data_5AMI # _model_server_result.job_id d1iw4cKUciUQZ8aV944jxA _model_server_result.datetime_utc '2024-12-02 07:41:08' _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 5ami # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":151}' # _entry.id 5AMI # _exptl.entry_id 5AMI _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 90 _cell.entry_id 5AMI _cell.length_a 57.25 _cell.length_b 59.656 _cell.length_c 86.728 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AMI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,I 1 1 B,F,G,J 2 1 C,H,K 3 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 E N N ? 3 G 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 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc2 A SG CYS 28 A CYS 27 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc3 A SG CYS 91 A CYS 90 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc4 A SG CYS 94 A CYS 93 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc5 B SG CYS 25 B CYS 24 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc6 B SG CYS 28 B CYS 27 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc7 B SG CYS 91 B CYS 90 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc8 B SG CYS 94 B CYS 93 1_555 F ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc9 C SG CYS 25 C CYS 24 1_555 H ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc10 C SG CYS 28 C CYS 27 1_555 H ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc11 C SG CYS 91 C CYS 90 1_555 H ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc12 C SG CYS 94 C CYS 93 1_555 H ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? # _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 83 n n C02 N03 EF2 sing 84 n n C02 C08 EF2 sing 85 n n N03 C04 EF2 sing 86 n n C04 O05 EF2 doub 87 n n C04 C06 EF2 sing 88 n n C06 C07 EF2 sing 89 n n C07 C08 EF2 sing 90 n n C08 N09 EF2 sing 91 n n N09 C3 EF2 sing 92 n n N09 C4 EF2 sing 93 n n C11 C12 EF2 sing 94 n y C11 C20 EF2 doub 95 n y C12 C13 EF2 doub 96 n y C13 C14 EF2 sing 97 n y C13 C4 EF2 sing 98 n n C14 C19 EF2 doub 99 n y C14 C3 EF2 sing 100 n n O16 C4 EF2 doub 101 n n O18 C3 EF2 doub 102 n n C19 C20 EF2 sing 103 n y N03 H03 EF2 sing 104 n n C08 H08 EF2 sing 105 n n C06 H061 EF2 sing 106 n n C06 H062 EF2 sing 107 n n C07 H071 EF2 sing 108 n n C07 H072 EF2 sing 109 n n C11 H11 EF2 sing 110 n n C12 H12 EF2 sing 111 n n C20 H20 EF2 sing 112 n n C19 H19 EF2 sing 113 n n # _atom_sites.entry_id 5AMI _atom_sites.fract_transf_matrix[1][1] 0.017467 _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] 0.016763 _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] 0.01153 _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 2 ZN A 1 150 150 ZN ZN . E 3 EF2 A 1 151 151 EF2 EF2 . F 2 ZN B 1 150 150 ZN ZN . G 3 EF2 B 1 151 151 EF2 EF2 . H 2 ZN C 1 150 150 ZN ZN . I 4 HOH A 1 2001 2001 HOH HOH . I 4 HOH A 2 2002 2002 HOH HOH . I 4 HOH A 3 2003 2003 HOH HOH . I 4 HOH A 4 2004 2004 HOH HOH . I 4 HOH A 5 2005 2005 HOH HOH . I 4 HOH A 6 2006 2006 HOH HOH . I 4 HOH A 7 2007 2007 HOH HOH . I 4 HOH A 8 2008 2008 HOH HOH . I 4 HOH A 9 2009 2009 HOH HOH . I 4 HOH A 10 2010 2010 HOH HOH . I 4 HOH A 11 2011 2011 HOH HOH . I 4 HOH A 12 2012 2012 HOH HOH . I 4 HOH A 13 2013 2013 HOH HOH . I 4 HOH A 14 2014 2014 HOH HOH . I 4 HOH A 15 2015 2015 HOH HOH . I 4 HOH A 16 2016 2016 HOH HOH . I 4 HOH A 17 2017 2017 HOH HOH . I 4 HOH A 18 2018 2018 HOH HOH . I 4 HOH A 19 2019 2019 HOH HOH . I 4 HOH A 20 2020 2020 HOH HOH . I 4 HOH A 21 2021 2021 HOH HOH . I 4 HOH A 22 2022 2022 HOH HOH . I 4 HOH A 23 2023 2023 HOH HOH . I 4 HOH A 24 2024 2024 HOH HOH . I 4 HOH A 25 2025 2025 HOH HOH . I 4 HOH A 26 2026 2026 HOH HOH . I 4 HOH A 27 2027 2027 HOH HOH . I 4 HOH A 28 2028 2028 HOH HOH . I 4 HOH A 29 2029 2029 HOH HOH . I 4 HOH A 30 2030 2030 HOH HOH . I 4 HOH A 31 2031 2031 HOH HOH . I 4 HOH A 32 2032 2032 HOH HOH . I 4 HOH A 33 2033 2033 HOH HOH . I 4 HOH A 34 2034 2034 HOH HOH . I 4 HOH A 35 2035 2035 HOH HOH . I 4 HOH A 36 2036 2036 HOH HOH . I 4 HOH A 37 2037 2037 HOH HOH . I 4 HOH A 38 2038 2038 HOH HOH . I 4 HOH A 39 2039 2039 HOH HOH . I 4 HOH A 40 2040 2040 HOH HOH . I 4 HOH A 41 2041 2041 HOH HOH . I 4 HOH A 42 2042 2042 HOH HOH . I 4 HOH A 43 2043 2043 HOH HOH . I 4 HOH A 44 2044 2044 HOH HOH . I 4 HOH A 45 2045 2045 HOH HOH . I 4 HOH A 46 2046 2046 HOH HOH . I 4 HOH A 47 2047 2047 HOH HOH . I 4 HOH A 48 2048 2048 HOH HOH . I 4 HOH A 49 2049 2049 HOH HOH . I 4 HOH A 50 2050 2050 HOH HOH . I 4 HOH A 51 2051 2051 HOH HOH . I 4 HOH A 52 2052 2052 HOH HOH . I 4 HOH A 53 2053 2053 HOH HOH . J 4 HOH B 1 2001 2001 HOH HOH . J 4 HOH B 2 2002 2002 HOH HOH . J 4 HOH B 3 2003 2003 HOH HOH . J 4 HOH B 4 2004 2004 HOH HOH . J 4 HOH B 5 2005 2005 HOH HOH . J 4 HOH B 6 2006 2006 HOH HOH . J 4 HOH B 7 2007 2007 HOH HOH . J 4 HOH B 8 2008 2008 HOH HOH . J 4 HOH B 9 2009 2009 HOH HOH . J 4 HOH B 10 2010 2010 HOH HOH . J 4 HOH B 11 2011 2011 HOH HOH . J 4 HOH B 12 2012 2012 HOH HOH . J 4 HOH B 13 2013 2013 HOH HOH . J 4 HOH B 14 2014 2014 HOH HOH . J 4 HOH B 15 2015 2015 HOH HOH . J 4 HOH B 16 2016 2016 HOH HOH . J 4 HOH B 17 2017 2017 HOH HOH . J 4 HOH B 18 2018 2018 HOH HOH . J 4 HOH B 19 2019 2019 HOH HOH . J 4 HOH B 20 2020 2020 HOH HOH . J 4 HOH B 21 2021 2021 HOH HOH . J 4 HOH B 22 2022 2022 HOH HOH . J 4 HOH B 23 2023 2023 HOH HOH . J 4 HOH B 24 2024 2024 HOH HOH . J 4 HOH B 25 2025 2025 HOH HOH . J 4 HOH B 26 2026 2026 HOH HOH . J 4 HOH B 27 2027 2027 HOH HOH . J 4 HOH B 28 2028 2028 HOH HOH . J 4 HOH B 29 2029 2029 HOH HOH . J 4 HOH B 30 2030 2030 HOH HOH . J 4 HOH B 31 2031 2031 HOH HOH . J 4 HOH B 32 2032 2032 HOH HOH . J 4 HOH B 33 2033 2033 HOH HOH . J 4 HOH B 34 2034 2034 HOH HOH . J 4 HOH B 35 2035 2035 HOH HOH . K 4 HOH C 1 2001 2001 HOH HOH . K 4 HOH C 2 2002 2002 HOH HOH . K 4 HOH C 3 2003 2003 HOH HOH . K 4 HOH C 4 2004 2004 HOH HOH . K 4 HOH C 5 2005 2005 HOH HOH . K 4 HOH C 6 2006 2006 HOH HOH . K 4 HOH C 7 2007 2007 HOH HOH . K 4 HOH C 8 2008 2008 HOH HOH . K 4 HOH C 9 2009 2009 HOH HOH . K 4 HOH C 10 2010 2010 HOH HOH . K 4 HOH C 11 2011 2011 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 . . . G 3 22.399 16.035 25.51 1 24.02 ? O01 EF2 151 B 1 HETATM 2 C C02 EF2 . . . G 3 23.086 15.122 25.999 1 24.61 ? C02 EF2 151 B 1 HETATM 3 N N03 EF2 . . . G 3 22.723 13.858 25.457 1 25.37 ? N03 EF2 151 B 1 HETATM 4 C C04 EF2 . . . G 3 23.448 12.627 25.746 1 24.68 ? C04 EF2 151 B 1 HETATM 5 O O05 EF2 . . . G 3 23.119 11.624 25.163 1 24.58 ? O05 EF2 151 B 1 HETATM 6 C C06 EF2 . . . G 3 24.572 12.784 26.723 1 23.39 ? C06 EF2 151 B 1 HETATM 7 C C07 EF2 . . . G 3 24.361 13.862 27.77 1 24.38 ? C07 EF2 151 B 1 HETATM 8 C C08 EF2 . . . G 3 24.262 15.208 27.053 1 24.39 ? C08 EF2 151 B 1 HETATM 9 N N09 EF2 . . . G 3 23.91 16.325 27.853 1 25.4 ? N09 EF2 151 B 1 HETATM 10 C C11 EF2 . . . G 3 23.323 20.42 30.099 1 36.04 ? C11 EF2 151 B 1 HETATM 11 C C12 EF2 . . . G 3 24.264 19.795 29.264 1 33.43 ? C12 EF2 151 B 1 HETATM 12 C C13 EF2 . . . G 3 23.951 18.482 28.852 1 30.42 ? C13 EF2 151 B 1 HETATM 13 C C14 EF2 . . . G 3 22.747 17.884 29.199 1 30.32 ? C14 EF2 151 B 1 HETATM 14 O O16 EF2 . . . G 3 25.847 17.548 27.424 1 24.81 ? O16 EF2 151 B 1 HETATM 15 O O18 EF2 . . . G 3 21.752 15.643 28.625 1 29.35 ? O18 EF2 151 B 1 HETATM 16 C C19 EF2 . . . G 3 21.794 18.495 30.013 1 32.5 ? C19 EF2 151 B 1 HETATM 17 C C20 EF2 . . . G 3 22.08 19.817 30.434 1 36.79 ? C20 EF2 151 B 1 HETATM 18 C C3 EF2 . . . G 3 22.757 16.53 28.667 1 27.05 ? C3 EF2 151 B 1 HETATM 19 C C4 EF2 . . . G 3 24.705 17.469 28.107 1 25.89 ? C4 EF2 151 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 473 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 19 #