data_1YNT # _model_server_result.job_id hpWsqiMvgEXVwUqHqiRV7A _model_server_result.datetime_utc '2025-07-05 21:17:39' _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 1ynt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":4002}' # _entry.id 1YNT # _exptl.entry_id 1YNT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 112.411 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CADMIUM ION' _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 89.97 _cell.angle_gamma 90 _cell.entry_id 1YNT _cell.length_a 71.034 _cell.length_b 198.285 _cell.length_c 128.366 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YNT _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 H N N ? 5 I 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 23 A CYS 23 1_555 A SG CYS 88 A CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 A SG CYS 134 A CYS 134 1_555 A SG CYS 194 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 B SG CYS 22 B CYS 522 1_555 B SG CYS 96 B CYS 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 B SG CYS 145 B CYS 645 1_555 B SG CYS 200 B CYS 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf5 C SG CYS 23 C CYS 1023 1_555 C SG CYS 88 C CYS 1088 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf6 C SG CYS 134 C CYS 1134 1_555 C SG CYS 194 C CYS 1194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 D SG CYS 22 D CYS 1522 1_555 D SG CYS 96 D CYS 1596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 D SG CYS 145 D CYS 1645 1_555 D SG CYS 200 D CYS 1700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 F SG CYS 11 F CYS 2012 1_555 F SG CYS 121 F CYS 2122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf10 F SG CYS 33 F CYS 2034 1_555 F SG CYS 112 F CYS 2113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf11 F SG CYS 53 F CYS 2054 1_555 F SG CYS 61 F CYS 2062 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 F SG CYS 141 F CYS 2142 1_555 F SG CYS 246 F CYS 2247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf13 F SG CYS 166 F CYS 2167 1_555 F SG CYS 236 F CYS 2237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf14 F SG CYS 181 F CYS 2182 1_555 F SG CYS 189 F CYS 2190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 G SG CYS 11 G CYS 3012 1_555 G SG CYS 121 G CYS 3122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf16 G SG CYS 33 G CYS 3034 1_555 G SG CYS 112 G CYS 3113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf17 G SG CYS 53 G CYS 3054 1_555 G SG CYS 61 G CYS 3062 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf18 G SG CYS 141 G CYS 3142 1_555 G SG CYS 246 G CYS 3247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf19 G SG CYS 166 G CYS 3167 1_555 G SG CYS 236 G CYS 3237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf20 G SG CYS 181 G CYS 3182 1_555 G SG CYS 189 G CYS 3190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _chem_comp.formula 'Cd 2' _chem_comp.formula_weight 112.411 _chem_comp.id CD _chem_comp.mon_nstd_flag . _chem_comp.name 'CADMIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1YNT _atom_sites.fract_transf_matrix[1][1] 0.014078 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] -0.000007 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005043 _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] 0.00779 _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 H 5 CD B 1 4001 4001 CD CD . I 5 CD D 1 4002 4002 CD CD . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CD _atom_site.label_atom_id CD _atom_site.label_comp_id CD _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id I _atom_site.label_entity_id 5 _atom_site.Cartn_x -2.393 _atom_site.Cartn_y -55.134 _atom_site.Cartn_z 71.435 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 115.34 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CD _atom_site.auth_comp_id CD _atom_site.auth_seq_id 4002 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #