data_3KPC # _model_server_result.job_id 99IlcHSb6uX4D0SYd4vJwA _model_server_result.datetime_utc '2024-11-29 18:14:32' _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 3kpc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":3615}' # _entry.id 3KPC # _exptl.entry_id 3KPC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.334 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXY-5'-METHYLTHIOADENOSINE" _entity.pdbx_number_of_molecules 1 _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 3KPC _cell.length_a 50.964 _cell.length_b 71.483 _cell.length_c 86.366 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KPC _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_545 -x+1/2,-y-1/2,z -1 0 0 0 -1 0 0 0 1 25.482 -35.7415 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H15 N5 O3 S' _chem_comp.formula_weight 297.334 _chem_comp.id MTA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXY-5'-METHYLTHIOADENOSINE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag CS S5' MTA sing 224 n n CS HCS1 MTA sing 225 n n CS HCS2 MTA sing 226 n n CS HCS3 MTA sing 227 n n S5' C5' MTA sing 228 n n C5' C4' MTA sing 229 n n C5' "H5'1" MTA sing 230 n n C5' "H5'2" MTA sing 231 n n C4' O4' MTA sing 232 n n C4' C3' MTA sing 233 n n C4' H4' MTA sing 234 n n O4' C1' MTA sing 235 n n C2' O2' MTA sing 236 n n C2' C3' MTA sing 237 n n C2' C1' MTA sing 238 n n C2' H2' MTA sing 239 n n O2' HO2' MTA sing 240 n n C3' O3' MTA sing 241 n n C3' H3' MTA sing 242 n n O3' H3T MTA sing 243 n n C1' N9 MTA sing 244 n n C1' H1' MTA sing 245 n n N9 C8 MTA sing 246 n y N9 C4 MTA sing 247 n y C8 N7 MTA doub 248 n y C8 H8 MTA sing 249 n n N7 C5 MTA sing 250 n y C5 C6 MTA sing 251 n y C5 C4 MTA doub 252 n y C6 N6 MTA sing 253 n n C6 N1 MTA doub 254 n y N6 H61 MTA sing 255 n n N6 H62 MTA sing 256 n n N1 C2 MTA sing 257 n y C2 N3 MTA doub 258 n y C2 H2 MTA sing 259 n n N3 C4 MTA sing 260 n y # _atom_sites.entry_id 3KPC _atom_sites.fract_transf_matrix[1][1] 0.019622 _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] 0.013989 _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] 0.011579 _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 B 2 SAM A 1 1000 1000 SAM SAM . C 3 MTA A 1 3615 3615 MTA MTA . D 4 HOH A 1 1 1 HOH HOH . D 4 HOH A 2 2 2 HOH HOH . D 4 HOH A 3 3 3 HOH HOH . D 4 HOH A 4 4 4 HOH HOH . D 4 HOH A 5 5 5 HOH HOH . D 4 HOH A 6 7 7 HOH HOH . D 4 HOH A 7 8 8 HOH HOH . D 4 HOH A 8 9 9 HOH HOH . D 4 HOH A 9 10 10 HOH HOH . D 4 HOH A 10 11 11 HOH HOH . D 4 HOH A 11 12 12 HOH HOH . D 4 HOH A 12 13 13 HOH HOH . D 4 HOH A 13 14 14 HOH HOH . D 4 HOH A 14 15 15 HOH HOH . D 4 HOH A 15 16 16 HOH HOH . D 4 HOH A 16 19 19 HOH HOH . D 4 HOH A 17 20 20 HOH HOH . D 4 HOH A 18 21 21 HOH HOH . D 4 HOH A 19 22 22 HOH HOH . D 4 HOH A 20 23 23 HOH HOH . D 4 HOH A 21 24 24 HOH HOH . D 4 HOH A 22 25 25 HOH HOH . D 4 HOH A 23 26 26 HOH HOH . D 4 HOH A 24 27 27 HOH HOH . D 4 HOH A 25 28 28 HOH HOH . D 4 HOH A 26 29 29 HOH HOH . D 4 HOH A 27 30 30 HOH HOH . D 4 HOH A 28 31 31 HOH HOH . D 4 HOH A 29 32 32 HOH HOH . D 4 HOH A 30 33 33 HOH HOH . D 4 HOH A 31 34 34 HOH HOH . D 4 HOH A 32 36 36 HOH HOH . D 4 HOH A 33 37 37 HOH HOH . D 4 HOH A 34 39 39 HOH HOH . D 4 HOH A 35 40 40 HOH HOH . D 4 HOH A 36 41 41 HOH HOH . D 4 HOH A 37 42 42 HOH HOH . D 4 HOH A 38 43 43 HOH HOH . D 4 HOH A 39 45 45 HOH HOH . D 4 HOH A 40 47 47 HOH HOH . D 4 HOH A 41 48 48 HOH HOH . D 4 HOH A 42 49 49 HOH HOH . D 4 HOH A 43 50 50 HOH HOH . D 4 HOH A 44 51 51 HOH HOH . D 4 HOH A 45 52 52 HOH HOH . D 4 HOH A 46 53 53 HOH HOH . D 4 HOH A 47 54 54 HOH HOH . D 4 HOH A 48 55 55 HOH HOH . D 4 HOH A 49 56 56 HOH HOH . D 4 HOH A 50 57 57 HOH HOH . D 4 HOH A 51 58 58 HOH HOH . D 4 HOH A 52 59 59 HOH HOH . D 4 HOH A 53 60 60 HOH HOH . D 4 HOH A 54 61 61 HOH HOH . D 4 HOH A 55 64 64 HOH HOH . D 4 HOH A 56 65 65 HOH HOH . D 4 HOH A 57 68 68 HOH HOH . D 4 HOH A 58 69 69 HOH HOH . D 4 HOH A 59 70 70 HOH HOH . D 4 HOH A 60 71 71 HOH HOH . D 4 HOH A 61 72 72 HOH HOH . D 4 HOH A 62 76 76 HOH HOH . D 4 HOH A 63 78 78 HOH HOH . D 4 HOH A 64 82 82 HOH HOH . D 4 HOH A 65 84 84 HOH HOH . D 4 HOH A 66 85 85 HOH HOH . D 4 HOH A 67 86 86 HOH HOH . D 4 HOH A 68 88 88 HOH HOH . D 4 HOH A 69 90 90 HOH HOH . D 4 HOH A 70 91 91 HOH HOH . D 4 HOH A 71 92 92 HOH HOH . D 4 HOH A 72 93 93 HOH HOH . D 4 HOH A 73 94 94 HOH HOH . D 4 HOH A 74 95 95 HOH HOH . D 4 HOH A 75 96 96 HOH HOH . D 4 HOH A 76 99 99 HOH HOH . D 4 HOH A 77 102 102 HOH HOH . D 4 HOH A 78 103 103 HOH HOH . D 4 HOH A 79 104 104 HOH HOH . D 4 HOH A 80 105 105 HOH HOH . D 4 HOH A 81 110 110 HOH HOH . D 4 HOH A 82 114 114 HOH HOH . D 4 HOH A 83 115 115 HOH HOH . D 4 HOH A 84 116 116 HOH HOH . D 4 HOH A 85 118 118 HOH HOH . D 4 HOH A 86 123 123 HOH HOH . D 4 HOH A 87 127 127 HOH HOH . D 4 HOH A 88 129 129 HOH HOH . D 4 HOH A 89 131 131 HOH HOH . D 4 HOH A 90 132 132 HOH HOH . D 4 HOH A 91 138 138 HOH HOH . D 4 HOH A 92 139 139 HOH HOH . D 4 HOH A 93 141 141 HOH HOH . D 4 HOH A 94 143 143 HOH HOH . D 4 HOH A 95 144 144 HOH HOH . D 4 HOH A 96 145 145 HOH HOH . D 4 HOH A 97 146 146 HOH HOH . D 4 HOH A 98 147 147 HOH HOH . D 4 HOH A 99 148 148 HOH HOH . D 4 HOH A 100 150 150 HOH HOH . D 4 HOH A 101 151 151 HOH HOH . D 4 HOH A 102 152 152 HOH HOH . D 4 HOH A 103 154 154 HOH HOH . D 4 HOH A 104 155 155 HOH HOH . D 4 HOH A 105 156 156 HOH HOH . D 4 HOH A 106 157 157 HOH HOH . D 4 HOH A 107 158 158 HOH HOH . D 4 HOH A 108 159 159 HOH HOH . D 4 HOH A 109 160 160 HOH HOH . D 4 HOH A 110 161 161 HOH HOH . D 4 HOH A 111 162 162 HOH HOH . D 4 HOH A 112 163 163 HOH HOH . D 4 HOH A 113 164 164 HOH HOH . D 4 HOH A 114 165 165 HOH HOH . D 4 HOH A 115 166 166 HOH HOH . D 4 HOH A 116 167 167 HOH HOH . D 4 HOH A 117 168 168 HOH HOH . D 4 HOH A 118 169 169 HOH HOH . D 4 HOH A 119 170 170 HOH HOH . D 4 HOH A 120 171 171 HOH HOH . D 4 HOH A 121 172 172 HOH HOH . D 4 HOH A 122 173 173 HOH HOH . D 4 HOH A 123 174 174 HOH HOH . D 4 HOH A 124 175 175 HOH HOH . D 4 HOH A 125 176 176 HOH HOH . D 4 HOH A 126 177 177 HOH HOH . D 4 HOH A 127 178 178 HOH HOH . D 4 HOH A 128 179 179 HOH HOH . D 4 HOH A 129 180 180 HOH HOH . D 4 HOH A 130 181 181 HOH HOH . D 4 HOH A 131 183 183 HOH HOH . D 4 HOH A 132 184 184 HOH HOH . D 4 HOH A 133 185 185 HOH HOH . D 4 HOH A 134 186 186 HOH HOH . D 4 HOH A 135 187 187 HOH HOH . D 4 HOH A 136 188 188 HOH HOH . D 4 HOH A 137 189 189 HOH HOH . D 4 HOH A 138 190 190 HOH HOH . D 4 HOH A 139 191 191 HOH HOH . D 4 HOH A 140 192 192 HOH HOH . D 4 HOH A 141 193 193 HOH HOH . D 4 HOH A 142 194 194 HOH HOH . D 4 HOH A 143 195 195 HOH HOH . D 4 HOH A 144 196 196 HOH HOH . D 4 HOH A 145 197 197 HOH HOH . D 4 HOH A 146 198 198 HOH HOH . D 4 HOH A 147 199 199 HOH HOH . D 4 HOH A 148 200 200 HOH HOH . D 4 HOH A 149 201 201 HOH HOH . D 4 HOH A 150 202 202 HOH HOH . D 4 HOH A 151 203 203 HOH HOH . D 4 HOH A 152 204 204 HOH HOH . D 4 HOH A 153 205 205 HOH HOH . D 4 HOH A 154 206 206 HOH HOH . D 4 HOH A 155 207 207 HOH HOH . D 4 HOH A 156 208 208 HOH HOH . D 4 HOH A 157 209 209 HOH HOH . D 4 HOH A 158 210 210 HOH HOH . D 4 HOH A 159 211 211 HOH HOH . D 4 HOH A 160 212 212 HOH HOH . D 4 HOH A 161 213 213 HOH HOH . D 4 HOH A 162 214 214 HOH HOH . D 4 HOH A 163 215 215 HOH HOH . D 4 HOH A 164 216 216 HOH HOH . D 4 HOH A 165 217 217 HOH HOH . D 4 HOH A 166 218 218 HOH HOH . D 4 HOH A 167 219 219 HOH HOH . D 4 HOH A 168 220 220 HOH HOH . D 4 HOH A 169 221 221 HOH HOH . D 4 HOH A 170 222 222 HOH HOH . D 4 HOH A 171 223 223 HOH HOH . D 4 HOH A 172 224 224 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C CS MTA . . . C 3 6.568 -16.174 -23.299 1 26.47 ? CS MTA 3615 A 1 HETATM 2 S S5' MTA . . . C 3 7.405 -15.143 -22.123 1 28.54 ? S5' MTA 3615 A 1 HETATM 3 C C5' MTA . . . C 3 6.292 -13.666 -22.217 1 29.08 ? C5' MTA 3615 A 1 HETATM 4 C C4' MTA . . . C 3 5.416 -13.397 -20.945 1 29.69 ? C4' MTA 3615 A 1 HETATM 5 O O4' MTA . . . C 3 4.033 -13.16 -21.351 1 29.5 ? O4' MTA 3615 A 1 HETATM 6 C C2' MTA . . . C 3 4.018 -15.186 -20.039 1 29.54 ? C2' MTA 3615 A 1 HETATM 7 O O2' MTA . . . C 3 3.396 -15.287 -18.689 1 29.3 ? O2' MTA 3615 A 1 HETATM 8 C C3' MTA . . . C 3 5.427 -14.593 -19.983 1 29.87 ? C3' MTA 3615 A 1 HETATM 9 O O3' MTA . . . C 3 5.761 -14.15 -18.61 1 30.21 ? O3' MTA 3615 A 1 HETATM 10 C C1' MTA . . . C 3 3.204 -14.301 -20.976 1 29.18 ? C1' MTA 3615 A 1 HETATM 11 N N9 MTA . . . C 3 2.848 -15.27 -22.066 1 28.58 ? N9 MTA 3615 A 1 HETATM 12 C C8 MTA . . . C 3 3.666 -16.125 -22.689 1 28.16 ? C8 MTA 3615 A 1 HETATM 13 N N7 MTA . . . C 3 2.99 -16.841 -23.586 1 27.97 ? N7 MTA 3615 A 1 HETATM 14 C C5 MTA . . . C 3 1.724 -16.449 -23.531 1 27.97 ? C5 MTA 3615 A 1 HETATM 15 C C6 MTA . . . C 3 0.571 -16.82 -24.206 1 27.71 ? C6 MTA 3615 A 1 HETATM 16 N N6 MTA . . . C 3 0.606 -17.77 -25.141 1 26.2 ? N6 MTA 3615 A 1 HETATM 17 N N1 MTA . . . C 3 -0.586 -16.214 -23.89 1 28.1 ? N1 MTA 3615 A 1 HETATM 18 C C2 MTA . . . C 3 -0.634 -15.262 -22.969 1 28.53 ? C2 MTA 3615 A 1 HETATM 19 N N3 MTA . . . C 3 0.447 -14.887 -22.303 1 28.57 ? N3 MTA 3615 A 1 HETATM 20 C C4 MTA . . . C 3 1.634 -15.458 -22.564 1 28.4 ? C4 MTA 3615 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #