data_5JDM # _model_server_result.job_id lhNELZfAwCwGkaPbNQmi-g _model_server_result.datetime_utc '2024-11-15 03:51:00' _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":"P","auth_seq_id":415}' # _entry.id 5JDM # _exptl.entry_id 5JDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 238.278 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PENTAETHYLENE GLYCOL' _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 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 P N N ? 6 R 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 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 '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 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 O OH2 1PE . . . P 6 11.084 36.162 10.144 1 80.5 ? OH2 1PE 415 A 1 HETATM 2 C C12 1PE . . . P 6 10.484 36.653 11.347 1 82.89 ? C12 1PE 415 A 1 HETATM 3 C C22 1PE . . . P 6 9.821 35.499 12.106 1 76.24 ? C22 1PE 415 A 1 HETATM 4 O OH3 1PE . . . P 6 10.802 34.511 12.438 1 69.93 ? OH3 1PE 415 A 1 HETATM 5 C C13 1PE . . . P 6 11.236 32.442 13.634 1 64.84 ? C13 1PE 415 A 1 HETATM 6 C C23 1PE . . . P 6 10.193 33.494 13.242 1 60.98 ? C23 1PE 415 A 1 HETATM 7 O OH4 1PE . . . P 6 11.796 31.817 12.472 1 59.71 ? OH4 1PE 415 A 1 HETATM 8 C C14 1PE . . . P 6 13.45 30.224 11.677 1 51.01 ? C14 1PE 415 A 1 HETATM 9 C C24 1PE . . . P 6 12.828 30.918 12.889 1 45.09 ? C24 1PE 415 A 1 HETATM 10 O OH5 1PE . . . P 6 14.022 31.176 10.778 1 59.97 ? OH5 1PE 415 A 1 HETATM 11 C C15 1PE . . . P 6 15.155 31.465 8.651 1 75.21 ? C15 1PE 415 A 1 HETATM 12 C C25 1PE . . . P 6 14.645 30.469 9.697 1 64.79 ? C25 1PE 415 A 1 HETATM 13 O OH6 1PE . . . P 6 14.055 32.226 8.141 1 80.54 ? OH6 1PE 415 A 1 HETATM 14 C C16 1PE . . . P 6 13.264 34.442 7.559 1 74.48 ? C16 1PE 415 A 1 HETATM 15 C C26 1PE . . . P 6 14.459 33.59 7.991 1 79.18 ? C26 1PE 415 A 1 HETATM 16 O OH7 1PE . . . P 6 13.664 35.807 7.432 1 93.84 ? OH7 1PE 415 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 16 #