data_5EBM # _model_server_result.job_id LjG8OfM3q2J-TUxg-9Iv3Q _model_server_result.datetime_utc '2025-03-04 23:18:14' _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 5ebm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1002}' # _entry.id 5EBM # _exptl.entry_id 5EBM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 144.254 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NONAN-1-OL _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 5EBM _cell.length_a 155.72 _cell.length_b 155.72 _cell.length_c 75.556 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EBM _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K 1 1 A,B,C,D,E,F,G,H,I,J,K 1 2 A,B,C,D,E,F,G,H,I,J,K 1 3 A,B,C,D,E,F,G,H,I,J,K 1 4 # 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_595 -x,-y+4,z -1 0 0 0 -1 0 0 0 1 0 622.88 0 3 'crystal symmetry operation' 3_775 -y+2,x+2,z 0 -1 0 1 0 0 0 0 1 311.44 311.44 0 4 'crystal symmetry operation' 4_375 y-2,-x+2,z 0 1 0 -1 0 0 0 0 1 -311.44 311.44 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 disulf ? disulf1 A SG CYS 22 A CYS 22 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 145 A CYS 145 1_555 A SG CYS 200 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 B SG CYS 23 B CYS 23 1_555 B SG CYS 88 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 B SG CYS 134 B CYS 134 1_555 B SG CYS 194 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc1 C O GLY 75 C GLY 75 1_555 G K K . C K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.774 ? metalc ? metalc2 C O GLY 75 C GLY 75 1_555 G K K . C K 1004 3_775 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc3 C O GLY 77 C GLY 77 1_555 F K K . C K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc4 C O GLY 77 C GLY 77 1_555 F K K . C K 1003 4_375 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? # _chem_comp.formula 'C9 H20 O' _chem_comp.formula_weight 144.254 _chem_comp.id F09 _chem_comp.mon_nstd_flag . _chem_comp.name NONAN-1-OL _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 C1 C2 F09 sing 202 n n C1 H11 F09 sing 203 n n C1 H12 F09 sing 204 n n C1 H13 F09 sing 205 n n C2 C3 F09 sing 206 n n C2 H21 F09 sing 207 n n C2 H22 F09 sing 208 n n C3 C4 F09 sing 209 n n C3 H31 F09 sing 210 n n C3 H32 F09 sing 211 n n C4 C5 F09 sing 212 n n C4 H41 F09 sing 213 n n C4 H42 F09 sing 214 n n C5 C6 F09 sing 215 n n C5 H51 F09 sing 216 n n C5 H52 F09 sing 217 n n C6 C7 F09 sing 218 n n C6 H61 F09 sing 219 n n C6 H62 F09 sing 220 n n C7 C8 F09 sing 221 n n C7 H71 F09 sing 222 n n C7 H72 F09 sing 223 n n C8 C9 F09 sing 224 n n C8 H81 F09 sing 225 n n C8 H82 F09 sing 226 n n C9 OXT F09 sing 227 n n C9 H91 F09 sing 228 n n C9 H92 F09 sing 229 n n OXT HXT F09 sing 230 n n # _atom_sites.entry_id 5EBM _atom_sites.fract_transf_matrix[1][1] 0.006422 _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] 0.006422 _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] 0.013235 _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 D 4 DGA C 1 1001 1001 DGA DGA . E 5 F09 C 1 1002 1002 F09 F09 . F 6 K C 1 1003 1 K K . G 6 K C 1 1004 2 K K . H 6 K C 1 1005 3 K K . I 7 HOH A 1 301 120 HOH HOH . I 7 HOH A 2 302 96 HOH HOH . I 7 HOH A 3 303 44 HOH HOH . I 7 HOH A 4 304 90 HOH HOH . I 7 HOH A 5 305 29 HOH HOH . I 7 HOH A 6 306 73 HOH HOH . I 7 HOH A 7 307 68 HOH HOH . I 7 HOH A 8 308 20 HOH HOH . I 7 HOH A 9 309 78 HOH HOH . I 7 HOH A 10 310 67 HOH HOH . I 7 HOH A 11 311 86 HOH HOH . I 7 HOH A 12 312 83 HOH HOH . I 7 HOH A 13 313 35 HOH HOH . I 7 HOH A 14 314 31 HOH HOH . I 7 HOH A 15 315 76 HOH HOH . I 7 HOH A 16 316 82 HOH HOH . I 7 HOH A 17 317 92 HOH HOH . I 7 HOH A 18 318 95 HOH HOH . I 7 HOH A 19 319 58 HOH HOH . I 7 HOH A 20 320 126 HOH HOH . I 7 HOH A 21 321 116 HOH HOH . I 7 HOH A 22 322 50 HOH HOH . I 7 HOH A 23 323 4 HOH HOH . I 7 HOH A 24 324 63 HOH HOH . I 7 HOH A 25 325 11 HOH HOH . I 7 HOH A 26 326 15 HOH HOH . I 7 HOH A 27 327 113 HOH HOH . I 7 HOH A 28 328 37 HOH HOH . I 7 HOH A 29 329 38 HOH HOH . I 7 HOH A 30 330 87 HOH HOH . I 7 HOH A 31 331 127 HOH HOH . I 7 HOH A 32 332 69 HOH HOH . I 7 HOH A 33 333 39 HOH HOH . I 7 HOH A 34 334 85 HOH HOH . J 7 HOH B 1 301 71 HOH HOH . J 7 HOH B 2 302 64 HOH HOH . J 7 HOH B 3 303 124 HOH HOH . J 7 HOH B 4 304 18 HOH HOH . J 7 HOH B 5 305 36 HOH HOH . J 7 HOH B 6 306 13 HOH HOH . J 7 HOH B 7 307 19 HOH HOH . J 7 HOH B 8 308 27 HOH HOH . J 7 HOH B 9 309 3 HOH HOH . J 7 HOH B 10 310 12 HOH HOH . J 7 HOH B 11 311 80 HOH HOH . J 7 HOH B 12 312 100 HOH HOH . J 7 HOH B 13 313 5 HOH HOH . J 7 HOH B 14 314 23 HOH HOH . J 7 HOH B 15 315 21 HOH HOH . J 7 HOH B 16 316 16 HOH HOH . J 7 HOH B 17 317 42 HOH HOH . J 7 HOH B 18 318 10 HOH HOH . J 7 HOH B 19 319 22 HOH HOH . J 7 HOH B 20 320 65 HOH HOH . J 7 HOH B 21 321 123 HOH HOH . J 7 HOH B 22 322 46 HOH HOH . J 7 HOH B 23 323 25 HOH HOH . J 7 HOH B 24 324 97 HOH HOH . J 7 HOH B 25 325 111 HOH HOH . J 7 HOH B 26 326 121 HOH HOH . J 7 HOH B 27 327 103 HOH HOH . J 7 HOH B 28 328 105 HOH HOH . J 7 HOH B 29 329 17 HOH HOH . J 7 HOH B 30 330 49 HOH HOH . J 7 HOH B 31 331 57 HOH HOH . J 7 HOH B 32 332 43 HOH HOH . J 7 HOH B 33 333 91 HOH HOH . J 7 HOH B 34 334 104 HOH HOH . K 7 HOH C 1 1101 128 HOH HOH . K 7 HOH C 2 1102 129 HOH HOH . K 7 HOH C 3 1103 8 HOH HOH . K 7 HOH C 4 1104 53 HOH HOH . K 7 HOH C 5 1105 130 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 C1 F09 . . . E 5 -1.626 289.288 36.949 1 82.31 ? C1 F09 1002 C 1 HETATM 2 C C2 F09 . . . E 5 -0.958 287.97 36.621 1 82.23 ? C2 F09 1002 C 1 HETATM 3 C C3 F09 . . . E 5 -1.016 287.687 35.125 1 82.01 ? C3 F09 1002 C 1 HETATM 4 C C4 F09 . . . E 5 0.287 287.066 34.635 1 81.5 ? C4 F09 1002 C 1 HETATM 5 C C5 F09 . . . E 5 0.419 287.196 33.122 1 81.34 ? C5 F09 1002 C 1 HETATM 6 C C6 F09 . . . E 5 -0.327 286.075 32.41 1 80.85 ? C6 F09 1002 C 1 HETATM 7 C C7 F09 . . . E 5 -0.045 286.096 30.913 1 80.33 ? C7 F09 1002 C 1 HETATM 8 C C8 F09 . . . E 5 -1.313 285.819 30.114 1 80.5 ? C8 F09 1002 C 1 HETATM 9 C C9 F09 . . . E 5 -0.982 285.197 28.762 1 80.15 ? C9 F09 1002 C 1 HETATM 10 O OXT F09 . . . E 5 -2.18 284.691 28.163 1 80.42 ? OXT F09 1002 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 10 #