data_3DYL # _model_server_result.job_id 21FubnrGtrcHCu3VoeJZ-g _model_server_result.datetime_utc '2024-11-23 04:49:42' _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 3dyl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":902}' # _entry.id 3DYL # _exptl.entry_id 3DYL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 24.305 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM 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 90 _cell.angle_gamma 90 _cell.entry_id 3DYL _cell.length_a 103.787 _cell.length_b 103.787 _cell.length_c 269.799 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DYL _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # 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 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,J 1 1 B,F,G,H,I,K 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 ? 3 D N N ? 3 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 OD2 ASP 116 A ASP 293 1_555 C MN MN . A MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc2 A OD1 ASP 116 A ASP 293 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc3 A OD1 ASP 225 A ASP 402 1_555 C MN MN . A MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc4 E O1A PCG . A PCG 900 1_555 C MN MN . A MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc5 E O2A PCG . A PCG 900 1_555 D MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? metalc ? metalc6 C MN MN . A MN 901 1_555 J O HOH . A HOH 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? metalc ? metalc7 D MG MG . A MG 902 1_555 J O HOH . A HOH 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc8 D MG MG . A MG 902 1_555 J O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc9 D MG MG . A MG 902 1_555 J O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? metalc ? metalc10 D MG MG . A MG 902 1_555 J O HOH . A HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc11 K O HOH . B HOH 0 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc12 I O1 FMT . B FMT 1 1_555 F MN MN . B MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc13 K O HOH . B HOH 2 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc14 K O HOH . B HOH 3 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc15 K O HOH . B HOH 4 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc16 K O HOH . B HOH 5 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.786 ? metalc ? metalc17 B OD2 ASP 116 B ASP 293 1_555 F MN MN . B MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc18 B OD1 ASP 116 B ASP 293 1_555 G MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc19 B OD1 ASP 225 B ASP 402 1_555 F MN MN . B MN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? # _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 3DYL _atom_sites.fract_transf_matrix[1][1] 0.009635 _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] 0.009635 _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] 0.003706 _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 MN A 1 901 901 MN MN . D 3 MG A 1 902 902 MG MG . E 4 PCG A 1 900 900 PCG PCG . F 2 MN B 1 901 901 MN MN . G 3 MG B 1 902 902 MG MG . H 5 IBM B 1 900 900 IBM IBM . I 6 FMT B 1 1 1 FMT FMT . J 7 HOH A 1 1 1 HOH HOH . J 7 HOH A 2 2 2 HOH HOH . J 7 HOH A 3 3 3 HOH HOH . J 7 HOH A 4 4 4 HOH HOH . J 7 HOH A 5 5 5 HOH HOH . J 7 HOH A 6 9 9 HOH HOH . J 7 HOH A 7 10 10 HOH HOH . J 7 HOH A 8 12 12 HOH HOH . J 7 HOH A 9 13 13 HOH HOH . J 7 HOH A 10 15 15 HOH HOH . J 7 HOH A 11 16 16 HOH HOH . J 7 HOH A 12 17 17 HOH HOH . J 7 HOH A 13 20 20 HOH HOH . J 7 HOH A 14 22 22 HOH HOH . J 7 HOH A 15 23 23 HOH HOH . J 7 HOH A 16 25 25 HOH HOH . J 7 HOH A 17 29 29 HOH HOH . J 7 HOH A 18 30 30 HOH HOH . J 7 HOH A 19 32 32 HOH HOH . J 7 HOH A 20 34 34 HOH HOH . J 7 HOH A 21 35 35 HOH HOH . J 7 HOH A 22 37 37 HOH HOH . J 7 HOH A 23 39 39 HOH HOH . J 7 HOH A 24 41 41 HOH HOH . J 7 HOH A 25 43 43 HOH HOH . J 7 HOH A 26 44 44 HOH HOH . J 7 HOH A 27 46 46 HOH HOH . J 7 HOH A 28 47 47 HOH HOH . J 7 HOH A 29 48 48 HOH HOH . J 7 HOH A 30 50 50 HOH HOH . J 7 HOH A 31 51 51 HOH HOH . J 7 HOH A 32 55 55 HOH HOH . J 7 HOH A 33 58 58 HOH HOH . J 7 HOH A 34 61 61 HOH HOH . J 7 HOH A 35 67 67 HOH HOH . J 7 HOH A 36 72 72 HOH HOH . J 7 HOH A 37 73 73 HOH HOH . J 7 HOH A 38 75 75 HOH HOH . J 7 HOH A 39 77 77 HOH HOH . J 7 HOH A 40 78 78 HOH HOH . J 7 HOH A 41 80 80 HOH HOH . J 7 HOH A 42 81 81 HOH HOH . J 7 HOH A 43 82 82 HOH HOH . J 7 HOH A 44 83 83 HOH HOH . J 7 HOH A 45 84 84 HOH HOH . J 7 HOH A 46 87 87 HOH HOH . J 7 HOH A 47 88 88 HOH HOH . J 7 HOH A 48 90 90 HOH HOH . J 7 HOH A 49 92 92 HOH HOH . J 7 HOH A 50 93 93 HOH HOH . J 7 HOH A 51 94 94 HOH HOH . J 7 HOH A 52 97 97 HOH HOH . J 7 HOH A 53 98 98 HOH HOH . J 7 HOH A 54 102 102 HOH HOH . J 7 HOH A 55 105 105 HOH HOH . J 7 HOH A 56 106 106 HOH HOH . J 7 HOH A 57 107 107 HOH HOH . J 7 HOH A 58 109 109 HOH HOH . J 7 HOH A 59 110 110 HOH HOH . J 7 HOH A 60 113 113 HOH HOH . J 7 HOH A 61 115 115 HOH HOH . J 7 HOH A 62 117 117 HOH HOH . J 7 HOH A 63 119 119 HOH HOH . J 7 HOH A 64 121 121 HOH HOH . J 7 HOH A 65 123 123 HOH HOH . J 7 HOH A 66 125 125 HOH HOH . J 7 HOH A 67 127 127 HOH HOH . J 7 HOH A 68 128 128 HOH HOH . J 7 HOH A 69 129 129 HOH HOH . J 7 HOH A 70 131 131 HOH HOH . J 7 HOH A 71 132 132 HOH HOH . J 7 HOH A 72 133 133 HOH HOH . J 7 HOH A 73 136 136 HOH HOH . J 7 HOH A 74 137 137 HOH HOH . J 7 HOH A 75 139 139 HOH HOH . J 7 HOH A 76 140 140 HOH HOH . J 7 HOH A 77 143 143 HOH HOH . J 7 HOH A 78 144 144 HOH HOH . J 7 HOH A 79 145 145 HOH HOH . J 7 HOH A 80 149 149 HOH HOH . J 7 HOH A 81 152 152 HOH HOH . J 7 HOH A 82 154 154 HOH HOH . J 7 HOH A 83 155 155 HOH HOH . J 7 HOH A 84 156 156 HOH HOH . J 7 HOH A 85 160 160 HOH HOH . J 7 HOH A 86 161 161 HOH HOH . J 7 HOH A 87 162 162 HOH HOH . J 7 HOH A 88 163 163 HOH HOH . J 7 HOH A 89 164 164 HOH HOH . J 7 HOH A 90 165 165 HOH HOH . J 7 HOH A 91 166 166 HOH HOH . J 7 HOH A 92 169 169 HOH HOH . J 7 HOH A 93 1000 1000 HOH HOH . J 7 HOH A 94 1003 1003 HOH HOH . J 7 HOH A 95 1004 1004 HOH HOH . J 7 HOH A 96 1005 1005 HOH HOH . K 7 HOH B 1 0 0 HOH HOH . K 7 HOH B 2 2 2 HOH HOH . K 7 HOH B 3 3 3 HOH HOH . K 7 HOH B 4 4 4 HOH HOH . K 7 HOH B 5 5 5 HOH HOH . K 7 HOH B 6 6 6 HOH HOH . K 7 HOH B 7 7 7 HOH HOH . K 7 HOH B 8 8 8 HOH HOH . K 7 HOH B 9 11 11 HOH HOH . K 7 HOH B 10 14 14 HOH HOH . K 7 HOH B 11 18 18 HOH HOH . K 7 HOH B 12 19 19 HOH HOH . K 7 HOH B 13 21 21 HOH HOH . K 7 HOH B 14 24 24 HOH HOH . K 7 HOH B 15 26 26 HOH HOH . K 7 HOH B 16 27 27 HOH HOH . K 7 HOH B 17 28 28 HOH HOH . K 7 HOH B 18 31 31 HOH HOH . K 7 HOH B 19 33 33 HOH HOH . K 7 HOH B 20 36 36 HOH HOH . K 7 HOH B 21 38 38 HOH HOH . K 7 HOH B 22 40 40 HOH HOH . K 7 HOH B 23 42 42 HOH HOH . K 7 HOH B 24 45 45 HOH HOH . K 7 HOH B 25 49 49 HOH HOH . K 7 HOH B 26 52 52 HOH HOH . K 7 HOH B 27 53 53 HOH HOH . K 7 HOH B 28 54 54 HOH HOH . K 7 HOH B 29 56 56 HOH HOH . K 7 HOH B 30 57 57 HOH HOH . K 7 HOH B 31 59 59 HOH HOH . K 7 HOH B 32 60 60 HOH HOH . K 7 HOH B 33 62 62 HOH HOH . K 7 HOH B 34 63 63 HOH HOH . K 7 HOH B 35 64 64 HOH HOH . K 7 HOH B 36 65 65 HOH HOH . K 7 HOH B 37 66 66 HOH HOH . K 7 HOH B 38 69 69 HOH HOH . K 7 HOH B 39 70 70 HOH HOH . K 7 HOH B 40 71 71 HOH HOH . K 7 HOH B 41 74 74 HOH HOH . K 7 HOH B 42 76 76 HOH HOH . K 7 HOH B 43 79 79 HOH HOH . K 7 HOH B 44 85 85 HOH HOH . K 7 HOH B 45 86 86 HOH HOH . K 7 HOH B 46 89 89 HOH HOH . K 7 HOH B 47 91 91 HOH HOH . K 7 HOH B 48 95 95 HOH HOH . K 7 HOH B 49 96 96 HOH HOH . K 7 HOH B 50 99 99 HOH HOH . K 7 HOH B 51 100 100 HOH HOH . K 7 HOH B 52 101 101 HOH HOH . K 7 HOH B 53 103 103 HOH HOH . K 7 HOH B 54 104 104 HOH HOH . K 7 HOH B 55 108 108 HOH HOH . K 7 HOH B 56 111 111 HOH HOH . K 7 HOH B 57 112 112 HOH HOH . K 7 HOH B 58 114 114 HOH HOH . K 7 HOH B 59 116 116 HOH HOH . K 7 HOH B 60 118 118 HOH HOH . K 7 HOH B 61 120 120 HOH HOH . K 7 HOH B 62 122 122 HOH HOH . K 7 HOH B 63 124 124 HOH HOH . K 7 HOH B 64 126 126 HOH HOH . K 7 HOH B 65 130 130 HOH HOH . K 7 HOH B 66 134 134 HOH HOH . K 7 HOH B 67 135 135 HOH HOH . K 7 HOH B 68 138 138 HOH HOH . K 7 HOH B 69 141 141 HOH HOH . K 7 HOH B 70 142 142 HOH HOH . K 7 HOH B 71 146 146 HOH HOH . K 7 HOH B 72 147 147 HOH HOH . K 7 HOH B 73 148 148 HOH HOH . K 7 HOH B 74 150 150 HOH HOH . K 7 HOH B 75 151 151 HOH HOH . K 7 HOH B 76 153 153 HOH HOH . K 7 HOH B 77 157 157 HOH HOH . K 7 HOH B 78 158 158 HOH HOH . K 7 HOH B 79 159 159 HOH HOH . K 7 HOH B 80 167 167 HOH HOH . K 7 HOH B 81 168 168 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 3 _atom_site.Cartn_x 85.231 _atom_site.Cartn_y 47.384 _atom_site.Cartn_z 38.907 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 39.12 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 902 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 1 #