data_5JDF # _model_server_result.job_id Ogly-mACW-7dnnKZNTQXDQ _model_server_result.datetime_utc '2024-11-15 02:36:57' _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 5jdf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":414}' # _entry.id 5JDF # _exptl.entry_id 5JDF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 238.278 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PENTAETHYLENE GLYCOL' _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 5JDF _cell.length_a 49.801 _cell.length_b 72.258 _cell.length_c 95.803 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JDF _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 _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 O _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 THR 50 A THR 50 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 A OE1 GLU 54 A GLU 54 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.323 ? metalc ? metalc3 A OE2 GLU 54 A GLU 54 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.202 ? metalc ? metalc4 A OE2 GLU 54 A GLU 54 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.45 ? metalc ? metalc5 A O ILE 118 A ILE 118 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc6 A OD1 ASP 121 A ASP 121 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? metalc ? metalc7 A O GLY 122 A GLY 122 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc8 A OD2 ASP 127 A ASP 127 1_555 B CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? metalc ? metalc9 A O THR 209 A THR 209 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.352 ? metalc ? metalc10 A OE1 GLU 213 A GLU 213 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.408 ? metalc ? metalc11 A OE2 GLU 213 A GLU 213 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.104 ? metalc ? metalc12 A OE2 GLU 213 A GLU 213 1_555 C CA CA . A CA 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.348 ? metalc ? metalc13 A OD1 ASP 240 A ASP 240 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 3.096 ? metalc ? metalc14 A OD2 ASP 240 A ASP 240 1_555 C CA CA . A CA 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.807 ? metalc ? metalc15 B CA CA . A CA 401 1_555 H O25 OLC . A OLC 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc16 B CA CA . A CA 401 1_555 P O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? # _chem_comp.formula 'C10 H22 O6' _chem_comp.formula_weight 238.278 _chem_comp.id 1PE _chem_comp.mon_nstd_flag . _chem_comp.name 'PENTAETHYLENE GLYCOL' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms PEG400 # 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 OH2 C12 1PE sing 1 n n OH2 HO2 1PE sing 2 n n C12 C22 1PE sing 3 n n C12 H121 1PE sing 4 n n C12 H122 1PE sing 5 n n C22 OH3 1PE sing 6 n n C22 H221 1PE sing 7 n n C22 H222 1PE sing 8 n n OH3 C23 1PE sing 9 n n C13 C23 1PE sing 10 n n C13 OH4 1PE sing 11 n n C13 H131 1PE sing 12 n n C13 H132 1PE sing 13 n n C23 H231 1PE sing 14 n n C23 H232 1PE sing 15 n n OH4 C24 1PE sing 16 n n C14 C24 1PE sing 17 n n C14 OH5 1PE sing 18 n n C14 H141 1PE sing 19 n n C14 H142 1PE sing 20 n n C24 H241 1PE sing 21 n n C24 H242 1PE sing 22 n n OH5 C25 1PE sing 23 n n C15 C25 1PE sing 24 n n C15 OH6 1PE sing 25 n n C15 H151 1PE sing 26 n n C15 H152 1PE sing 27 n n C25 H251 1PE sing 28 n n C25 H252 1PE sing 29 n n OH6 C26 1PE sing 30 n n C16 C26 1PE sing 31 n n C16 OH7 1PE sing 32 n n C16 H161 1PE sing 33 n n C16 H162 1PE sing 34 n n C26 H261 1PE sing 35 n n C26 H262 1PE sing 36 n n OH7 HO7 1PE sing 37 n n # _atom_sites.entry_id 5JDF _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] 0.013839 _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] 0.010438 _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 CA A 1 401 1 CA CA . C 2 CA A 1 402 2 CA CA . D 3 OLC A 1 403 1 OLC MON . E 3 OLC A 1 404 3 OLC MON . F 3 OLC A 1 405 4 OLC MON . G 3 OLC A 1 406 5 OLC MON . H 3 OLC A 1 407 6 OLC MON . I 4 MYS A 1 408 15 MYS FAT . J 4 MYS A 1 409 20 MYS FAT . K 4 MYS A 1 410 24 MYS FAT . L 4 MYS A 1 411 25 MYS FAT . M 4 MYS A 1 412 26 MYS FAT . N 4 MYS A 1 413 28 MYS FAT . O 5 1PE A 1 414 1 1PE PEG . P 6 HOH A 1 501 10 HOH HOH . P 6 HOH A 2 502 21 HOH HOH . P 6 HOH A 3 503 12 HOH HOH . P 6 HOH A 4 504 8 HOH HOH . P 6 HOH A 5 505 14 HOH HOH . P 6 HOH A 6 506 24 HOH HOH . P 6 HOH A 7 507 3 HOH HOH . P 6 HOH A 8 508 16 HOH HOH . P 6 HOH A 9 509 5 HOH HOH . P 6 HOH A 10 510 2 HOH HOH . P 6 HOH A 11 511 9 HOH HOH . P 6 HOH A 12 512 11 HOH HOH . P 6 HOH A 13 513 19 HOH HOH . P 6 HOH A 14 514 23 HOH HOH . P 6 HOH A 15 515 17 HOH HOH . P 6 HOH A 16 516 18 HOH HOH . P 6 HOH A 17 517 22 HOH HOH . P 6 HOH A 18 518 20 HOH HOH . P 6 HOH A 19 519 4 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 O OH3 1PE . . . O 5 13.568 34.027 8.052 1 91.9 ? OH3 1PE 414 A 1 HETATM 2 C C13 1PE . . . O 5 15.159 32.245 8.442 1 95.42 ? C13 1PE 414 A 1 HETATM 3 C C23 1PE . . . O 5 14.37 33.04 7.399 1 98.7 ? C23 1PE 414 A 1 HETATM 4 O OH4 1PE . . . O 5 14.275 31.584 9.362 1 87.59 ? OH4 1PE 414 A 1 HETATM 5 C C14 1PE . . . O 5 14.545 30.712 11.666 1 72.21 ? C14 1PE 414 A 1 HETATM 6 C C24 1PE . . . O 5 15.131 30.86 10.252 1 78.07 ? C24 1PE 414 A 1 HETATM 7 O OH5 1PE . . . O 5 13.311 29.99 11.684 1 79.97 ? OH5 1PE 414 A 1 HETATM 8 C C15 1PE . . . O 5 12.077 31.646 13.003 1 76.5 ? C15 1PE 414 A 1 HETATM 9 C C25 1PE . . . O 5 12.16 30.838 11.709 1 81.31 ? C25 1PE 414 A 1 HETATM 10 O OH6 1PE . . . O 5 10.898 32.455 12.939 1 93.23 ? OH6 1PE 414 A 1 HETATM 11 C C16 1PE . . . O 5 10.739 34.85 13.15 1 81.62 ? C16 1PE 414 A 1 HETATM 12 C C26 1PE . . . O 5 10.956 33.524 13.885 1 80.65 ? C26 1PE 414 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 12 #