data_4CI1 # _model_server_result.job_id Hh_OzQkhUnN3l0IQxV4Yew _model_server_result.datetime_utc '2024-12-02 00:32:46' _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 4ci1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1429}' # _entry.id 4CI1 # _exptl.entry_id 4CI1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 258.229 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-Thalidomide _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 4CI1 _cell.length_a 172.18 _cell.length_b 172.18 _cell.length_c 140.09 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CI1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 ALA 104 A ALA 86 1_555 A N CAF 105 A CAF 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale2 A C CAF 105 A CAF 87 1_555 A N ILE 106 A ILE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? covale ? covale3 A C VAL 994 A VAL 976 1_555 A N CAF 995 A CAF 977 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale4 A C CAF 995 A CAF 977 1_555 A N GLN 996 A GLN 978 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale5 B C ARG 335 B ARG 311 1_555 B N CAF 336 B CAF 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale6 B C CAF 336 B CAF 312 1_555 B N GLU 337 B GLU 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale7 B C LYS 343 B LYS 319 1_555 B N CAF 344 B CAF 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale8 B C CAF 344 B CAF 320 1_555 B N THR 345 B THR 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? metalc ? metalc1 B SG CYS 349 B CYS 325 1_555 C ZN ZN . B ZN 1428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc2 B SG CYS 352 B CYS 328 1_555 C ZN ZN . B ZN 1428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc3 B SG CYS 417 B CYS 393 1_555 C ZN ZN . B ZN 1428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc4 B SG CYS 420 B CYS 396 1_555 C ZN ZN . B ZN 1428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? # _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 105 n n C02 N03 EF2 sing 106 n n C02 C08 EF2 sing 107 n n N03 C04 EF2 sing 108 n n C04 O05 EF2 doub 109 n n C04 C06 EF2 sing 110 n n C06 C07 EF2 sing 111 n n C07 C08 EF2 sing 112 n n C08 N09 EF2 sing 113 n n N09 C3 EF2 sing 114 n n N09 C4 EF2 sing 115 n n C11 C12 EF2 sing 116 n y C11 C20 EF2 doub 117 n y C12 C13 EF2 doub 118 n y C13 C14 EF2 sing 119 n y C13 C4 EF2 sing 120 n n C14 C19 EF2 doub 121 n y C14 C3 EF2 sing 122 n n O16 C4 EF2 doub 123 n n O18 C3 EF2 doub 124 n n C19 C20 EF2 sing 125 n y N03 H03 EF2 sing 126 n n C08 H08 EF2 sing 127 n n C06 H061 EF2 sing 128 n n C06 H062 EF2 sing 129 n n C07 H071 EF2 sing 130 n n C07 H072 EF2 sing 131 n n C11 H11 EF2 sing 132 n n C12 H12 EF2 sing 133 n n C20 H20 EF2 sing 134 n n C19 H19 EF2 sing 135 n n # _atom_sites.entry_id 4CI1 _atom_sites.fract_transf_matrix[1][1] 0.005808 _atom_sites.fract_transf_matrix[1][2] 0.003353 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006706 _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] 0.007138 _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 3 ZN B 1 1428 1428 ZN ZN . D 4 EF2 B 1 1429 1429 EF2 EF2 . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . F 5 HOH B 1 2001 2001 HOH HOH . F 5 HOH B 2 2002 2002 HOH HOH . F 5 HOH B 3 2003 2003 HOH HOH . F 5 HOH B 4 2004 2004 HOH HOH . F 5 HOH B 5 2005 2005 HOH HOH . F 5 HOH B 6 2006 2006 HOH HOH . F 5 HOH B 7 2007 2007 HOH HOH . F 5 HOH B 8 2008 2008 HOH HOH . F 5 HOH B 9 2009 2009 HOH HOH . F 5 HOH B 10 2010 2010 HOH HOH . F 5 HOH B 11 2011 2011 HOH HOH . F 5 HOH B 12 2012 2012 HOH HOH . F 5 HOH B 13 2013 2013 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 O01 EF2 . . . D 4 -1.923 7.695 11.553 1 55.43 ? O01 EF2 1429 B 1 HETATM 2 C C02 EF2 . . . D 4 -1.715 8.198 12.649 1 55.37 ? C02 EF2 1429 B 1 HETATM 3 N N03 EF2 . . . D 4 -1.294 9.48 12.795 1 56.72 ? N03 EF2 1429 B 1 HETATM 4 C C04 EF2 . . . D 4 -1.071 10.098 13.979 1 55.85 ? C04 EF2 1429 B 1 HETATM 5 O O05 EF2 . . . D 4 -0.693 11.248 14.006 1 60.02 ? O05 EF2 1429 B 1 HETATM 6 C C06 EF2 . . . D 4 -1.306 9.377 15.284 1 52.16 ? C06 EF2 1429 B 1 HETATM 7 C C07 EF2 . . . D 4 -1.111 7.854 15.077 1 52.64 ? C07 EF2 1429 B 1 HETATM 8 C C08 EF2 . . . D 4 -2.001 7.399 13.899 1 54.53 ? C08 EF2 1429 B 1 HETATM 9 N N09 EF2 . . . D 4 -1.896 5.966 13.669 1 55.35 ? N09 EF2 1429 B 1 HETATM 10 C C11 EF2 . . . D 4 -1.16 1.494 12.472 1 46.02 ? C11 EF2 1429 B 1 HETATM 11 C C12 EF2 . . . D 4 -0.521 2.751 12.388 1 48.48 ? C12 EF2 1429 B 1 HETATM 12 C C13 EF2 . . . D 4 -1.227 3.848 12.907 1 53.33 ? C13 EF2 1429 B 1 HETATM 13 C C14 EF2 . . . D 4 -2.505 3.704 13.476 1 50.9 ? C14 EF2 1429 B 1 HETATM 14 O O16 EF2 . . . D 4 0.186 5.793 12.604 1 63.42 ? O16 EF2 1429 B 1 HETATM 15 O O18 EF2 . . . D 4 -3.993 5.348 14.401 1 49.65 ? O18 EF2 1429 B 1 HETATM 16 C C19 EF2 . . . D 4 -3.147 2.454 13.535 1 47.53 ? C19 EF2 1429 B 1 HETATM 17 C C20 EF2 . . . D 4 -2.454 1.343 13.013 1 45.68 ? C20 EF2 1429 B 1 HETATM 18 C C3 EF2 . . . D 4 -2.9 5.091 13.926 1 51.75 ? C3 EF2 1429 B 1 HETATM 19 C C4 EF2 . . . D 4 -0.868 5.316 13.043 1 58.89 ? C4 EF2 1429 B 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #