data_2Y58 # _model_server_result.job_id NlBDiSSQrkFXCHOKrknJKQ _model_server_result.datetime_utc '2024-11-22 13:18:11' _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 2y58 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":301}' # _entry.id 2Y58 # _exptl.entry_id 2Y58 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 366.473 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(1R,5S)-8-[(2R)-2-HYDROXY-2-PHENYL-ETHYL]-8-METHYL-8-AZONIABICYCLO[3.2.1]OCTAN-3-YL] BENZOATE' _entity.pdbx_number_of_molecules 5 _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 2Y58 _cell.length_a 213.33 _cell.length_b 213.33 _cell.length_c 213.33 _cell.Z_PDB 120 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Y58 _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,T _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 ? 2 F N N ? 2 J N N ? 2 N N N ? 2 P N N ? 2 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 disulf ? disulf1 A SG CYS 125 A CYS 125 1_555 A SG CYS 138 A CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf2 A SG CYS 188 A CYS 188 1_555 A SG CYS 189 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf3 B SG CYS 125 B CYS 125 1_555 B SG CYS 138 B CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 B SG CYS 188 B CYS 188 1_555 B SG CYS 189 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf5 C SG CYS 125 C CYS 125 1_555 C SG CYS 138 C CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf6 C SG CYS 188 C CYS 188 1_555 C SG CYS 189 C CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf7 D SG CYS 125 D CYS 125 1_555 D SG CYS 138 D CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 D SG CYS 188 D CYS 188 1_555 D SG CYS 189 D CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf9 E SG CYS 125 E CYS 125 1_555 E SG CYS 138 E CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf10 E SG CYS 188 E CYS 188 1_555 E SG CYS 189 E CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? # _chem_comp.formula 'C23 H28 N O3 1' _chem_comp.formula_weight 366.473 _chem_comp.id V38 _chem_comp.mon_nstd_flag . _chem_comp.name '[(1R,5S)-8-[(2R)-2-HYDROXY-2-PHENYL-ETHYL]-8-METHYL-8-AZONIABICYCLO[3.2.1]OCTAN-3-YL] BENZOATE' _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 N C10 V38 sing 360 n n N C11 V38 sing 361 n n N C15 V38 sing 362 n n N C23 V38 sing 363 n n C1 O1 V38 sing 364 n n C1 C2 V38 sing 365 n n C1 O2 V38 doub 366 n n O1 C8 V38 sing 367 n n C2 C3 V38 doub 368 n y C2 C7 V38 sing 369 n y C3 C4 V38 sing 370 n y O3 C16 V38 sing 371 n n C4 C5 V38 doub 372 n y C5 C6 V38 sing 373 n y C6 C7 V38 doub 374 n y C8 C9 V38 sing 375 n n C8 C12 V38 sing 376 n n C9 C10 V38 sing 377 n n C10 C14 V38 sing 378 n n C11 C12 V38 sing 379 n n C11 C13 V38 sing 380 n n C13 C14 V38 sing 381 n n C15 C16 V38 sing 382 n n C16 C17 V38 sing 383 n n C17 C18 V38 doub 384 n y C17 C22 V38 sing 385 n y C18 C19 V38 sing 386 n y C19 C20 V38 doub 387 n y C20 C21 V38 sing 388 n y C21 C22 V38 doub 389 n y C7 H7 V38 sing 390 n n C3 H3 V38 sing 391 n n C6 H6 V38 sing 392 n n C5 H5 V38 sing 393 n n C4 H4 V38 sing 394 n n C8 H8 V38 sing 395 n n C12 H121 V38 sing 396 n n C12 H122 V38 sing 397 n n C9 H91C V38 sing 398 n n C9 H92C V38 sing 399 n n C11 H11 V38 sing 400 n n C13 H131 V38 sing 401 n n C13 H132 V38 sing 402 n n C14 H141 V38 sing 403 n n C14 H142 V38 sing 404 n n C10 H10 V38 sing 405 n n C23 H231 V38 sing 406 n n C23 H232 V38 sing 407 n n C23 H233 V38 sing 408 n n C15 H151 V38 sing 409 n n C15 H152 V38 sing 410 n n C16 H16 V38 sing 411 n n O3 HA V38 sing 412 n n C22 H22 V38 sing 413 n n C18 H18 V38 sing 414 n n C21 H21 V38 sing 415 n n C20 H20 V38 sing 416 n n C19 H19 V38 sing 417 n n # _atom_sites.entry_id 2Y58 _atom_sites.fract_transf_matrix[1][1] 0.004688 _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] 0.004688 _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] 0.004688 _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 F 2 V38 A 1 301 301 V38 V38 . G 3 CL A 1 501 501 CL CL . H 4 SO4 A 1 601 601 SO4 SO4 . I 4 SO4 A 1 602 602 SO4 SO4 . J 2 V38 B 1 301 301 V38 V38 . K 3 CL B 1 501 501 CL CL . L 3 CL B 1 502 502 CL CL . M 4 SO4 B 1 601 601 SO4 SO4 . N 2 V38 C 1 301 301 V38 V38 . O 3 CL C 1 501 501 CL CL . P 2 V38 D 1 301 301 V38 V38 . Q 3 CL D 1 501 501 CL CL . R 2 V38 E 1 301 301 V38 V38 . S 3 CL E 1 501 501 CL CL . T 4 SO4 E 1 601 601 SO4 SO4 . # 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 O2 V38 . . . J 2 -55.39 -33.847 -33.055 1 67.52 ? O2 V38 301 B 1 HETATM 2 C C1 V38 . . . J 2 -56.214 -33.376 -32.265 1 66.01 ? C1 V38 301 B 1 HETATM 3 C C2 V38 . . . J 2 -55.816 -32.87 -30.911 1 66.8 ? C2 V38 301 B 1 HETATM 4 C C7 V38 . . . J 2 -56.846 -32.496 -30.019 1 67.83 ? C7 V38 301 B 1 HETATM 5 C C6 V38 . . . J 2 -56.546 -31.941 -28.771 1 67.44 ? C6 V38 301 B 1 HETATM 6 C C5 V38 . . . J 2 -55.201 -31.746 -28.444 1 67.24 ? C5 V38 301 B 1 HETATM 7 C C4 V38 . . . J 2 -54.181 -32.107 -29.342 1 65.34 ? C4 V38 301 B 1 HETATM 8 C C3 V38 . . . J 2 -54.471 -32.648 -30.595 1 64.01 ? C3 V38 301 B 1 HETATM 9 O O1 V38 . . . J 2 -57.622 -33.139 -32.575 1 61.41 ? O1 V38 301 B 1 HETATM 10 C C8 V38 . . . J 2 -58.182 -33.565 -33.806 1 60.64 ? C8 V38 301 B 1 HETATM 11 C C12 V38 . . . J 2 -58.099 -35.083 -33.972 1 60.41 ? C12 V38 301 B 1 HETATM 12 C C11 V38 . . . J 2 -59.181 -35.843 -33.21 1 59.82 ? C11 V38 301 B 1 HETATM 13 C C13 V38 . . . J 2 -59.021 -35.44 -31.757 1 63.03 ? C13 V38 301 B 1 HETATM 14 C C14 V38 . . . J 2 -59.963 -34.251 -31.598 1 64.96 ? C14 V38 301 B 1 HETATM 15 C C10 V38 . . . J 2 -60.577 -34.036 -32.982 1 62.23 ? C10 V38 301 B 1 HETATM 16 C C9 V38 . . . J 2 -59.636 -33.097 -33.75 1 61.91 ? C9 V38 301 B 1 HETATM 17 N N V38 . . . J 2 -60.52 -35.357 -33.613 1 57.87 ? N V38 301 B 1 HETATM 18 C C23 V38 . . . J 2 -61.579 -36.212 -33.068 1 54.37 ? C23 V38 301 B 1 HETATM 19 C C15 V38 . . . J 2 -60.726 -35.197 -35.059 1 59.28 ? C15 V38 301 B 1 HETATM 20 C C16 V38 . . . J 2 -60.864 -36.508 -35.81 1 64.18 ? C16 V38 301 B 1 HETATM 21 O O3 V38 . . . J 2 -59.791 -37.374 -35.448 1 67.24 ? O3 V38 301 B 1 HETATM 22 C C17 V38 . . . J 2 -60.678 -36.203 -37.235 1 66.63 ? C17 V38 301 B 1 HETATM 23 C C22 V38 . . . J 2 -59.662 -36.835 -37.948 1 67.44 ? C22 V38 301 B 1 HETATM 24 C C21 V38 . . . J 2 -59.473 -36.539 -39.292 1 68.47 ? C21 V38 301 B 1 HETATM 25 C C20 V38 . . . J 2 -60.276 -35.585 -39.909 1 70.24 ? C20 V38 301 B 1 HETATM 26 C C19 V38 . . . J 2 -61.295 -34.951 -39.201 1 71.32 ? C19 V38 301 B 1 HETATM 27 C C18 V38 . . . J 2 -61.5 -35.272 -37.858 1 69.67 ? C18 V38 301 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 379 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #