data_5JDM # _model_server_result.job_id WNVTPjcwPsgc75XIOgSm6w _model_server_result.datetime_utc '2024-11-15 03:50:52' _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 5jdm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":416}' # _entry.id 5JDM # _exptl.entry_id 5JDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 250.332 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3,6,9,12,15-PENTAOXAHEPTADECANE _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 5JDM _cell.length_a 49.802 _cell.length_b 72.267 _cell.length_c 94.839 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JDM _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,G,H,I,J,K,L,M,N,O,P,Q,R,S _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 7 _struct_asym.id Q _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 A O ALA 47 A ALA 47 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc2 A OG1 THR 50 A THR 50 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc3 A O THR 50 A THR 50 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc4 A OG SER 51 A SER 51 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc5 A OE1 GLU 54 A GLU 54 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc6 A OE2 GLU 54 A GLU 54 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc7 A O ILE 118 A ILE 118 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc8 A OD1 ASP 121 A ASP 121 1_555 D SR SR . A SR 403 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc9 A OD2 ASP 121 A ASP 121 1_555 D SR SR . A SR 403 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc10 A OD2 ASP 127 A ASP 127 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc11 A O THR 209 A THR 209 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc12 A OE2 GLU 213 A GLU 213 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc13 A OE1 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc14 A OE2 GLU 213 A GLU 213 1_555 C NA NA . A NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc15 A OG SER 236 A SER 236 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? # _chem_comp.formula 'C12 H26 O5' _chem_comp.formula_weight 250.332 _chem_comp.id P3G _chem_comp.mon_nstd_flag . _chem_comp.name 3,6,9,12,15-PENTAOXAHEPTADECANE _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 C5 C6 P3G sing 384 n n C5 H51 P3G sing 385 n n C5 H5 P3G sing 386 n n C5 H52 P3G sing 387 n n C6 O3 P3G sing 388 n n C6 H61 P3G sing 389 n n C6 H62 P3G sing 390 n n O3 C7 P3G sing 391 n n C7 C8 P3G sing 392 n n C7 H71 P3G sing 393 n n C7 H72 P3G sing 394 n n C8 O4 P3G sing 395 n n C8 H81 P3G sing 396 n n C8 H82 P3G sing 397 n n O4 C9 P3G sing 398 n n C9 C10 P3G sing 399 n n C9 H91 P3G sing 400 n n C9 H92 P3G sing 401 n n C10 O5 P3G sing 402 n n C10 H101 P3G sing 403 n n C10 H102 P3G sing 404 n n O5 C11 P3G sing 405 n n C11 C12 P3G sing 406 n n C11 H111 P3G sing 407 n n C11 H112 P3G sing 408 n n C12 O6 P3G sing 409 n n C12 H121 P3G sing 410 n n C12 H122 P3G sing 411 n n O6 C13 P3G sing 412 n n C13 C14 P3G sing 413 n n C13 H131 P3G sing 414 n n C13 H132 P3G sing 415 n n C14 O7 P3G sing 416 n n C14 H141 P3G sing 417 n n C14 H142 P3G sing 418 n n O7 C15 P3G sing 419 n n C15 C16 P3G sing 420 n n C15 H151 P3G sing 421 n n C15 H152 P3G sing 422 n n C16 H16 P3G sing 423 n n C16 H162 P3G sing 424 n n C16 H161 P3G sing 425 n n # _atom_sites.entry_id 5JDM _atom_sites.fract_transf_matrix[1][1] 0.02008 _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] 0.013838 _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] 0.010544 _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 NA A 1 401 1 NA NA . C 2 NA A 1 402 2 NA NA . D 3 SR A 1 403 1 SR SR . E 4 OLC A 1 404 1 OLC MON . F 4 OLC A 1 405 2 OLC MON . G 5 MYS A 1 406 1 MYS FAT . H 5 MYS A 1 407 3 MYS FAT . I 5 MYS A 1 408 4 MYS FAT . J 5 MYS A 1 409 5 MYS FAT . K 5 MYS A 1 410 6 MYS FAT . L 5 MYS A 1 411 7 MYS FAT . M 5 MYS A 1 412 8 MYS FAT . N 5 MYS A 1 413 9 MYS FAT . O 5 MYS A 1 414 11 MYS FAT . P 6 1PE A 1 415 1 1PE PEG . Q 7 P3G A 1 416 2 P3G PEG . R 6 1PE A 1 417 3 1PE PEG . S 8 HOH A 1 501 1 HOH HOH . S 8 HOH A 2 502 5 HOH HOH . S 8 HOH A 3 503 4 HOH HOH . S 8 HOH A 4 504 3 HOH HOH . S 8 HOH A 5 505 2 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 C6 P3G . . . Q 7 18.559 41.177 13.71 1 91.83 ? C6 P3G 416 A 1 HETATM 2 O O3 P3G . . . Q 7 19.47 40.074 13.704 1 86.05 ? O3 P3G 416 A 1 HETATM 3 C C7 P3G . . . Q 7 18.721 38.859 13.654 1 90.29 ? C7 P3G 416 A 1 HETATM 4 C C8 P3G . . . Q 7 19.658 37.65 13.792 1 87.47 ? C8 P3G 416 A 1 HETATM 5 O O4 P3G . . . Q 7 18.886 36.443 13.753 1 73.3 ? O4 P3G 416 A 1 HETATM 6 C C9 P3G . . . Q 7 17.913 36.504 14.803 1 80.21 ? C9 P3G 416 A 1 HETATM 7 C C10 P3G . . . Q 7 18.572 36.289 16.176 1 78.65 ? C10 P3G 416 A 1 HETATM 8 O O5 P3G . . . Q 7 17.596 36.384 17.23 1 87.34 ? O5 P3G 416 A 1 HETATM 9 C C11 P3G . . . Q 7 16.396 35.663 16.917 1 88.96 ? C11 P3G 416 A 1 HETATM 10 C C12 P3G . . . Q 7 15.196 36.617 17.001 1 99.31 ? C12 P3G 416 A 1 HETATM 11 O O6 P3G . . . Q 7 13.992 35.916 16.663 1 98.97 ? O6 P3G 416 A 1 HETATM 12 C C13 P3G . . . Q 7 13.21 36.74 15.788 1 95.81 ? C13 P3G 416 A 1 HETATM 13 C C14 P3G . . . Q 7 14.031 37.072 14.536 1 92.02 ? C14 P3G 416 A 1 HETATM 14 O O7 P3G . . . Q 7 13.278 37.895 13.643 1 91.48 ? O7 P3G 416 A 1 HETATM 15 C C15 P3G . . . Q 7 14.113 38.268 12.541 1 84.8 ? C15 P3G 416 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #