data_1NLY # _model_server_result.job_id jjk6QVKhQOu6Ez-cQnZqpw _model_server_result.datetime_utc '2025-03-05 01:53:37' _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 1nly # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":403}' # _entry.id 1NLY # _exptl.entry_id 1NLY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 414.488 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NONAETHYLENE 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 120 _cell.entry_id 1NLY _cell.length_a 110.82 _cell.length_b 110.82 _cell.length_c 230.91 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NLY _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 55.41 95.972935 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -55.41 95.972935 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _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 covale ? covale1 A C LYS 41 A LYS 41 1_555 A N MSE 42 A MSE 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 A C MSE 42 A MSE 42 1_555 A N GLU 43 A GLU 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C LEU 81 A LEU 81 1_555 A N MSE 82 A MSE 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C MSE 82 A MSE 82 1_555 A N HIS 83 A HIS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C ILE 191 A ILE 191 1_555 A N MSE 192 A MSE 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 A C MSE 192 A MSE 192 1_555 A N GLU 193 A GLU 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale7 A C ARG 238 A ARG 238 1_555 A N MSE 239 A MSE 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale8 A C MSE 239 A MSE 239 1_555 A N ARG 240 A ARG 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale9 A C ASN 286 A ASN 286 1_555 A N MSE 287 A MSE 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale10 A C MSE 287 A MSE 287 1_555 A N SER 288 A SER 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale11 A C ASP 311 A ASP 311 1_555 A N MSE 312 A MSE 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale12 A C MSE 312 A MSE 312 1_555 A N ILE 313 A ILE 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 B C LYS 41 B LYS 41 1_555 B N MSE 42 B MSE 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale14 B C MSE 42 B MSE 42 1_555 B N GLU 43 B GLU 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale15 B C LEU 81 B LEU 81 1_555 B N MSE 82 B MSE 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 B C MSE 82 B MSE 82 1_555 B N HIS 83 B HIS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale17 B C ILE 191 B ILE 191 1_555 B N MSE 192 B MSE 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale18 B C MSE 192 B MSE 192 1_555 B N GLU 193 B GLU 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale19 B C ARG 238 B ARG 238 1_555 B N MSE 239 B MSE 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale20 B C MSE 239 B MSE 239 1_555 B N ARG 240 B ARG 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale21 B C ASN 286 B ASN 286 1_555 B N MSE 287 B MSE 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale22 B C MSE 287 B MSE 287 1_555 B N SER 288 B SER 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale23 B C ASP 311 B ASP 311 1_555 B N MSE 312 B MSE 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale24 B C MSE 312 B MSE 312 1_555 B N ILE 313 B ILE 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A OG1 THR 185 A THR 185 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.718 ? metalc ? metalc2 C MG MG . A MG 401 1_555 D O2B AGS . A AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? metalc ? metalc3 C MG MG . A MG 401 1_555 H O HOH . A HOH 1022 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? # _chem_comp.formula 'C18 H38 O10' _chem_comp.formula_weight 414.488 _chem_comp.id 2PE _chem_comp.mon_nstd_flag . _chem_comp.name 'NONAETHYLENE GLYCOL' _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 O1 C2 2PE sing 1 n n O1 HO1 2PE sing 2 n n C2 C3 2PE sing 3 n n C2 H21 2PE sing 4 n n C2 H22 2PE sing 5 n n C3 O4 2PE sing 6 n n C3 H31 2PE sing 7 n n C3 H32 2PE sing 8 n n O4 C5 2PE sing 9 n n C5 C6 2PE sing 10 n n C5 H51 2PE sing 11 n n C5 H52 2PE sing 12 n n C6 O7 2PE sing 13 n n C6 H61 2PE sing 14 n n C6 H62 2PE sing 15 n n O7 C8 2PE sing 16 n n C8 C9 2PE sing 17 n n C8 H81 2PE sing 18 n n C8 H82 2PE sing 19 n n C9 O10 2PE sing 20 n n C9 H91 2PE sing 21 n n C9 H92 2PE sing 22 n n O10 C11 2PE sing 23 n n C11 C12 2PE sing 24 n n C11 H111 2PE sing 25 n n C11 H112 2PE sing 26 n n C12 O13 2PE sing 27 n n C12 H121 2PE sing 28 n n C12 H122 2PE sing 29 n n O13 C14 2PE sing 30 n n C14 C15 2PE sing 31 n n C14 H141 2PE sing 32 n n C14 H142 2PE sing 33 n n C15 O16 2PE sing 34 n n C15 H151 2PE sing 35 n n C15 H152 2PE sing 36 n n O16 C17 2PE sing 37 n n C17 C18 2PE sing 38 n n C17 H171 2PE sing 39 n n C17 H172 2PE sing 40 n n C18 O19 2PE sing 41 n n C18 H181 2PE sing 42 n n C18 H182 2PE sing 43 n n O19 C20 2PE sing 44 n n C20 C21 2PE sing 45 n n C20 H201 2PE sing 46 n n C20 H202 2PE sing 47 n n C21 O22 2PE sing 48 n n C21 H211 2PE sing 49 n n C21 H212 2PE sing 50 n n O22 C23 2PE sing 51 n n C23 C24 2PE sing 52 n n C23 H231 2PE sing 53 n n C23 H232 2PE sing 54 n n C24 O25 2PE sing 55 n n C24 H241 2PE sing 56 n n C24 H242 2PE sing 57 n n O25 C26 2PE sing 58 n n C26 C27 2PE sing 59 n n C26 H261 2PE sing 60 n n C26 H262 2PE sing 61 n n C27 O28 2PE sing 62 n n C27 H271 2PE sing 63 n n C27 H272 2PE sing 64 n n O28 HO2 2PE sing 65 n n # _atom_sites.entry_id 1NLY _atom_sites.fract_transf_matrix[1][1] 0.009024 _atom_sites.fract_transf_matrix[1][2] 0.00521 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01042 _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] 0.004331 _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 C 2 MG A 1 401 700 MG MG2 . D 3 AGS A 1 402 400 AGS ATG . E 4 SO4 B 1 401 800 SO4 SO4 . F 3 AGS B 1 402 500 AGS ATG . G 5 2PE B 1 403 600 2PE PEG . H 6 HOH A 1 1001 1001 HOH HOH . H 6 HOH A 2 1002 1002 HOH HOH . H 6 HOH A 3 1003 1003 HOH HOH . H 6 HOH A 4 1004 1004 HOH HOH . H 6 HOH A 5 1005 1005 HOH HOH . H 6 HOH A 6 1006 1006 HOH HOH . H 6 HOH A 7 1007 1007 HOH HOH . H 6 HOH A 8 1008 1008 HOH HOH . H 6 HOH A 9 1009 1010 HOH HOH . H 6 HOH A 10 1010 1011 HOH HOH . H 6 HOH A 11 1011 1012 HOH HOH . H 6 HOH A 12 1012 1013 HOH HOH . H 6 HOH A 13 1013 1015 HOH HOH . H 6 HOH A 14 1014 1025 HOH HOH . H 6 HOH A 15 1015 1027 HOH HOH . H 6 HOH A 16 1016 1032 HOH HOH . H 6 HOH A 17 1017 1033 HOH HOH . H 6 HOH A 18 1018 1034 HOH HOH . H 6 HOH A 19 1019 1035 HOH HOH . H 6 HOH A 20 1020 1036 HOH HOH . H 6 HOH A 21 1021 1041 HOH HOH . H 6 HOH A 22 1022 1042 HOH HOH . I 6 HOH B 1 501 1009 HOH HOH . I 6 HOH B 2 502 1014 HOH HOH . I 6 HOH B 3 503 1016 HOH HOH . I 6 HOH B 4 504 1017 HOH HOH . I 6 HOH B 5 505 1018 HOH HOH . I 6 HOH B 6 506 1019 HOH HOH . I 6 HOH B 7 507 1020 HOH HOH . I 6 HOH B 8 508 1021 HOH HOH . I 6 HOH B 9 509 1022 HOH HOH . I 6 HOH B 10 510 1023 HOH HOH . I 6 HOH B 11 511 1024 HOH HOH . I 6 HOH B 12 512 1026 HOH HOH . I 6 HOH B 13 513 1028 HOH HOH . I 6 HOH B 14 514 1029 HOH HOH . I 6 HOH B 15 515 1030 HOH HOH . I 6 HOH B 16 516 1031 HOH HOH . I 6 HOH B 17 517 1037 HOH HOH . I 6 HOH B 18 518 1038 HOH HOH . I 6 HOH B 19 519 1039 HOH HOH . I 6 HOH B 20 520 1040 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 O1 2PE . . . G 5 -37.543 23.549 33.4 1 55.72 ? O1 2PE 403 B 1 HETATM 2 C C2 2PE . . . G 5 -36.574 22.542 33.47 1 59.24 ? C2 2PE 403 B 1 HETATM 3 C C3 2PE . . . G 5 -35.831 22.558 32.137 1 60.61 ? C3 2PE 403 B 1 HETATM 4 O O4 2PE . . . G 5 -34.854 21.522 32.252 1 65.02 ? O4 2PE 403 B 1 HETATM 5 C C5 2PE . . . G 5 -35.334 20.09 32.263 1 66.99 ? C5 2PE 403 B 1 HETATM 6 C C6 2PE . . . G 5 -34.225 19.029 32.383 1 67.03 ? C6 2PE 403 B 1 HETATM 7 O O7 2PE . . . G 5 -33.827 18.876 33.781 1 65.99 ? O7 2PE 403 B 1 HETATM 8 C C8 2PE . . . G 5 -32.787 17.898 33.929 1 61.78 ? C8 2PE 403 B 1 HETATM 9 C C9 2PE . . . G 5 -32.487 17.864 35.415 1 58.32 ? C9 2PE 403 B 1 HETATM 10 O O10 2PE . . . G 5 -31.134 17.529 35.724 1 54.56 ? O10 2PE 403 B 1 HETATM 11 C C11 2PE . . . G 5 -30.379 18.045 36.819 1 49.34 ? C11 2PE 403 B 1 HETATM 12 C C12 2PE . . . G 5 -28.927 17.54 36.923 1 48.35 ? C12 2PE 403 B 1 HETATM 13 O O13 2PE . . . G 5 -28.748 16.167 36.429 1 46.31 ? O13 2PE 403 B 1 HETATM 14 C C14 2PE . . . G 5 -27.429 15.885 35.954 1 43.33 ? C14 2PE 403 B 1 HETATM 15 C C15 2PE . . . G 5 -27.157 14.458 36.417 1 45.32 ? C15 2PE 403 B 1 HETATM 16 O O16 2PE . . . G 5 -25.744 14.401 36.548 1 43.27 ? O16 2PE 403 B 1 HETATM 17 C C17 2PE . . . G 5 -25.155 13.109 36.739 1 43.36 ? C17 2PE 403 B 1 HETATM 18 C C18 2PE . . . G 5 -23.674 13.346 36.693 1 42.75 ? C18 2PE 403 B 1 HETATM 19 O O19 2PE . . . G 5 -23.304 13.373 35.278 1 45.01 ? O19 2PE 403 B 1 HETATM 20 C C20 2PE . . . G 5 -21.886 13.116 35.168 1 46.6 ? C20 2PE 403 B 1 HETATM 21 C C21 2PE . . . G 5 -21.403 13.137 33.706 1 48.11 ? C21 2PE 403 B 1 HETATM 22 O O22 2PE . . . G 5 -21.188 11.759 33.27 1 49 ? O22 2PE 403 B 1 HETATM 23 C C23 2PE . . . G 5 -20.722 11.737 31.868 1 51.14 ? C23 2PE 403 B 1 HETATM 24 C C24 2PE . . . G 5 -20.484 10.308 31.346 1 51.45 ? C24 2PE 403 B 1 HETATM 25 O O25 2PE . . . G 5 -19.81 9.389 32.326 1 52.12 ? O25 2PE 403 B 1 HETATM 26 C C26 2PE . . . G 5 -18.977 8.351 31.778 1 52.93 ? C26 2PE 403 B 1 HETATM 27 C C27 2PE . . . G 5 -18.413 7.584 32.997 1 54 ? C27 2PE 403 B 1 HETATM 28 O O28 2PE . . . G 5 -16.998 7.713 32.975 1 56.4 ? O28 2PE 403 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #