data_2YDF # _model_server_result.job_id mgIFwpJGvJv98BuRdxzgNw _model_server_result.datetime_utc '2024-11-26 05:31:14' _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 2ydf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2003}' # _entry.id 2YDF # _exptl.entry_id 2YDF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 571.917 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'IOPHENOXIC ACID' _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 81 _cell.angle_beta 90.83 _cell.angle_gamma 64.52 _cell.entry_id 2YDF _cell.length_a 55.072 _cell.length_b 55.44 _cell.length_c 119.845 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YDF _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # 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 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,K 1 1 B,G,H,I,J,L 2 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 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J 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 53 A CYS 53 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 90 A CYS 90 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 124 A CYS 124 1_555 A SG CYS 169 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 168 A CYS 168 1_555 A SG CYS 177 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 A SG CYS 200 A CYS 200 1_555 A SG CYS 246 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 A SG CYS 245 A CYS 245 1_555 A SG CYS 253 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 A SG CYS 265 A CYS 265 1_555 A SG CYS 279 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf9 A SG CYS 278 A CYS 278 1_555 A SG CYS 289 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 A SG CYS 316 A CYS 316 1_555 A SG CYS 361 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 A SG CYS 360 A CYS 360 1_555 A SG CYS 369 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 A SG CYS 392 A CYS 392 1_555 A SG CYS 438 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf13 A SG CYS 437 A CYS 437 1_555 A SG CYS 448 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf14 A SG CYS 461 A CYS 461 1_555 A SG CYS 477 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf15 A SG CYS 476 A CYS 476 1_555 A SG CYS 487 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf16 A SG CYS 514 A CYS 514 1_555 A SG CYS 559 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf17 A SG CYS 558 A CYS 558 1_555 A SG CYS 567 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf18 B SG CYS 53 B CYS 53 1_555 B SG CYS 62 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf19 B SG CYS 75 B CYS 75 1_555 B SG CYS 91 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf20 B SG CYS 90 B CYS 90 1_555 B SG CYS 101 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf21 B SG CYS 124 B CYS 124 1_555 B SG CYS 169 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf22 B SG CYS 168 B CYS 168 1_555 B SG CYS 177 B CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf23 B SG CYS 200 B CYS 200 1_555 B SG CYS 246 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf24 B SG CYS 245 B CYS 245 1_555 B SG CYS 253 B CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf25 B SG CYS 265 B CYS 265 1_555 B SG CYS 279 B CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf26 B SG CYS 278 B CYS 278 1_555 B SG CYS 289 B CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf27 B SG CYS 316 B CYS 316 1_555 B SG CYS 361 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf28 B SG CYS 360 B CYS 360 1_555 B SG CYS 369 B CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf29 B SG CYS 392 B CYS 392 1_555 B SG CYS 438 B CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf30 B SG CYS 437 B CYS 437 1_555 B SG CYS 448 B CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf31 B SG CYS 461 B CYS 461 1_555 B SG CYS 477 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf32 B SG CYS 476 B CYS 476 1_555 B SG CYS 487 B CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf33 B SG CYS 514 B CYS 514 1_555 B SG CYS 559 B CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf34 B SG CYS 558 B CYS 558 1_555 B SG CYS 567 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? # _chem_comp.formula 'C11 H11 I3 O3' _chem_comp.formula_weight 571.917 _chem_comp.id IO3 _chem_comp.mon_nstd_flag . _chem_comp.name 'IOPHENOXIC ACID' _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 O2 C9 IO3 doub 173 n n O3 C9 IO3 sing 174 n n C9 C8 IO3 sing 175 n n C11 C10 IO3 sing 176 n n C10 C8 IO3 sing 177 n n C8 C7 IO3 sing 178 n n C7 C1 IO3 sing 179 n n I3 C6 IO3 sing 180 n n I1 C2 IO3 sing 181 n n C1 C6 IO3 doub 182 n y C1 C2 IO3 sing 183 n y C6 C5 IO3 sing 184 n y C2 C3 IO3 doub 185 n y C5 O1 IO3 sing 186 n n C5 C4 IO3 doub 187 n y C3 C4 IO3 sing 188 n y C4 I2 IO3 sing 189 n n O1 H1 IO3 sing 190 n n O3 H2 IO3 sing 191 n n C3 H3 IO3 sing 192 n n C7 H4 IO3 sing 193 n n C7 H5 IO3 sing 194 n n C8 H6 IO3 sing 195 n n C10 H7 IO3 sing 196 n n C10 H8 IO3 sing 197 n n C11 H9 IO3 sing 198 n n C11 H10 IO3 sing 199 n n C11 H11 IO3 sing 200 n n # _atom_sites.entry_id 2YDF _atom_sites.fract_transf_matrix[1][1] 0.018158 _atom_sites.fract_transf_matrix[1][2] -0.008653 _atom_sites.fract_transf_matrix[1][3] 0.001853 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019981 _atom_sites.fract_transf_matrix[2][3] -0.003661 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008484 _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 2 IO3 A 1 2001 2001 IO3 IO3 . D 2 IO3 A 1 2002 2002 IO3 IO3 . E 2 IO3 A 1 2003 2003 IO3 IO3 . F 2 IO3 A 1 2004 2004 IO3 IO3 . G 2 IO3 B 1 2001 2001 IO3 IO3 . H 2 IO3 B 1 2002 2002 IO3 IO3 . I 2 IO3 B 1 2003 2003 IO3 IO3 . J 2 IO3 B 1 2004 2004 IO3 IO3 . K 3 HOH A 1 2006 2006 HOH HOH . K 3 HOH A 2 2007 2007 HOH HOH . K 3 HOH A 3 2008 2008 HOH HOH . K 3 HOH A 4 2009 2009 HOH HOH . K 3 HOH A 5 2010 2010 HOH HOH . K 3 HOH A 6 2011 2011 HOH HOH . K 3 HOH A 7 2012 2012 HOH HOH . K 3 HOH A 8 2013 2013 HOH HOH . K 3 HOH A 9 2014 2014 HOH HOH . K 3 HOH A 10 2015 2015 HOH HOH . K 3 HOH A 11 2016 2016 HOH HOH . K 3 HOH A 12 2017 2017 HOH HOH . L 3 HOH B 1 2006 2006 HOH HOH . L 3 HOH B 2 2007 2007 HOH HOH . L 3 HOH B 3 2008 2008 HOH HOH . L 3 HOH B 4 2009 2009 HOH HOH . L 3 HOH B 5 2010 2010 HOH HOH . L 3 HOH B 6 2011 2011 HOH HOH . L 3 HOH B 7 2012 2012 HOH HOH . L 3 HOH B 8 2013 2013 HOH HOH . L 3 HOH B 9 2014 2014 HOH HOH . L 3 HOH B 10 2015 2015 HOH HOH . L 3 HOH B 11 2016 2016 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 I I1 IO3 . . . E 2 0.537 7.645 7.361 1 82.39 ? I1 IO3 2003 A 1 HETATM 2 I I2 IO3 . . . E 2 3.747 10.321 11.71 1 201.39 ? I2 IO3 2003 A 1 HETATM 3 I I3 IO3 . . . E 2 0.397 13.72 8.092 1 184.49 ? I3 IO3 2003 A 1 HETATM 4 O O1 IO3 . . . E 2 2.355 12.816 10.373 1 71.7 ? O1 IO3 2003 A 1 HETATM 5 O O2 IO3 . . . E 2 -0.501 9.071 4.042 1 88.18 ? O2 IO3 2003 A 1 HETATM 6 O O3 IO3 . . . E 2 -1.884 10.745 4.267 1 87.03 ? O3 IO3 2003 A 1 HETATM 7 C C1 IO3 . . . E 2 0.655 10.679 7.957 1 86.08 ? C1 IO3 2003 A 1 HETATM 8 C C2 IO3 . . . E 2 1.119 9.422 8.348 1 86.78 ? C2 IO3 2003 A 1 HETATM 9 C C3 IO3 . . . E 2 1.998 9.314 9.416 1 82.6 ? C3 IO3 2003 A 1 HETATM 10 C C4 IO3 . . . E 2 2.409 10.451 10.09 1 77.47 ? C4 IO3 2003 A 1 HETATM 11 C C5 IO3 . . . E 2 1.945 11.69 9.704 1 74.31 ? C5 IO3 2003 A 1 HETATM 12 C C6 IO3 . . . E 2 1.072 11.805 8.646 1 78.98 ? C6 IO3 2003 A 1 HETATM 13 C C7 IO3 . . . E 2 -0.298 10.85 6.82 1 87.78 ? C7 IO3 2003 A 1 HETATM 14 C C8 IO3 . . . E 2 0.206 10.898 5.416 1 88.13 ? C8 IO3 2003 A 1 HETATM 15 C C9 IO3 . . . E 2 -0.776 10.2 4.529 1 87.74 ? C9 IO3 2003 A 1 HETATM 16 C C10 IO3 . . . E 2 0.319 12.322 4.979 1 88.59 ? C10 IO3 2003 A 1 HETATM 17 C C11 IO3 . . . E 2 1.612 12.813 4.418 1 86.61 ? C11 IO3 2003 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 17 #