data_2YDF
#
_model_server_result.job_id            awrpHmHt6VpSq0HqR9iAYw 
_model_server_result.datetime_utc      '2024-11-04 22:18:48' 
_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":"D","auth_seq_id":2002}' 
#
_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 . . . D 2 9.684 -2.357 -15.115 1 37.12 ? I1 IO3 2002 A 1 
HETATM 2 I I2 IO3 . . . D 2 13.693 1.002 -12.392 1 41.84 ? I2 IO3 2002 A 1 
HETATM 3 I I3 IO3 . . . D 2 8.469 3.521 -14.226 1 48.59 ? I3 IO3 2002 A 1 
HETATM 4 O O1 IO3 . . . D 2 11.409 3.224 -12.925 1 33.84 ? O1 IO3 2002 A 1 
HETATM 5 O O2 IO3 . . . D 2 5.703 0.679 -17.748 1 29.28 ? O2 IO3 2002 A 1 
HETATM 6 O O3 IO3 . . . D 2 6.569 2.349 -16.646 1 25.74 ? O3 IO3 2002 A 1 
HETATM 7 C C1 IO3 . . . D 2 9.346 0.646 -14.542 1 28.09 ? C1 IO3 2002 A 1 
HETATM 8 C C2 IO3 . . . D 2 10.186 -0.444 -14.406 1 30.11 ? C2 IO3 2002 A 1 
HETATM 9 C C3 IO3 . . . D 2 11.409 -0.306 -13.795 1 34.35 ? C3 IO3 2002 A 1 
HETATM 10 C C4 IO3 . . . D 2 11.809 0.911 -13.307 1 33.03 ? C4 IO3 2002 A 1 
HETATM 11 C C5 IO3 . . . D 2 10.991 2.012 -13.42 1 30.61 ? C5 IO3 2002 A 1 
HETATM 12 C C6 IO3 . . . D 2 9.756 1.87 -14.035 1 27.41 ? C6 IO3 2002 A 1 
HETATM 13 C C7 IO3 . . . D 2 8.002 0.509 -15.181 1 25.88 ? C7 IO3 2002 A 1 
HETATM 14 C C8 IO3 . . . D 2 7.796 0.302 -16.64 1 26.64 ? C8 IO3 2002 A 1 
HETATM 15 C C9 IO3 . . . D 2 6.633 1.154 -17.042 1 25.8 ? C9 IO3 2002 A 1 
HETATM 16 C C10 IO3 . . . D 2 9.018 0.721 -17.379 1 35.68 ? C10 IO3 2002 A 1 
HETATM 17 C C11 IO3 . . . D 2 8.978 0.593 -18.868 1 39.85 ? C11 IO3 2002 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           17 
#