data_5YFE
#
_model_server_result.job_id            Z4s-cPQibBl7yhZ4QGwY1g 
_model_server_result.datetime_utc      '2025-01-10 07:45:35' 
_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          5yfe 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":304}' 
#
_entry.id    5YFE 
#
_exptl.entry_id    5YFE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_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            5YFE 
_cell.length_a            50.945 
_cell.length_b            56.644 
_cell.length_c            80.611 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YFE 
_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 
_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 
#
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 177 A CYS 177 1_555 A SG CYS 213 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf2 A SG CYS 247 A CYS 247 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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
C1 O1 GOL sing 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     5YFE 
_atom_sites.fract_transf_matrix[1][1]    0.019629 
_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]    0.017654 
_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]    0.012405 
_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 SO4 A 1 301 2 SO4 SO4 . 
C 2 SO4 A 1 302 6 SO4 SO4 . 
D 3 GOL A 1 303 15 GOL GOL . 
E 3 GOL A 1 304 16 GOL GOL . 
F 4 HOH A 1 401 65 HOH HOH . 
F 4 HOH A 2 402 417 HOH HOH . 
F 4 HOH A 3 403 262 HOH HOH . 
F 4 HOH A 4 404 284 HOH HOH . 
F 4 HOH A 5 405 19 HOH HOH . 
F 4 HOH A 6 406 272 HOH HOH . 
F 4 HOH A 7 407 45 HOH HOH . 
F 4 HOH A 8 408 243 HOH HOH . 
F 4 HOH A 9 409 399 HOH HOH . 
F 4 HOH A 10 410 402 HOH HOH . 
F 4 HOH A 11 411 415 HOH HOH . 
F 4 HOH A 12 412 407 HOH HOH . 
F 4 HOH A 13 413 432 HOH HOH . 
F 4 HOH A 14 414 410 HOH HOH . 
F 4 HOH A 15 415 172 HOH HOH . 
F 4 HOH A 16 416 24 HOH HOH . 
F 4 HOH A 17 417 23 HOH HOH . 
F 4 HOH A 18 418 305 HOH HOH . 
F 4 HOH A 19 419 11 HOH HOH . 
F 4 HOH A 20 420 8 HOH HOH . 
F 4 HOH A 21 421 431 HOH HOH . 
F 4 HOH A 22 422 247 HOH HOH . 
F 4 HOH A 23 423 159 HOH HOH . 
F 4 HOH A 24 424 405 HOH HOH . 
F 4 HOH A 25 425 202 HOH HOH . 
F 4 HOH A 26 426 424 HOH HOH . 
F 4 HOH A 27 427 414 HOH HOH . 
F 4 HOH A 28 428 141 HOH HOH . 
F 4 HOH A 29 429 404 HOH HOH . 
F 4 HOH A 30 430 397 HOH HOH . 
F 4 HOH A 31 431 266 HOH HOH . 
F 4 HOH A 32 432 422 HOH HOH . 
F 4 HOH A 33 433 279 HOH HOH . 
F 4 HOH A 34 434 310 HOH HOH . 
F 4 HOH A 35 435 428 HOH HOH . 
F 4 HOH A 36 436 251 HOH HOH . 
F 4 HOH A 37 437 418 HOH HOH . 
F 4 HOH A 38 438 162 HOH HOH . 
F 4 HOH A 39 439 241 HOH HOH . 
F 4 HOH A 40 440 433 HOH HOH . 
F 4 HOH A 41 441 31 HOH HOH . 
F 4 HOH A 42 442 412 HOH HOH . 
F 4 HOH A 43 443 426 HOH HOH . 
F 4 HOH A 44 444 411 HOH HOH . 
F 4 HOH A 45 445 164 HOH HOH . 
F 4 HOH A 46 446 129 HOH HOH . 
F 4 HOH A 47 447 423 HOH HOH . 
F 4 HOH A 48 448 38 HOH HOH . 
F 4 HOH A 49 449 248 HOH HOH . 
F 4 HOH A 50 450 409 HOH HOH . 
F 4 HOH A 51 451 264 HOH HOH . 
F 4 HOH A 52 452 271 HOH HOH . 
F 4 HOH A 53 453 300 HOH HOH . 
F 4 HOH A 54 454 240 HOH HOH . 
F 4 HOH A 55 455 400 HOH HOH . 
F 4 HOH A 56 456 117 HOH HOH . 
F 4 HOH A 57 457 62 HOH HOH . 
F 4 HOH A 58 458 294 HOH HOH . 
F 4 HOH A 59 459 242 HOH HOH . 
F 4 HOH A 60 460 255 HOH HOH . 
F 4 HOH A 61 461 287 HOH HOH . 
F 4 HOH A 62 462 256 HOH HOH . 
F 4 HOH A 63 463 301 HOH HOH . 
F 4 HOH A 64 464 419 HOH HOH . 
F 4 HOH A 65 465 274 HOH HOH . 
F 4 HOH A 66 466 286 HOH HOH . 
F 4 HOH A 67 467 403 HOH HOH . 
F 4 HOH A 68 468 283 HOH HOH . 
F 4 HOH A 69 469 408 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 C1 GOL . . . E 3 -2.136 52.008 21.625 1 19.07 ? C1 GOL 304 A 1 
HETATM 2 O O1 GOL . . . E 3 -0.873 51.412 21.429 1 24.15 ? O1 GOL 304 A 1 
HETATM 3 C C2 GOL . . . E 3 -1.983 53.508 21.564 1 17.33 ? C2 GOL 304 A 1 
HETATM 4 O O2 GOL . . . E 3 -1.254 53.943 22.676 1 19.07 ? O2 GOL 304 A 1 
HETATM 5 C C3 GOL . . . E 3 -1.321 53.782 20.261 1 20.88 ? C3 GOL 304 A 1 
HETATM 6 O O3 GOL . . . E 3 -1.369 55.163 20.111 1 18.22 ? O3 GOL 304 A 1 
HETATM 7 H H11 GOL . . . E 3 -2.538 51.715 22.595 1 22.88 ? H11 GOL 304 A 1 
HETATM 8 H H12 GOL . . . E 3 -2.828 51.674 20.852 1 22.88 ? H12 GOL 304 A 1 
HETATM 9 H HO1 GOL . . . E 3 -0.931 50.448 21.584 1 28.98 ? HO1 GOL 304 A 1 
HETATM 10 H H2 GOL . . . E 3 -2.973 53.965 21.562 1 20.8 ? H2 GOL 304 A 1 
HETATM 11 H HO2 GOL . . . E 3 -0.304 53.823 22.494 1 22.88 ? HO2 GOL 304 A 1 
HETATM 12 H H31 GOL . . . E 3 -1.853 53.289 19.448 1 25.06 ? H31 GOL 304 A 1 
HETATM 13 H H32 GOL . . . E 3 -0.284 53.446 20.266 1 25.06 ? H32 GOL 304 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           215 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           13 
#