data_5AMK # _model_server_result.job_id -j0WXtgBPlfgQlHM9_07Mw _model_server_result.datetime_utc '2024-12-03 10:43:27' _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 5amk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":151}' # _entry.id 5AMK # _exptl.entry_id 5AMK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 258.229 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-Thalidomide _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 120 _cell.entry_id 5AMK _cell.length_a 137.86 _cell.length_b 137.86 _cell.length_c 154.39 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AMK _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F 1 1 B,G,H 2 1 C,I,J 3 1 D,K 4 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 F N N ? 3 H 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 SG CYS 25 A CYS 24 1_555 E ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc2 A SG CYS 28 A CYS 27 1_555 E ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc3 A SG CYS 91 A CYS 90 1_555 E ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc4 A SG CYS 94 A CYS 93 1_555 E ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc5 B SG CYS 25 B CYS 24 1_555 G ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc6 B SG CYS 28 B CYS 27 1_555 G ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc7 B SG CYS 91 B CYS 90 1_555 G ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc8 B SG CYS 94 B CYS 93 1_555 G ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc9 C SG CYS 25 C CYS 24 1_555 I ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc10 C SG CYS 28 C CYS 27 1_555 I ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc11 C SG CYS 91 C CYS 90 1_555 I ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc12 C SG CYS 94 C CYS 93 1_555 I ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc13 D SG CYS 25 D CYS 24 1_555 K ZN ZN . D ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc14 D SG CYS 28 D CYS 27 1_555 K ZN ZN . D ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc15 D SG CYS 91 D CYS 90 1_555 K ZN ZN . D ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc16 D SG CYS 94 D CYS 93 1_555 K ZN ZN . D ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? # _chem_comp.formula 'C13 H10 N2 O4' _chem_comp.formula_weight 258.229 _chem_comp.id EF2 _chem_comp.mon_nstd_flag . _chem_comp.name S-Thalidomide _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 O01 C02 EF2 doub 92 n n C02 N03 EF2 sing 93 n n C02 C08 EF2 sing 94 n n N03 C04 EF2 sing 95 n n C04 O05 EF2 doub 96 n n C04 C06 EF2 sing 97 n n C06 C07 EF2 sing 98 n n C07 C08 EF2 sing 99 n n C08 N09 EF2 sing 100 n n N09 C3 EF2 sing 101 n n N09 C4 EF2 sing 102 n n C11 C12 EF2 sing 103 n y C11 C20 EF2 doub 104 n y C12 C13 EF2 doub 105 n y C13 C14 EF2 sing 106 n y C13 C4 EF2 sing 107 n n C14 C19 EF2 doub 108 n y C14 C3 EF2 sing 109 n n O16 C4 EF2 doub 110 n n O18 C3 EF2 doub 111 n n C19 C20 EF2 sing 112 n y N03 H03 EF2 sing 113 n n C08 H08 EF2 sing 114 n n C06 H061 EF2 sing 115 n n C06 H062 EF2 sing 116 n n C07 H071 EF2 sing 117 n n C07 H072 EF2 sing 118 n n C11 H11 EF2 sing 119 n n C12 H12 EF2 sing 120 n n C20 H20 EF2 sing 121 n n C19 H19 EF2 sing 122 n n # _atom_sites.entry_id 5AMK _atom_sites.fract_transf_matrix[1][1] 0.007254 _atom_sites.fract_transf_matrix[1][2] 0.004188 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008376 _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] 0.006477 _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 E 2 ZN A 1 150 150 ZN ZN . F 3 EF2 A 1 151 151 EF2 EF2 . G 2 ZN B 1 150 150 ZN ZN . H 3 EF2 B 1 151 151 EF2 EF2 . I 2 ZN C 1 150 150 ZN ZN . J 4 DMS C 1 151 151 DMS DMS . K 2 ZN D 1 150 150 ZN ZN . # 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 O01 EF2 . . . F 3 -25.098 -26.732 -2.046 1 32.64 ? O01 EF2 151 A 1 HETATM 2 C C02 EF2 . . . F 3 -23.88 -26.794 -2.066 1 31.54 ? C02 EF2 151 A 1 HETATM 3 N N03 EF2 . . . F 3 -23.145 -25.695 -2.661 1 32.3 ? N03 EF2 151 A 1 HETATM 4 C C04 EF2 . . . F 3 -21.695 -25.742 -2.722 1 33.12 ? C04 EF2 151 A 1 HETATM 5 O O05 EF2 . . . F 3 -21.06 -24.841 -3.234 1 36.57 ? O05 EF2 151 A 1 HETATM 6 C C06 EF2 . . . F 3 -20.996 -26.972 -2.144 1 31.87 ? C06 EF2 151 A 1 HETATM 7 C C07 EF2 . . . F 3 -21.879 -28.178 -2.404 1 30.28 ? C07 EF2 151 A 1 HETATM 8 C C08 EF2 . . . F 3 -23.065 -27.969 -1.49 1 30.33 ? C08 EF2 151 A 1 HETATM 9 N N09 EF2 . . . F 3 -24.039 -29.023 -1.393 1 30.92 ? N09 EF2 151 A 1 HETATM 10 C C11 EF2 . . . F 3 -27.339 -32.146 -0.526 1 35.33 ? C11 EF2 151 A 1 HETATM 11 C C12 EF2 . . . F 3 -26.498 -31.266 0.15 1 33.18 ? C12 EF2 151 A 1 HETATM 12 C C13 EF2 . . . F 3 -25.661 -30.5 -0.613 1 31.95 ? C13 EF2 151 A 1 HETATM 13 C C14 EF2 . . . F 3 -25.599 -30.668 -1.987 1 33.43 ? C14 EF2 151 A 1 HETATM 14 O O16 EF2 . . . F 3 -24.435 -29.055 1.06 1 28.4 ? O16 EF2 151 A 1 HETATM 15 O O18 EF2 . . . F 3 -24.249 -29.539 -3.843 1 35.63 ? O18 EF2 151 A 1 HETATM 16 C C19 EF2 . . . F 3 -26.461 -31.5 -2.697 1 35.29 ? C19 EF2 151 A 1 HETATM 17 C C20 EF2 . . . F 3 -27.341 -32.25 -1.931 1 35.69 ? C20 EF2 151 A 1 HETATM 18 C C3 EF2 . . . F 3 -24.705 -29.646 -2.52 1 32.78 ? C3 EF2 151 A 1 HETATM 19 C C4 EF2 . . . F 3 -24.607 -29.581 -0.194 1 29.96 ? C4 EF2 151 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 495 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 19 #