data_5JDN # _model_server_result.job_id ESBBwNwvn4T5McLFCD38sA _model_server_result.datetime_utc '2024-11-15 03:36:32' _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 5jdn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":411}' # _entry.id 5JDN # _exptl.entry_id 5JDN _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 5JDN _cell.length_a 49.67 _cell.length_b 72.463 _cell.length_c 96.428 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JDN _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 _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 L N N ? 6 M 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc2 A OG1 THR 50 A THR 50 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc3 A O THR 50 A THR 50 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc4 A OG SER 51 A SER 51 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc5 A OE1 GLU 54 A GLU 54 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc6 A OE2 GLU 54 A GLU 54 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc7 A O ILE 118 A ILE 118 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc8 A OD1 ASP 121 A ASP 121 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc9 A O GLY 122 A GLY 122 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc10 A OD2 ASP 127 A ASP 127 1_555 D SR SR . A SR 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc11 A O THR 209 A THR 209 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc12 A OE2 GLU 213 A GLU 213 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc13 A OE1 GLU 213 A GLU 213 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc14 A OE2 GLU 213 A GLU 213 1_555 C SR SR . A SR 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc15 A OG SER 236 A SER 236 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc16 C SR SR . A SR 402 1_555 N O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.824 ? metalc ? metalc17 D SR SR . A SR 403 1_555 E O23 OLC . A OLC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc18 D SR SR . A SR 403 1_555 E O25 OLC . A OLC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? # _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 5JDN _atom_sites.fract_transf_matrix[1][1] 0.020133 _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] 0.0138 _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] 0.01037 _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 3 SR A 1 402 1 SR SR . D 3 SR A 1 403 2 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 2 MYS FAT . I 5 MYS A 1 408 3 MYS FAT . J 5 MYS A 1 409 4 MYS FAT . K 5 MYS A 1 410 5 MYS FAT . L 6 1PE A 1 411 1 1PE PEG . M 6 1PE A 1 412 2 1PE PEG . N 7 HOH A 1 501 8 HOH HOH . N 7 HOH A 2 502 12 HOH HOH . N 7 HOH A 3 503 9 HOH HOH . N 7 HOH A 4 504 25 HOH HOH . N 7 HOH A 5 505 13 HOH HOH . N 7 HOH A 6 506 1 HOH HOH . N 7 HOH A 7 507 7 HOH HOH . N 7 HOH A 8 508 4 HOH HOH . N 7 HOH A 9 509 2 HOH HOH . N 7 HOH A 10 510 26 HOH HOH . N 7 HOH A 11 511 11 HOH HOH . N 7 HOH A 12 512 27 HOH HOH . N 7 HOH A 13 513 5 HOH HOH . N 7 HOH A 14 514 15 HOH HOH . N 7 HOH A 15 515 19 HOH HOH . N 7 HOH A 16 516 28 HOH HOH . N 7 HOH A 17 517 6 HOH HOH . N 7 HOH A 18 518 14 HOH HOH . N 7 HOH A 19 519 17 HOH HOH . N 7 HOH A 20 520 30 HOH HOH . N 7 HOH A 21 521 18 HOH HOH . N 7 HOH A 22 522 10 HOH HOH . N 7 HOH A 23 523 23 HOH HOH . N 7 HOH A 24 524 3 HOH HOH . N 7 HOH A 25 525 24 HOH HOH . N 7 HOH A 26 526 16 HOH HOH . N 7 HOH A 27 527 21 HOH HOH . N 7 HOH A 28 528 20 HOH HOH . N 7 HOH A 29 529 32 HOH HOH . N 7 HOH A 30 530 22 HOH HOH . N 7 HOH A 31 531 31 HOH HOH . N 7 HOH A 32 532 29 HOH HOH . N 7 HOH A 33 533 33 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 . . . L 6 9.45 35.801 12.237 1 57.93 ? OH2 1PE 411 A 1 HETATM 2 C C12 1PE . . . L 6 10.654 35.093 12.557 1 63.84 ? C12 1PE 411 A 1 HETATM 3 C C22 1PE . . . L 6 10.305 33.641 12.908 1 62.53 ? C22 1PE 411 A 1 HETATM 4 O OH3 1PE . . . L 6 11.492 32.889 13.196 1 58.17 ? OH3 1PE 411 A 1 HETATM 5 C C13 1PE . . . L 6 12.456 30.666 12.943 1 44.4 ? C13 1PE 411 A 1 HETATM 6 C C23 1PE . . . L 6 11.184 31.507 12.984 1 46.7 ? C23 1PE 411 A 1 HETATM 7 O OH4 1PE . . . L 6 13.282 31.139 11.88 1 50.14 ? OH4 1PE 411 A 1 HETATM 8 C C14 1PE . . . L 6 15.106 30.704 10.402 1 49.29 ? C14 1PE 411 A 1 HETATM 9 C C24 1PE . . . L 6 14.09 30.103 11.352 1 46.11 ? C24 1PE 411 A 1 HETATM 10 O OH5 1PE . . . L 6 14.436 31.4 9.347 1 60.85 ? OH5 1PE 411 A 1 HETATM 11 C C15 1PE . . . L 6 14.931 32.794 7.398 1 75.52 ? C15 1PE 411 A 1 HETATM 12 C C25 1PE . . . L 6 15.41 31.678 8.328 1 70.45 ? C25 1PE 411 A 1 HETATM 13 O OH6 1PE . . . L 6 14.722 33.987 8.16 1 83.34 ? OH6 1PE 411 A 1 HETATM 14 C C16 1PE . . . L 6 13.462 35.022 6.355 1 80.66 ? C16 1PE 411 A 1 HETATM 15 C C26 1PE . . . L 6 14.675 35.12 7.282 1 80.96 ? C26 1PE 411 A 1 HETATM 16 O OH7 1PE . . . L 6 12.264 34.996 7.135 1 82.61 ? OH7 1PE 411 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 16 #