data_1YBU # _model_server_result.job_id 8DPn6wkxeh1jZYGzo_wHJQ _model_server_result.datetime_utc '2024-10-20 00:38:43' _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 1ybu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":502}' # _entry.id 1YBU # _exptl.entry_id 1YBU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) 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 1YBU _cell.length_a 91.067 _cell.length_b 48.923 _cell.length_c 68.198 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YBU _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,I,J 1 1 C,D,G,H,K,L 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 E 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 I O HOH . A HOH 3 1_555 E MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? metalc ? metalc2 A O ILE 25 A ILE 303 1_555 E MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? metalc ? metalc3 A OG SER 28 A SER 306 1_555 E MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc4 E MN MN . A MN 501 1_555 F O2A APC . A APC 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc5 E MN MN . A MN 501 1_555 F O1A APC . A APC 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc6 E MN MN . A MN 501 1_555 F PA APC . A APC 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc7 D O ILE 25 D ILE 303 1_555 G MN MN . D MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc8 D OG SER 28 D SER 306 1_555 G MN MN . D MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc9 G MN MN . D MN 502 1_555 H O1A APC . D APC 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc10 G MN MN . D MN 502 1_555 H O2A APC . D APC 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc11 G MN MN . D MN 502 1_555 H PA APC . D APC 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? # _chem_comp.formula 'Mn 2' _chem_comp.formula_weight 54.938 _chem_comp.id MN _chem_comp.mon_nstd_flag . _chem_comp.name 'MANGANESE (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1YBU _atom_sites.fract_transf_matrix[1][1] 0.010981 _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] 0.02044 _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] 0.014663 _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 E 2 MN A 1 501 501 MN MN . F 3 APC A 1 601 601 APC APC . G 2 MN D 1 502 502 MN MN . H 3 APC D 1 602 602 APC APC . I 4 HOH A 1 2 2 HOH HOH . I 4 HOH A 2 3 3 HOH HOH . I 4 HOH A 3 7 7 HOH HOH . I 4 HOH A 4 12 12 HOH HOH . I 4 HOH A 5 14 14 HOH HOH . I 4 HOH A 6 17 17 HOH HOH . I 4 HOH A 7 23 23 HOH HOH . I 4 HOH A 8 27 27 HOH HOH . I 4 HOH A 9 28 28 HOH HOH . I 4 HOH A 10 34 34 HOH HOH . I 4 HOH A 11 36 36 HOH HOH . I 4 HOH A 12 43 43 HOH HOH . I 4 HOH A 13 49 49 HOH HOH . I 4 HOH A 14 54 54 HOH HOH . I 4 HOH A 15 57 57 HOH HOH . I 4 HOH A 16 58 58 HOH HOH . I 4 HOH A 17 59 59 HOH HOH . I 4 HOH A 18 61 61 HOH HOH . I 4 HOH A 19 62 62 HOH HOH . I 4 HOH A 20 63 63 HOH HOH . I 4 HOH A 21 69 69 HOH HOH . I 4 HOH A 22 72 72 HOH HOH . I 4 HOH A 23 74 74 HOH HOH . I 4 HOH A 24 75 75 HOH HOH . I 4 HOH A 25 76 76 HOH HOH . I 4 HOH A 26 77 77 HOH HOH . I 4 HOH A 27 87 87 HOH HOH . I 4 HOH A 28 89 89 HOH HOH . I 4 HOH A 29 90 90 HOH HOH . I 4 HOH A 30 92 92 HOH HOH . I 4 HOH A 31 93 93 HOH HOH . I 4 HOH A 32 95 95 HOH HOH . I 4 HOH A 33 96 96 HOH HOH . I 4 HOH A 34 99 99 HOH HOH . I 4 HOH A 35 106 106 HOH HOH . I 4 HOH A 36 115 115 HOH HOH . I 4 HOH A 37 119 119 HOH HOH . I 4 HOH A 38 120 120 HOH HOH . I 4 HOH A 39 128 128 HOH HOH . I 4 HOH A 40 133 133 HOH HOH . I 4 HOH A 41 141 141 HOH HOH . I 4 HOH A 42 146 146 HOH HOH . I 4 HOH A 43 148 148 HOH HOH . I 4 HOH A 44 153 153 HOH HOH . I 4 HOH A 45 154 154 HOH HOH . I 4 HOH A 46 158 158 HOH HOH . I 4 HOH A 47 168 168 HOH HOH . I 4 HOH A 48 171 171 HOH HOH . I 4 HOH A 49 172 172 HOH HOH . I 4 HOH A 50 176 176 HOH HOH . I 4 HOH A 51 177 177 HOH HOH . I 4 HOH A 52 179 179 HOH HOH . I 4 HOH A 53 180 180 HOH HOH . I 4 HOH A 54 183 183 HOH HOH . I 4 HOH A 55 187 187 HOH HOH . I 4 HOH A 56 192 192 HOH HOH . I 4 HOH A 57 193 193 HOH HOH . I 4 HOH A 58 197 197 HOH HOH . I 4 HOH A 59 203 203 HOH HOH . I 4 HOH A 60 204 204 HOH HOH . I 4 HOH A 61 213 213 HOH HOH . I 4 HOH A 62 217 217 HOH HOH . I 4 HOH A 63 218 218 HOH HOH . I 4 HOH A 64 220 220 HOH HOH . I 4 HOH A 65 221 221 HOH HOH . I 4 HOH A 66 223 223 HOH HOH . J 4 HOH B 1 1 1 HOH HOH . J 4 HOH B 2 6 6 HOH HOH . J 4 HOH B 3 9 9 HOH HOH . J 4 HOH B 4 18 18 HOH HOH . J 4 HOH B 5 21 21 HOH HOH . J 4 HOH B 6 22 22 HOH HOH . J 4 HOH B 7 29 29 HOH HOH . J 4 HOH B 8 32 32 HOH HOH . J 4 HOH B 9 33 33 HOH HOH . J 4 HOH B 10 39 39 HOH HOH . J 4 HOH B 11 40 40 HOH HOH . J 4 HOH B 12 41 41 HOH HOH . J 4 HOH B 13 44 44 HOH HOH . J 4 HOH B 14 48 48 HOH HOH . J 4 HOH B 15 50 50 HOH HOH . J 4 HOH B 16 53 53 HOH HOH . J 4 HOH B 17 55 55 HOH HOH . J 4 HOH B 18 64 64 HOH HOH . J 4 HOH B 19 66 66 HOH HOH . J 4 HOH B 20 70 70 HOH HOH . J 4 HOH B 21 73 73 HOH HOH . J 4 HOH B 22 79 79 HOH HOH . J 4 HOH B 23 80 80 HOH HOH . J 4 HOH B 24 98 98 HOH HOH . J 4 HOH B 25 101 101 HOH HOH . J 4 HOH B 26 102 102 HOH HOH . J 4 HOH B 27 109 109 HOH HOH . J 4 HOH B 28 116 116 HOH HOH . J 4 HOH B 29 123 123 HOH HOH . J 4 HOH B 30 126 126 HOH HOH . J 4 HOH B 31 131 131 HOH HOH . J 4 HOH B 32 132 132 HOH HOH . J 4 HOH B 33 134 134 HOH HOH . J 4 HOH B 34 135 135 HOH HOH . J 4 HOH B 35 136 136 HOH HOH . J 4 HOH B 36 157 157 HOH HOH . J 4 HOH B 37 165 165 HOH HOH . J 4 HOH B 38 166 166 HOH HOH . J 4 HOH B 39 167 167 HOH HOH . J 4 HOH B 40 170 170 HOH HOH . J 4 HOH B 41 181 181 HOH HOH . J 4 HOH B 42 191 191 HOH HOH . J 4 HOH B 43 194 194 HOH HOH . J 4 HOH B 44 195 195 HOH HOH . J 4 HOH B 45 196 196 HOH HOH . J 4 HOH B 46 200 200 HOH HOH . J 4 HOH B 47 202 202 HOH HOH . J 4 HOH B 48 205 205 HOH HOH . J 4 HOH B 49 206 206 HOH HOH . J 4 HOH B 50 209 209 HOH HOH . J 4 HOH B 51 211 211 HOH HOH . J 4 HOH B 52 214 214 HOH HOH . K 4 HOH C 1 5 5 HOH HOH . K 4 HOH C 2 11 11 HOH HOH . K 4 HOH C 3 13 13 HOH HOH . K 4 HOH C 4 15 15 HOH HOH . K 4 HOH C 5 16 16 HOH HOH . K 4 HOH C 6 20 20 HOH HOH . K 4 HOH C 7 26 26 HOH HOH . K 4 HOH C 8 35 35 HOH HOH . K 4 HOH C 9 38 38 HOH HOH . K 4 HOH C 10 42 42 HOH HOH . K 4 HOH C 11 45 45 HOH HOH . K 4 HOH C 12 46 46 HOH HOH . K 4 HOH C 13 52 52 HOH HOH . K 4 HOH C 14 60 60 HOH HOH . K 4 HOH C 15 65 65 HOH HOH . K 4 HOH C 16 67 67 HOH HOH . K 4 HOH C 17 68 68 HOH HOH . K 4 HOH C 18 83 83 HOH HOH . K 4 HOH C 19 86 86 HOH HOH . K 4 HOH C 20 91 91 HOH HOH . K 4 HOH C 21 97 97 HOH HOH . K 4 HOH C 22 100 100 HOH HOH . K 4 HOH C 23 104 104 HOH HOH . K 4 HOH C 24 105 105 HOH HOH . K 4 HOH C 25 108 108 HOH HOH . K 4 HOH C 26 112 112 HOH HOH . K 4 HOH C 27 113 113 HOH HOH . K 4 HOH C 28 118 118 HOH HOH . K 4 HOH C 29 124 124 HOH HOH . K 4 HOH C 30 127 127 HOH HOH . K 4 HOH C 31 129 129 HOH HOH . K 4 HOH C 32 130 130 HOH HOH . K 4 HOH C 33 137 137 HOH HOH . K 4 HOH C 34 139 139 HOH HOH . K 4 HOH C 35 140 140 HOH HOH . K 4 HOH C 36 144 144 HOH HOH . K 4 HOH C 37 145 145 HOH HOH . K 4 HOH C 38 147 147 HOH HOH . K 4 HOH C 39 156 156 HOH HOH . K 4 HOH C 40 160 160 HOH HOH . K 4 HOH C 41 161 161 HOH HOH . K 4 HOH C 42 162 162 HOH HOH . K 4 HOH C 43 163 163 HOH HOH . K 4 HOH C 44 164 164 HOH HOH . K 4 HOH C 45 174 174 HOH HOH . K 4 HOH C 46 175 175 HOH HOH . K 4 HOH C 47 178 178 HOH HOH . K 4 HOH C 48 188 188 HOH HOH . K 4 HOH C 49 189 189 HOH HOH . K 4 HOH C 50 190 190 HOH HOH . K 4 HOH C 51 198 198 HOH HOH . K 4 HOH C 52 199 199 HOH HOH . K 4 HOH C 53 201 201 HOH HOH . K 4 HOH C 54 207 207 HOH HOH . K 4 HOH C 55 208 208 HOH HOH . K 4 HOH C 56 215 215 HOH HOH . K 4 HOH C 57 216 216 HOH HOH . K 4 HOH C 58 219 219 HOH HOH . L 4 HOH D 1 4 4 HOH HOH . L 4 HOH D 2 8 8 HOH HOH . L 4 HOH D 3 10 10 HOH HOH . L 4 HOH D 4 19 19 HOH HOH . L 4 HOH D 5 24 24 HOH HOH . L 4 HOH D 6 25 25 HOH HOH . L 4 HOH D 7 30 30 HOH HOH . L 4 HOH D 8 31 31 HOH HOH . L 4 HOH D 9 37 37 HOH HOH . L 4 HOH D 10 47 47 HOH HOH . L 4 HOH D 11 51 51 HOH HOH . L 4 HOH D 12 56 56 HOH HOH . L 4 HOH D 13 71 71 HOH HOH . L 4 HOH D 14 78 78 HOH HOH . L 4 HOH D 15 81 81 HOH HOH . L 4 HOH D 16 82 82 HOH HOH . L 4 HOH D 17 84 84 HOH HOH . L 4 HOH D 18 85 85 HOH HOH . L 4 HOH D 19 88 88 HOH HOH . L 4 HOH D 20 94 94 HOH HOH . L 4 HOH D 21 103 103 HOH HOH . L 4 HOH D 22 107 107 HOH HOH . L 4 HOH D 23 110 110 HOH HOH . L 4 HOH D 24 111 111 HOH HOH . L 4 HOH D 25 114 114 HOH HOH . L 4 HOH D 26 117 117 HOH HOH . L 4 HOH D 27 121 121 HOH HOH . L 4 HOH D 28 122 122 HOH HOH . L 4 HOH D 29 125 125 HOH HOH . L 4 HOH D 30 138 138 HOH HOH . L 4 HOH D 31 142 142 HOH HOH . L 4 HOH D 32 143 143 HOH HOH . L 4 HOH D 33 149 149 HOH HOH . L 4 HOH D 34 150 150 HOH HOH . L 4 HOH D 35 151 151 HOH HOH . L 4 HOH D 36 152 152 HOH HOH . L 4 HOH D 37 155 155 HOH HOH . L 4 HOH D 38 159 159 HOH HOH . L 4 HOH D 39 169 169 HOH HOH . L 4 HOH D 40 173 173 HOH HOH . L 4 HOH D 41 182 182 HOH HOH . L 4 HOH D 42 184 184 HOH HOH . L 4 HOH D 43 185 185 HOH HOH . L 4 HOH D 44 186 186 HOH HOH . L 4 HOH D 45 210 210 HOH HOH . L 4 HOH D 46 212 212 HOH HOH . L 4 HOH D 47 224 224 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MN _atom_site.label_atom_id MN _atom_site.label_comp_id MN _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 2 _atom_site.Cartn_x 26.053 _atom_site.Cartn_y 58.951 _atom_site.Cartn_z 59.578 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 111.26 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 502 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #