 1 502 2 MG MG . 
F 6 GDP B 1 501 1 GDP GDP . 
G 7 POU B 1 502 3 POU POU . 
#
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 C27 POU . . . G 7 375.03 456.635 292.252 1 47.59 ? C27 POU 502 B 1 
HETATM 2 C C20 POU . . . G 7 376.744 453.106 292.363 1 42.89 ? C20 POU 502 B 1 
HETATM 3 C C16 POU . . . G 7 381.517 455.785 286.577 1 45.25 ? C16 POU 502 B 1 
HETATM 4 C C17 POU . . . G 7 381.33 446.847 286.47 1 53.84 ? C17 POU 502 B 1 
HETATM 5 C C25 POU . . . G 7 378.9 457.77 289.458 1 33.35 ? C25 POU 502 B 1 
HETATM 6 C C18 POU . . . G 7 382.548 451.19 290.377 1 41.09 ? C18 POU 502 B 1 
HETATM 7 C C19 POU . . . G 7 381.2 449.147 290.869 1 43.77 ? C19 POU 502 B 1 
HETATM 8 C C22 POU . . . G 7 376.269 457.548 289.56 1 23.19 ? C22 POU 502 B 1 
HETATM 9 C C26 POU . . . G 7 374.198 456.98 291.002 1 41.28 ? C26 POU 502 B 1 
HETATM 10 C C24 POU . . . G 7 374.037 457.074 288.563 1 29.96 ? C24 POU 502 B 1 
HETATM 11 C C12 POU . . . G 7 379.981 452.917 290.417 1 43.01 ? C12 POU 502 B 1 
HETATM 12 C C14 POU . . . G 7 378.631 455.046 291.19 1 55.12 ? C14 POU 502 B 1 
HETATM 13 C C4 POU . . . G 7 380.888 453.085 286.023 1 46.34 ? C4 POU 502 B 1 
HETATM 14 C C6 POU . . . G 7 381.472 450.543 285.792 1 60.45 ? C6 POU 502 B 1 
HETATM 15 C C21 POU . . . G 7 377.676 456.873 289.626 1 31.78 ? C21 POU 502 B 1 
HETATM 16 O O1 POU . . . G 7 376.77 454.854 287.189 1 41.17 ? O1 POU 502 B 1 
HETATM 17 O O24 POU . . . G 7 372.892 456.228 288.657 1 24.41 ? O24 POU 502 B 1 
HETATM 18 O O11 POU . . . G 7 380.46 451.542 292.32 1 47.22 ? O11 POU 502 B 1 
HETATM 19 O O2 POU . . . G 7 378.24 453.692 285.391 1 55.69 ? O2 POU 502 B 1 
HETATM 20 O O8 POU . . . G 7 383.02 449.454 287.995 1 78.95 ? O8 POU 502 B 1 
HETATM 21 O O91 POU . . . G 7 379.473 449.989 288.601 1 81.06 ? O91 POU 502 B 1 
HETATM 22 O O13 POU . . . G 7 377.615 452.795 291.28 1 38.93 ? O13 POU 502 B 1 
HETATM 23 O O3 POU . . . G 7 380.174 455.337 286.423 1 40.44 ? O3 POU 502 B 1 
HETATM 24 O O7 POU . . . G 7 381.701 448.053 285.787 1 61.18 ? O7 POU 502 B 1 
HETATM 25 O O15 POU . . . G 7 378.431 454.589 288.747 1 42.8 ? O15 POU 502 B 1 
HETATM 26 O O9 POU . . . G 7 380.957 451.599 287.992 1 72.11 ? O9 POU 502 B 1 
HETATM 27 C C1 POU . . . G 7 377.838 454.389 287.549 1 43.35 ? C1 POU 502 B 1 
HETATM 28 C C23 POU . . . G 7 374.984 456.712 289.699 1 37.83 ? C23 POU 502 B 1 
HETATM 29 C C11 POU . . . G 7 380.152 451.487 290.886 1 48.87 ? C11 POU 502 B 1 
HETATM 30 C C13 POU . . . G 7 378.895 453.505 291.347 1 37.96 ? C13 POU 502 B 1 
HETATM 31 C C5 POU . . . G 7 380.704 451.629 286.556 1 67.46 ? C5 POU 502 B 1 
HETATM 32 C C2 POU . . . G 7 378.636 453.572 286.764 1 48.92 ? C2 POU 502 B 1 
HETATM 33 C C8 POU . . . G 7 381.609 449.227 287.962 1 77.64 ? C8 POU 502 B 1 
HETATM 34 C C15 POU . . . G 7 377.932 455.369 289.828 1 34.28 ? C15 POU 502 B 1 
HETATM 35 C C3 POU . . . G 7 380.051 453.998 286.884 1 44.22 ? C3 POU 502 B 1 
HETATM 36 C C7 POU . . . G 7 381.155 449.192 286.48 1 60.41 ? C7 POU 502 B 1 
HETATM 37 C C10 POU . . . G 7 381.184 450.518 290.202 1 44.42 ? C10 POU 502 B 1 
HETATM 38 C C9 POU . . . G 7 380.87 450.329 288.676 1 77 ? C9 POU 502 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           446 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           38 
#