data_5YPX # _model_server_result.job_id LKDtkzDRgfGcsgLkTUH12g _model_server_result.datetime_utc '2025-03-06 09:52:02' _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 5ypx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 5YPX # _exptl.entry_id 5YPX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 24.305 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM ION' _entity.pdbx_number_of_molecules 5 _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 5YPX _cell.length_a 65.258 _cell.length_b 65.258 _cell.length_c 113.203 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YPX _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 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 OD1 ASP 91 A ASP 71 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc2 A OD1 ASP 93 A ASP 73 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc3 A OD1 ASP 95 A ASP 75 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc4 A OD2 ASP 95 A ASP 75 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc5 A O TYR 97 A TYR 77 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc6 A OE1 GLU 102 A GLU 82 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc7 A OD1 ASP 127 A ASP 107 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc8 A OD1 ASN 129 A ASN 109 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc9 A OD1 ASP 131 A ASP 111 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc10 A O TYR 133 A TYR 113 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc11 A OE1 GLU 138 A GLU 118 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc12 A OE2 GLU 138 A GLU 118 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc13 B OD1 ASP 91 B ASP 71 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc14 B OD1 ASP 93 B ASP 73 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc15 B OD2 ASP 93 B ASP 73 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc16 B OD1 ASP 95 B ASP 75 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc17 B O TYR 97 B TYR 77 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc18 B OE1 GLU 102 B GLU 82 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc19 B OD1 ASP 127 B ASP 107 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc20 B OD1 ASN 129 B ASN 109 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc21 B OD1 ASP 131 B ASP 111 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc22 B O TYR 133 B TYR 113 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc23 B OE1 GLU 138 B GLU 118 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc24 B OE2 GLU 138 B GLU 118 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc25 B OD1 ASP 172 B ASP 152 1_555 G MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc26 B OD1 ASP 174 B ASP 154 1_555 G MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc27 B OD1 ASP 176 B ASP 156 1_555 G MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc28 B O ARG 178 B ARG 158 1_555 G MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? metalc ? metalc29 B OD2 ASP 183 B ASP 163 1_555 G MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? # _chem_comp.formula 'Mg 2' _chem_comp.formula_weight 24.305 _chem_comp.id MG _chem_comp.mon_nstd_flag . _chem_comp.name 'MAGNESIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5YPX _atom_sites.fract_transf_matrix[1][1] 0.015324 _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] 0.015324 _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] 0.008834 _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 MG A 1 301 1 MG MG . D 2 MG A 1 302 2 MG MG . E 2 MG B 1 301 3 MG MG . F 2 MG B 1 302 4 MG MG . G 2 MG B 1 303 5 MG MG . H 3 HOH A 1 401 19 HOH HOH . H 3 HOH A 2 402 8 HOH HOH . H 3 HOH A 3 403 4 HOH HOH . H 3 HOH A 4 404 17 HOH HOH . H 3 HOH A 5 405 26 HOH HOH . H 3 HOH A 6 406 40 HOH HOH . I 3 HOH B 1 401 5 HOH HOH . I 3 HOH B 2 402 30 HOH HOH . I 3 HOH B 3 403 41 HOH HOH . I 3 HOH B 4 404 9 HOH HOH . I 3 HOH B 5 405 27 HOH HOH . I 3 HOH B 6 406 11 HOH HOH . I 3 HOH B 7 407 33 HOH HOH . I 3 HOH B 8 408 43 HOH HOH . I 3 HOH B 9 409 22 HOH HOH . I 3 HOH B 10 410 13 HOH HOH . I 3 HOH B 11 411 2 HOH HOH . I 3 HOH B 12 412 6 HOH HOH . I 3 HOH B 13 413 28 HOH HOH . I 3 HOH B 14 414 10 HOH HOH . I 3 HOH B 15 415 7 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MG _atom_site.label_atom_id MG _atom_site.label_comp_id MG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 2 _atom_site.Cartn_x 24.76 _atom_site.Cartn_y -32.226 _atom_site.Cartn_z 13.065 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 29.84 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 302 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #