data_3PH5 # _model_server_result.job_id BiKZE3t6fQGl74M5QcD-jA _model_server_result.datetime_utc '2024-12-12 17:35:31' _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 3ph5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":4}' # _entry.id 3PH5 # _exptl.entry_id 3PH5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.906 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'YTTRIUM (III) ION' _entity.pdbx_number_of_molecules 4 _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 3PH5 _cell.length_a 40.8 _cell.length_b 63.57 _cell.length_c 134.03 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PH5 _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 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,I 1 1 B,G,H,J 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 G N N ? 2 H 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 65 A CYS 82 1_555 A SG CYS 159 A CYS 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 105 A CYS 122 1_555 A SG CYS 118 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 B SG CYS 65 B CYS 82 1_555 B SG CYS 159 B CYS 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 B SG CYS 105 B CYS 122 1_555 B SG CYS 118 B CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc1 C Y YT3 . A YT3 1 1_555 A OE1 GLU 50 A GLU 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.621 ? metalc ? metalc2 C Y YT3 . A YT3 1 1_555 A OD2 ASP 52 A ASP 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc3 C Y YT3 . A YT3 1 1_555 A OE2 GLU 73 A GLU 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc4 C Y YT3 . A YT3 1 3_554 A OE1 GLU 156 A GLU 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc5 D Y YT3 . A YT3 2 1_555 A OE2 GLU 126 A GLU 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc6 D Y YT3 . A YT3 2 1_555 A OE1 GLU 126 A GLU 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc7 G Y YT3 . B YT3 3 1_555 B OE2 GLU 64 B GLU 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc8 G Y YT3 . B YT3 3 1_555 B OE1 GLU 64 B GLU 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc9 H Y YT3 . B YT3 4 1_555 B OD2 ASP 129 B ASP 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc10 H Y YT3 . B YT3 4 1_555 B OD1 ASP 129 B ASP 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.352 ? # _chem_comp.formula 'Y 3' _chem_comp.formula_weight 88.906 _chem_comp.id YT3 _chem_comp.mon_nstd_flag . _chem_comp.name 'YTTRIUM (III) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3PH5 _atom_sites.fract_transf_matrix[1][1] 0.02451 _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] 0.015731 _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] 0.007461 _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 YT3 A 1 1 1 YT3 YT3 . D 2 YT3 A 1 2 2 YT3 YT3 . E 3 CL A 1 5 5 CL CL . F 3 CL A 1 6 6 CL CL . G 2 YT3 B 1 3 3 YT3 YT3 . H 2 YT3 B 1 4 4 YT3 YT3 . I 4 HOH A 1 3 3 HOH HOH . I 4 HOH A 2 4 4 HOH HOH . I 4 HOH A 3 8 8 HOH HOH . I 4 HOH A 4 10 10 HOH HOH . I 4 HOH A 5 11 11 HOH HOH . I 4 HOH A 6 12 12 HOH HOH . I 4 HOH A 7 13 13 HOH HOH . I 4 HOH A 8 14 14 HOH HOH . I 4 HOH A 9 16 16 HOH HOH . I 4 HOH A 10 179 1 HOH HOH . I 4 HOH A 11 180 2 HOH HOH . I 4 HOH A 12 181 5 HOH HOH . I 4 HOH A 13 182 22 HOH HOH . I 4 HOH A 14 183 23 HOH HOH . I 4 HOH A 15 184 32 HOH HOH . I 4 HOH A 16 185 35 HOH HOH . I 4 HOH A 17 186 37 HOH HOH . I 4 HOH A 18 187 40 HOH HOH . I 4 HOH A 19 188 41 HOH HOH . I 4 HOH A 20 189 44 HOH HOH . I 4 HOH A 21 190 49 HOH HOH . I 4 HOH A 22 191 50 HOH HOH . I 4 HOH A 23 192 53 HOH HOH . I 4 HOH A 24 193 54 HOH HOH . J 4 HOH B 1 15 15 HOH HOH . J 4 HOH B 2 179 19 HOH HOH . J 4 HOH B 3 180 20 HOH HOH . J 4 HOH B 4 181 21 HOH HOH . J 4 HOH B 5 182 27 HOH HOH . J 4 HOH B 6 183 28 HOH HOH . J 4 HOH B 7 184 29 HOH HOH . J 4 HOH B 8 185 31 HOH HOH . J 4 HOH B 9 186 36 HOH HOH . J 4 HOH B 10 187 38 HOH HOH . J 4 HOH B 11 188 42 HOH HOH . J 4 HOH B 12 189 46 HOH HOH . J 4 HOH B 13 190 48 HOH HOH . J 4 HOH B 14 191 51 HOH HOH . J 4 HOH B 15 192 52 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol Y _atom_site.label_atom_id Y _atom_site.label_comp_id YT3 _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id H _atom_site.label_entity_id 2 _atom_site.Cartn_x -4.857 _atom_site.Cartn_y -13.738 _atom_site.Cartn_z -1.304 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 34.45 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id Y _atom_site.auth_comp_id YT3 _atom_site.auth_seq_id 4 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 368 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #