data_2HDF # _model_server_result.job_id XDaiGjki0ezsU3uncVh1wg _model_server_result.datetime_utc '2024-12-21 12:53:41' _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 2hdf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":22}' # _entry.id 2HDF # _exptl.entry_id 2HDF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 206.345 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-OCTYL-2-HYDROXYETHYL SULFOXIDE' _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 109.16 _cell.angle_gamma 90 _cell.entry_id 2HDF _cell.length_a 90.593 _cell.length_b 84.336 _cell.length_c 99.458 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2HDF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 ? 3 C N N ? 3 D 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 disulf ? disulf1 A SG CYS 411 A CYS 435 1_555 A SG CYS 415 A CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A C THR 8 A THR 32 1_555 A N MSE 9 A MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 A C MSE 9 A MSE 33 1_555 A N VAL 10 A VAL 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C PRO 115 A PRO 139 1_555 A N MSE 116 A MSE 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale4 A C MSE 116 A MSE 140 1_555 A N SER 117 A SER 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 A C GLY 176 A GLY 200 1_555 A N MSE 177 A MSE 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 A C MSE 177 A MSE 201 1_555 A N LYS 178 A LYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale7 A C GLU 313 A GLU 337 1_555 A N MSE 314 A MSE 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale8 A C MSE 314 A MSE 338 1_555 A N ARG 315 A ARG 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 A C LYS 318 A LYS 342 1_555 A N MSE 319 A MSE 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale10 A C MSE 319 A MSE 343 1_555 A N SER 320 A SER 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale11 A C ARG 359 A ARG 383 1_555 A N MSE 360 A MSE 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale12 A C MSE 360 A MSE 384 1_555 A N ASP 361 A ASP 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale13 A C TYR 437 A TYR 461 1_555 A N MSE 438 A MSE 462 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale14 A C MSE 438 A MSE 462 1_555 A N GLY 439 A GLY 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 A C SER 564 A SER 588 1_555 A N MSE 565 A MSE 589 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale16 A C MSE 565 A MSE 589 1_555 A N TYR 566 A TYR 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale17 A C TYR 566 A TYR 590 1_555 A N MSE 567 A MSE 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale18 A C MSE 567 A MSE 591 1_555 A N SER 568 A SER 592 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale19 A C PHE 632 A PHE 656 1_555 A N MSE 633 A MSE 657 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale20 A C MSE 633 A MSE 657 1_555 A N ALA 634 A ALA 658 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 B SR SR . A SR 23 1_555 A O ASN 99 A ASN 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.385 ? metalc ? metalc2 B SR SR . A SR 23 1_555 A OG SER 210 A SER 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? metalc ? metalc3 B SR SR . A SR 23 1_555 A OD2 ASP 212 A ASP 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.035 ? metalc ? metalc4 B SR SR . A SR 23 1_555 A OD1 ASP 234 A ASP 258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.93 ? # _chem_comp.formula 'C10 H22 O2 S' _chem_comp.formula_weight 206.345 _chem_comp.id OES _chem_comp.mon_nstd_flag . _chem_comp.name 'N-OCTYL-2-HYDROXYETHYL SULFOXIDE' _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 OES sing 256 n n C1 HC11 OES sing 257 n n C1 HC12 OES sing 258 n n C1 HC13 OES sing 259 n n C2 C3 OES sing 260 n n C2 HC21 OES sing 261 n n C2 HC22 OES sing 262 n n C3 C4 OES sing 263 n n C3 HC31 OES sing 264 n n C3 HC32 OES sing 265 n n C4 C5 OES sing 266 n n C4 HC41 OES sing 267 n n C4 HC42 OES sing 268 n n C5 C6 OES sing 269 n n C5 HC51 OES sing 270 n n C5 HC52 OES sing 271 n n C6 C7 OES sing 272 n n C6 HC61 OES sing 273 n n C6 HC62 OES sing 274 n n C7 C8 OES sing 275 n n C7 HC71 OES sing 276 n n C7 HC72 OES sing 277 n n C8 S2 OES sing 278 n n C8 HC81 OES sing 279 n n C8 HC82 OES sing 280 n n S2 C22 OES sing 281 n n S2 O2 OES doub 282 n n C22 C23 OES sing 283 n n C22 H221 OES sing 284 n n C22 H222 OES sing 285 n n C23 O3 OES sing 286 n n C23 H231 OES sing 287 n n C23 H232 OES sing 288 n n O3 HO31 OES sing 289 n n # _atom_sites.entry_id 2HDF _atom_sites.fract_transf_matrix[1][1] 0.011038 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003835 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011857 _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] 0.010644 _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 SR A 1 23 1 SR SR . C 3 OES A 1 21 1 OES OES . D 3 OES A 1 22 2 OES OES . E 4 HOH A 1 1 1 HOH HOH . E 4 HOH A 2 2 2 HOH HOH . E 4 HOH A 3 3 3 HOH HOH . E 4 HOH A 4 4 4 HOH HOH . E 4 HOH A 5 5 5 HOH HOH . E 4 HOH A 6 6 6 HOH HOH . E 4 HOH A 7 7 7 HOH HOH . E 4 HOH A 8 8 8 HOH HOH . E 4 HOH A 9 9 9 HOH HOH . E 4 HOH A 10 10 10 HOH HOH . E 4 HOH A 11 11 11 HOH HOH . E 4 HOH A 12 12 12 HOH HOH . E 4 HOH A 13 13 13 HOH HOH . E 4 HOH A 14 14 14 HOH HOH . E 4 HOH A 15 15 15 HOH HOH . E 4 HOH A 16 16 16 HOH HOH . E 4 HOH A 17 17 17 HOH HOH . E 4 HOH A 18 18 18 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 OES . . . D 3 1.092 -6.812 32.178 1 77.66 ? C1 OES 22 A 1 HETATM 2 C C2 OES . . . D 3 1.86 -7.069 30.897 1 84.24 ? C2 OES 22 A 1 HETATM 3 C C3 OES . . . D 3 1.255 -6.344 29.694 1 87.17 ? C3 OES 22 A 1 HETATM 4 C C4 OES . . . D 3 2.136 -6.472 28.45 1 89.54 ? C4 OES 22 A 1 HETATM 5 C C5 OES . . . D 3 1.341 -6.889 27.212 1 92.61 ? C5 OES 22 A 1 HETATM 6 C C6 OES . . . D 3 2.124 -7.877 26.346 1 96.28 ? C6 OES 22 A 1 HETATM 7 C C7 OES . . . D 3 1.346 -8.29 25.096 1 101.44 ? C7 OES 22 A 1 HETATM 8 C C8 OES . . . D 3 1.74 -7.466 23.868 1 105.96 ? C8 OES 22 A 1 HETATM 9 S S2 OES . . . D 3 1.186 -8.266 22.314 1 111.24 ? S2 OES 22 A 1 HETATM 10 C C22 OES . . . D 3 2.144 -9.816 22.1 1 109.05 ? C22 OES 22 A 1 HETATM 11 C C23 OES . . . D 3 2.808 -9.873 20.726 1 106.59 ? C23 OES 22 A 1 HETATM 12 O O2 OES . . . D 3 1.73 -7.055 21.097 1 106.53 ? O2 OES 22 A 1 HETATM 13 O O3 OES . . . D 3 2.007 -10.642 19.821 1 104.62 ? O3 OES 22 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #