data_7BAY
#
_model_server_result.job_id            D30r1PTFtKSJrWViBuc9pg 
_model_server_result.datetime_utc      '2025-07-08 01:08:58' 
_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          7bay 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":1411}' 
#
_entry.id    7BAY 
#
_exptl.entry_id    7BAY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              622.518 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'neutral Yb(III)-caged complex' 
_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            7BAY 
_cell.length_a            114.904 
_cell.length_b            52.207 
_cell.length_c            73.99 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7BAY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    'P 2 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             L 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C21 H29 N4 O7 Yb 4' 
_chem_comp.formula_weight    622.518 
_chem_comp.id                T7K 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'neutral Yb(III)-caged complex' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '8-[(4-hydroxyphenyl)methyl]-2,17,18-trioxa-5,8,11,14-tetraza-1(gamma)-ytterbatricyclo[9.6.3.25,14]docosane-3,16,19-trione;Yb(III) clathrochelate' 
#
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
C4 C3 T7K sing 333 n n 
C4 N3 T7K sing 334 n n 
C2 C1 T7K sing 335 n n 
C2 N2 T7K sing 336 n n 
C3 N2 T7K sing 337 n n 
C1 N1 T7K sing 338 n n 
C7 C8 T7K sing 339 n n 
C7 N4 T7K sing 340 n n 
C6 C5 T7K sing 341 n n 
C6 N4 T7K sing 342 n n 
C8 N1 T7K sing 343 n n 
C12 C11 T7K sing 344 n n 
C12 N2 T7K sing 345 n n 
C16 C01 T7K sing 346 n n 
C16 N4 T7K sing 347 n n 
C13 C14 T7K sing 348 n n 
C13 O6 T7K sing 349 n n 
C13 O5 T7K doub 350 n n 
C9 O2 T7K sing 351 n n 
C9 O1 T7K doub 352 n n 
C9 C10 T7K sing 353 n n 
C5 N3 T7K sing 354 n n 
C11 O3 T7K doub 355 n n 
C11 O4 T7K sing 356 n n 
N1 C10 T7K sing 357 n n 
YB N2 T7K sing 358 n n 
C01 C02 T7K doub 359 n y 
C01 C06 T7K sing 360 n y 
C02 C03 T7K sing 361 n y 
C03 C04 T7K doub 362 n y 
C04 C05 T7K sing 363 n y 
C04 O01 T7K sing 364 n n 
C05 C06 T7K doub 365 n y 
C14 N3 T7K sing 366 n n 
N1 YB T7K sing 367 n n 
YB N3 T7K sing 368 n n 
N4 YB T7K sing 369 n n 
YB O2 T7K sing 370 n n 
YB O4 T7K sing 371 n n 
YB O6 T7K sing 372 n n 
C4 H1 T7K sing 373 n n 
C4 H2 T7K sing 374 n n 
C2 H3 T7K sing 375 n n 
C2 H4 T7K sing 376 n n 
C3 H5 T7K sing 377 n n 
C3 H6 T7K sing 378 n n 
C1 H7 T7K sing 379 n n 
C1 H8 T7K sing 380 n n 
C7 H9 T7K sing 381 n n 
C7 H10 T7K sing 382 n n 
C6 H11 T7K sing 383 n n 
C6 H12 T7K sing 384 n n 
C8 H13 T7K sing 385 n n 
C8 H14 T7K sing 386 n n 
C12 H15 T7K sing 387 n n 
C12 H16 T7K sing 388 n n 
C16 H17 T7K sing 389 n n 
C16 H18 T7K sing 390 n n 
C5 H19 T7K sing 391 n n 
C5 H20 T7K sing 392 n n 
C02 H21 T7K sing 393 n n 
C03 H22 T7K sing 394 n n 
C05 H23 T7K sing 395 n n 
C06 H24 T7K sing 396 n n 
C10 H25 T7K sing 397 n n 
C10 H26 T7K sing 398 n n 
C14 H27 T7K sing 399 n n 
C14 H28 T7K sing 400 n n 
O01 H29 T7K sing 401 n n 
#
_atom_sites.entry_id                     7BAY 
_atom_sites.fract_transf_matrix[1][1]    0.008703 
_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]    0.019155 
_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]    0.013515 
_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 CHT AA 1 1401 1401 CHT CHT . 
C 2 CHT AA 1 1402 1501 CHT CHT . 
D 2 CHT AA 1 1403 1701 CHT CHT . 
E 3 PGE AA 1 1404 1801 PGE PGE . 
F 2 CHT AA 1 1405 1901 CHT CHT . 
G 2 CHT AA 1 1406 2001 CHT CHT . 
H 4 GOL AA 1 1407 2101 GOL GOL . 
I 2 CHT AA 1 1408 2201 CHT CHT . 
J 4 GOL AA 1 1409 2301 GOL GOL . 
K 4 GOL AA 1 1410 2401 GOL GOL . 
L 5 T7K AA 1 1411 2501 T7K 201 . 
M 6 HOH AA 1 1501 38 HOH HOH . 
M 6 HOH AA 2 1502 9 HOH HOH . 
M 6 HOH AA 3 1503 27 HOH HOH . 
M 6 HOH AA 4 1504 28 HOH HOH . 
M 6 HOH AA 5 1505 41 HOH HOH . 
M 6 HOH AA 6 1506 1 HOH HOH . 
M 6 HOH AA 7 1507 11 HOH HOH . 
M 6 HOH AA 8 1508 2 HOH HOH . 
M 6 HOH AA 9 1509 3 HOH HOH . 
M 6 HOH AA 10 1510 7 HOH HOH . 
M 6 HOH AA 11 1511 13 HOH HOH . 
M 6 HOH AA 12 1512 39 HOH HOH . 
M 6 HOH AA 13 1513 16 HOH HOH . 
M 6 HOH AA 14 1514 6 HOH HOH . 
M 6 HOH AA 15 1515 4 HOH HOH . 
M 6 HOH AA 16 1516 36 HOH HOH . 
M 6 HOH AA 17 1517 5 HOH HOH . 
M 6 HOH AA 18 1518 8 HOH HOH . 
M 6 HOH AA 19 1519 24 HOH HOH . 
M 6 HOH AA 20 1520 19 HOH HOH . 
M 6 HOH AA 21 1521 10 HOH HOH . 
M 6 HOH AA 22 1522 17 HOH HOH . 
M 6 HOH AA 23 1523 18 HOH HOH . 
M 6 HOH AA 24 1524 33 HOH HOH . 
M 6 HOH AA 25 1525 22 HOH HOH . 
M 6 HOH AA 26 1526 14 HOH HOH . 
M 6 HOH AA 27 1527 37 HOH HOH . 
M 6 HOH AA 28 1528 43 HOH HOH . 
M 6 HOH AA 29 1529 12 HOH HOH . 
M 6 HOH AA 30 1530 47 HOH HOH . 
M 6 HOH AA 31 1531 31 HOH HOH . 
M 6 HOH AA 32 1532 46 HOH HOH . 
M 6 HOH AA 33 1533 44 HOH HOH . 
M 6 HOH AA 34 1534 23 HOH HOH . 
M 6 HOH AA 35 1535 29 HOH HOH . 
M 6 HOH AA 36 1536 25 HOH HOH . 
M 6 HOH AA 37 1537 32 HOH HOH . 
M 6 HOH AA 38 1538 26 HOH HOH . 
M 6 HOH AA 39 1539 42 HOH HOH . 
M 6 HOH AA 40 1540 48 HOH HOH . 
M 6 HOH AA 41 1541 15 HOH HOH . 
M 6 HOH AA 42 1542 35 HOH HOH . 
M 6 HOH AA 43 1543 45 HOH HOH . 
M 6 HOH AA 44 1544 30 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 C4 T7K . . . L 5 5.13 -29.669 57.121 1 86.35 ? C4 T7K 1411 AA 1 
HETATM 2 C C2 T7K . . . L 5 5.994 -31.5 54.722 1 82.07 ? C2 T7K 1411 AA 1 
HETATM 3 C C3 T7K . . . L 5 5.597 -31.145 57.084 1 87.65 ? C3 T7K 1411 AA 1 
HETATM 4 C C1 T7K . . . L 5 5.47 -32.199 53.444 1 85.13 ? C1 T7K 1411 AA 1 
HETATM 5 C C7 T7K . . . L 5 3.624 -29.015 52.869 1 81.97 ? C7 T7K 1411 AA 1 
HETATM 6 C C6 T7K . . . L 5 3.752 -28.056 55.086 1 76.2 ? C6 T7K 1411 AA 1 
HETATM 7 C C8 T7K . . . L 5 4.885 -29.895 53.106 1 77.3 ? C8 T7K 1411 AA 1 
HETATM 8 C C12 T7K . . . L 5 5.036 -33.258 56.061 1 90.94 ? C12 T7K 1411 AA 1 
HETATM 9 C C16 T7K . . . L 5 1.62 -28.122 53.924 1 78.5 ? C16 T7K 1411 AA 1 
HETATM 10 C C13 T7K . . . L 5 1.519 -29.986 58.234 1 96.38 ? C13 T7K 1411 AA 1 
HETATM 11 C C9 T7K . . . L 5 2.82 -33.017 53.218 1 86.39 ? C9 T7K 1411 AA 1 
HETATM 12 C C5 T7K . . . L 5 3.237 -28.271 56.55 1 78.91 ? C5 T7K 1411 AA 1 
HETATM 13 C C11 T7K . . . L 5 4.023 -33.578 57.195 1 93.08 ? C11 T7K 1411 AA 1 
HETATM 14 O O3 T7K . . . L 5 4.417 -34.154 58.257 1 92.42 ? O3 T7K 1411 AA 1 
HETATM 15 N N1 T7K . . . L 5 4.635 -31.27 52.659 1 85.8 ? N1 T7K 1411 AA 1 
HETATM 16 O O2 T7K . . . L 5 3.613 -33.996 53.116 1 91.24 ? O2 T7K 1411 AA 1 
HETATM 17 O O1 T7K . . . L 5 1.659 -33.207 53.67 1 82.1 ? O1 T7K 1411 AA 1 
HETATM 18 YB YB T7K . . . L 5 2.952 -31.115 55.215 1 90.12 ? YB T7K 1411 AA 1 
HETATM 19 C C01 T7K . . . L 5 1.869 -26.698 53.329 1 81.83 ? C01 T7K 1411 AA 1 
HETATM 20 C C02 T7K . . . L 5 2.198 -25.511 54.268 1 76.81 ? C02 T7K 1411 AA 1 
HETATM 21 C C03 T7K . . . L 5 2.405 -24.305 53.766 1 80.26 ? C03 T7K 1411 AA 1 
HETATM 22 C C04 T7K . . . L 5 2.307 -24.078 52.26 1 89.63 ? C04 T7K 1411 AA 1 
HETATM 23 C C05 T7K . . . L 5 2.017 -25.091 51.453 1 85.21 ? C05 T7K 1411 AA 1 
HETATM 24 C C06 T7K . . . L 5 1.778 -26.502 52.039 1 85.68 ? C06 T7K 1411 AA 1 
HETATM 25 C C10 T7K . . . L 5 3.198 -31.575 52.794 1 80.57 ? C10 T7K 1411 AA 1 
HETATM 26 C C14 T7K . . . L 5 3.049 -29.846 58.351 1 95.13 ? C14 T7K 1411 AA 1 
HETATM 27 N N2 T7K . . . L 5 5.091 -31.803 55.85 1 87.93 ? N2 T7K 1411 AA 1 
HETATM 28 N N3 T7K . . . L 5 3.636 -29.604 57.021 1 86.3 ? N3 T7K 1411 AA 1 
HETATM 29 N N4 T7K . . . L 5 2.912 -28.825 54.147 1 84.28 ? N4 T7K 1411 AA 1 
HETATM 30 O O01 T7K . . . L 5 2.527 -22.783 51.726 1 83.4 ? O01 T7K 1411 AA 1 
HETATM 31 O O4 T7K . . . L 5 2.808 -33.268 57.059 1 94.86 ? O4 T7K 1411 AA 1 
HETATM 32 O O6 T7K . . . L 5 0.791 -29.782 59.242 1 98.9 ? O6 T7K 1411 AA 1 
HETATM 33 O O5 T7K . . . L 5 0.992 -30.304 57.132 1 93.92 ? O5 T7K 1411 AA 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           33 
#