data_5DNY # _model_server_result.job_id ssakOPgOu484zK6V5dNUGQ _model_server_result.datetime_utc '2024-11-05 01:00:16' _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 5dny # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 5DNY # _exptl.entry_id 5DNY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 24.305 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM 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 5DNY _cell.length_a 84.303 _cell.length_b 130.111 _cell.length_c 166.656 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DNY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,J,K,L,M,N _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 G N N ? 5 H N N ? 5 J N N ? 5 K 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 OD2 ASP 28 A ASP 8 1_555 G MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.902 ? metalc ? metalc2 A OD2 ASP 69 A ASP 49 1_555 G MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc3 A OD2 ASP 69 A ASP 49 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc4 C OD2 ASP 28 C ASP 8 1_555 K MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc5 C OD2 ASP 69 C ASP 49 1_555 J MG MG . C MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc6 C OD2 ASP 69 C ASP 49 1_555 K MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? hydrog WATSON-CRICK hydrog1 E N1 DG 4 E DG 4 1_555 F N3 DC 26 F DC -4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 E N2 DG 4 E DG 4 1_555 F O2 DC 26 F DC -4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 E O6 DG 4 E DG 4 1_555 F N4 DC 26 F DC -4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 E N3 DT 5 E DT 5 1_555 F N1 DA 25 F DA -5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 E O4 DT 5 E DT 5 1_555 F N6 DA 25 F DA -5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DC MISPAIR' hydrog6 E O4 DT 6 E DT 6 1_555 F N4 DC 23 F DC -7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 E N3 DT 6 E DT 6 1_555 F N1 DA 24 F DA -6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 E O4 DT 6 E DT 6 1_555 F N6 DA 24 F DA -6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog9 E O6 DG 7 E DG 7 1_555 F N4 DC 22 F DC -8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 E N1 DG 7 E DG 7 1_555 F N3 DC 23 F DC -7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 E N2 DG 7 E DG 7 1_555 F O2 DC 23 F DC -7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 E O6 DG 7 E DG 7 1_555 F N4 DC 23 F DC -7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 E N1 DG 8 E DG 8 1_555 F N3 DC 22 F DC -8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 E N2 DG 8 E DG 8 1_555 F O2 DC 22 F DC -8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 E O6 DG 8 E DG 8 1_555 F N4 DC 22 F DC -8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 E N1 DG 9 E DG 9 1_555 F N3 DC 21 F DC -9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 E N2 DG 9 E DG 9 1_555 F O2 DC 21 F DC -9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 E O6 DG 9 E DG 9 1_555 F N4 DC 21 F DC -9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog19 E N1 DA 10 E DA 10 1_555 F N3 DT 20 F DT -10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 E N3 DT 11 E DT 11 1_555 F N1 DA 19 F DA -11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 E O4 DT 11 E DT 11 1_555 F N6 DA 19 F DA -11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog22 E N3 DT 12 E DT 12 1_555 F N1 DA 18 F DA -12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog23 E N2 DG 13 E DG 13 1_555 F N3 DC 17 F DC -13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 E N1 DA 14 E DA 14 1_555 F N3 DT 16 F DT -14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 E N6 DA 14 E DA 14 1_555 F O4 DT 16 F DT -14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog26 E N2 DG 15 E DG 15 1_555 F O2 DC 15 F DC -15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog27 E N1 DA 16 E DA 16 1_555 F N3 DT 14 F DT -16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 E N3 DC 17 E DC 17 1_555 F N1 DG 13 F DG -17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 E N4 DC 17 E DC 17 1_555 F O6 DG 13 F DG -17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 E O2 DC 17 E DC 17 1_555 F N2 DG 13 F DG -17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog31 E N1 DA 18 E DA 18 1_555 F N3 DT 12 F DT -18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog32 E O2 DC 19 E DC 19 1_555 F N2 DG 11 F DG -19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 E N1 DA 20 E DA 20 1_555 F N3 DT 10 F DT -20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 E N6 DA 20 E DA 20 1_555 F O4 DT 10 F DT -20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog35 E N3 DC 21 E DC 21 1_555 F N2 DG 9 F DG -21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 E N1 DA 22 E DA 22 1_555 F N3 DT 8 F DT -22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 E N6 DA 22 E DA 22 1_555 F O4 DT 8 F DT -22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 E N3 DT 23 E DT 23 1_555 F N1 DA 7 F DA -23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 E O4 DT 23 E DT 23 1_555 F N6 DA 7 F DA -23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog40 E O2 DC 25 E DC 25 1_555 F N2 DG 5 F DG -25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 5DNY _atom_sites.fract_transf_matrix[1][1] 0.011862 _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] 0.007686 _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] 0.006 _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 G 5 MG A 1 401 1 MG MG . H 5 MG A 1 402 1 MG MG . I 6 AGS B 1 1101 1006 AGS AGS . J 5 MG C 1 401 1 MG MG . K 5 MG C 1 402 1 MG MG . L 6 AGS D 1 1101 1006 AGS AGS . M 7 HOH A 1 501 2 HOH HOH . N 7 HOH C 1 501 1 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 G _atom_site.label_entity_id 5 _atom_site.Cartn_x -23.969 _atom_site.Cartn_y 27.285 _atom_site.Cartn_z -62.258 _atom_site.occupancy 0.83 _atom_site.B_iso_or_equiv 92.17 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 401 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #