data_1JDT # _model_server_result.job_id ntaNW8J3mm0K_Yva58fEsA _model_server_result.datetime_utc '2024-10-12 06:16:16' _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 1jdt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":2260}' # _entry.id 1JDT # _exptl.entry_id 1JDT _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 3 _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 1JDT _cell.length_a 101.6 _cell.length_b 176.3 _cell.length_c 87.1 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JDT _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 101.6 0 43.55 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 G N N ? 3 I 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 disulf ? disulf1 A SG CYS 125 A CYS 125 1_555 C SG CYS 125 C CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 B SG CYS 125 B CYS 125 1_555 B SG CYS 125 B CYS 125 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? # _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 237 n n CS HCS1 MTA sing 238 n n CS HCS2 MTA sing 239 n n CS HCS3 MTA sing 240 n n S5' C5' MTA sing 241 n n C5' C4' MTA sing 242 n n C5' "H5'1" MTA sing 243 n n C5' "H5'2" MTA sing 244 n n C4' O4' MTA sing 245 n n C4' C3' MTA sing 246 n n C4' H4' MTA sing 247 n n O4' C1' MTA sing 248 n n C2' O2' MTA sing 249 n n C2' C3' MTA sing 250 n n C2' C1' MTA sing 251 n n C2' H2' MTA sing 252 n n O2' HO2' MTA sing 253 n n C3' O3' MTA sing 254 n n C3' H3' MTA sing 255 n n O3' H3T MTA sing 256 n n C1' N9 MTA sing 257 n n C1' H1' MTA sing 258 n n N9 C8 MTA sing 259 n y N9 C4 MTA sing 260 n y C8 N7 MTA doub 261 n y C8 H8 MTA sing 262 n n N7 C5 MTA sing 263 n y C5 C6 MTA sing 264 n y C5 C4 MTA doub 265 n y C6 N6 MTA sing 266 n n C6 N1 MTA doub 267 n y N6 H61 MTA sing 268 n n N6 H62 MTA sing 269 n n N1 C2 MTA sing 270 n y C2 N3 MTA doub 271 n y C2 H2 MTA sing 272 n n N3 C4 MTA sing 273 n y # _atom_sites.entry_id 1JDT _atom_sites.fract_transf_matrix[1][1] 0.009843 _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] 0.005672 _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] 0.011481 _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 D 2 SO4 A 1 1250 1250 SO4 SO4 . E 3 MTA A 1 1260 1260 MTA MTA . F 2 SO4 B 1 2250 2250 SO4 SO4 . G 3 MTA B 1 2260 2260 MTA MTA . H 2 SO4 C 1 3250 3250 SO4 SO4 . I 3 MTA C 1 3260 3260 MTA MTA . J 4 HOH A 1 1261 1 HOH HOH . J 4 HOH A 2 1262 5 HOH HOH . J 4 HOH A 3 1263 7 HOH HOH . J 4 HOH A 4 1264 9 HOH HOH . J 4 HOH A 5 1265 12 HOH HOH . J 4 HOH A 6 1266 13 HOH HOH . J 4 HOH A 7 1267 14 HOH HOH . J 4 HOH A 8 1268 20 HOH HOH . J 4 HOH A 9 1269 24 HOH HOH . J 4 HOH A 10 1270 27 HOH HOH . J 4 HOH A 11 1271 28 HOH HOH . J 4 HOH A 12 1272 33 HOH HOH . J 4 HOH A 13 1273 34 HOH HOH . J 4 HOH A 14 1274 35 HOH HOH . J 4 HOH A 15 1275 37 HOH HOH . J 4 HOH A 16 1276 45 HOH HOH . J 4 HOH A 17 1277 50 HOH HOH . J 4 HOH A 18 1278 51 HOH HOH . J 4 HOH A 19 1279 55 HOH HOH . J 4 HOH A 20 1280 56 HOH HOH . J 4 HOH A 21 1281 57 HOH HOH . J 4 HOH A 22 1282 59 HOH HOH . J 4 HOH A 23 1283 66 HOH HOH . J 4 HOH A 24 1284 68 HOH HOH . J 4 HOH A 25 1285 69 HOH HOH . J 4 HOH A 26 1286 74 HOH HOH . J 4 HOH A 27 1287 75 HOH HOH . J 4 HOH A 28 1288 76 HOH HOH . J 4 HOH A 29 1289 77 HOH HOH . J 4 HOH A 30 1290 79 HOH HOH . J 4 HOH A 31 1291 80 HOH HOH . J 4 HOH A 32 1292 83 HOH HOH . J 4 HOH A 33 1293 85 HOH HOH . J 4 HOH A 34 1294 86 HOH HOH . J 4 HOH A 35 1295 87 HOH HOH . J 4 HOH A 36 1296 92 HOH HOH . J 4 HOH A 37 1297 98 HOH HOH . J 4 HOH A 38 1298 101 HOH HOH . J 4 HOH A 39 1299 104 HOH HOH . J 4 HOH A 40 1300 108 HOH HOH . J 4 HOH A 41 1301 110 HOH HOH . J 4 HOH A 42 1302 111 HOH HOH . J 4 HOH A 43 1303 112 HOH HOH . J 4 HOH A 44 1304 113 HOH HOH . J 4 HOH A 45 1305 119 HOH HOH . J 4 HOH A 46 1306 120 HOH HOH . J 4 HOH A 47 1307 129 HOH HOH . J 4 HOH A 48 1308 133 HOH HOH . J 4 HOH A 49 1309 135 HOH HOH . J 4 HOH A 50 1310 141 HOH HOH . J 4 HOH A 51 1311 146 HOH HOH . J 4 HOH A 52 1312 150 HOH HOH . J 4 HOH A 53 1313 153 HOH HOH . J 4 HOH A 54 1314 159 HOH HOH . J 4 HOH A 55 1315 160 HOH HOH . J 4 HOH A 56 1316 161 HOH HOH . J 4 HOH A 57 1317 162 HOH HOH . J 4 HOH A 58 1318 163 HOH HOH . J 4 HOH A 59 1319 167 HOH HOH . K 4 HOH B 1 2261 6 HOH HOH . K 4 HOH B 2 2262 8 HOH HOH . K 4 HOH B 3 2263 10 HOH HOH . K 4 HOH B 4 2264 11 HOH HOH . K 4 HOH B 5 2265 17 HOH HOH . K 4 HOH B 6 2266 19 HOH HOH . K 4 HOH B 7 2267 21 HOH HOH . K 4 HOH B 8 2268 22 HOH HOH . K 4 HOH B 9 2269 30 HOH HOH . K 4 HOH B 10 2270 32 HOH HOH . K 4 HOH B 11 2271 40 HOH HOH . K 4 HOH B 12 2272 41 HOH HOH . K 4 HOH B 13 2273 42 HOH HOH . K 4 HOH B 14 2274 44 HOH HOH . K 4 HOH B 15 2275 48 HOH HOH . K 4 HOH B 16 2276 49 HOH HOH . K 4 HOH B 17 2277 52 HOH HOH . K 4 HOH B 18 2278 54 HOH HOH . K 4 HOH B 19 2279 62 HOH HOH . K 4 HOH B 20 2280 65 HOH HOH . K 4 HOH B 21 2281 67 HOH HOH . K 4 HOH B 22 2282 70 HOH HOH . K 4 HOH B 23 2283 73 HOH HOH . K 4 HOH B 24 2284 81 HOH HOH . K 4 HOH B 25 2285 82 HOH HOH . K 4 HOH B 26 2286 88 HOH HOH . K 4 HOH B 27 2287 90 HOH HOH . K 4 HOH B 28 2288 93 HOH HOH . K 4 HOH B 29 2289 94 HOH HOH . K 4 HOH B 30 2290 99 HOH HOH . K 4 HOH B 31 2291 103 HOH HOH . K 4 HOH B 32 2292 105 HOH HOH . K 4 HOH B 33 2293 106 HOH HOH . K 4 HOH B 34 2294 107 HOH HOH . K 4 HOH B 35 2295 109 HOH HOH . K 4 HOH B 36 2296 114 HOH HOH . K 4 HOH B 37 2297 117 HOH HOH . K 4 HOH B 38 2298 118 HOH HOH . K 4 HOH B 39 2299 122 HOH HOH . K 4 HOH B 40 2300 125 HOH HOH . K 4 HOH B 41 2301 127 HOH HOH . K 4 HOH B 42 2302 128 HOH HOH . K 4 HOH B 43 2303 130 HOH HOH . K 4 HOH B 44 2304 131 HOH HOH . K 4 HOH B 45 2305 132 HOH HOH . K 4 HOH B 46 2306 138 HOH HOH . K 4 HOH B 47 2307 139 HOH HOH . K 4 HOH B 48 2308 143 HOH HOH . K 4 HOH B 49 2309 144 HOH HOH . K 4 HOH B 50 2310 145 HOH HOH . K 4 HOH B 51 2311 147 HOH HOH . K 4 HOH B 52 2312 148 HOH HOH . K 4 HOH B 53 2313 149 HOH HOH . K 4 HOH B 54 2314 154 HOH HOH . K 4 HOH B 55 2315 156 HOH HOH . K 4 HOH B 56 2316 165 HOH HOH . K 4 HOH B 57 2317 166 HOH HOH . L 4 HOH C 1 3261 2 HOH HOH . L 4 HOH C 2 3262 3 HOH HOH . L 4 HOH C 3 3263 4 HOH HOH . L 4 HOH C 4 3264 15 HOH HOH . L 4 HOH C 5 3265 16 HOH HOH . L 4 HOH C 6 3266 18 HOH HOH . L 4 HOH C 7 3267 23 HOH HOH . L 4 HOH C 8 3268 25 HOH HOH . L 4 HOH C 9 3269 26 HOH HOH . L 4 HOH C 10 3270 29 HOH HOH . L 4 HOH C 11 3271 31 HOH HOH . L 4 HOH C 12 3272 36 HOH HOH . L 4 HOH C 13 3273 38 HOH HOH . L 4 HOH C 14 3274 39 HOH HOH . L 4 HOH C 15 3275 43 HOH HOH . L 4 HOH C 16 3276 46 HOH HOH . L 4 HOH C 17 3277 47 HOH HOH . L 4 HOH C 18 3278 53 HOH HOH . L 4 HOH C 19 3279 58 HOH HOH . L 4 HOH C 20 3280 60 HOH HOH . L 4 HOH C 21 3281 61 HOH HOH . L 4 HOH C 22 3282 63 HOH HOH . L 4 HOH C 23 3283 64 HOH HOH . L 4 HOH C 24 3284 71 HOH HOH . L 4 HOH C 25 3285 72 HOH HOH . L 4 HOH C 26 3286 78 HOH HOH . L 4 HOH C 27 3287 84 HOH HOH . L 4 HOH C 28 3288 89 HOH HOH . L 4 HOH C 29 3289 91 HOH HOH . L 4 HOH C 30 3290 95 HOH HOH . L 4 HOH C 31 3291 96 HOH HOH . L 4 HOH C 32 3292 97 HOH HOH . L 4 HOH C 33 3293 100 HOH HOH . L 4 HOH C 34 3294 102 HOH HOH . L 4 HOH C 35 3295 115 HOH HOH . L 4 HOH C 36 3296 116 HOH HOH . L 4 HOH C 37 3297 121 HOH HOH . L 4 HOH C 38 3298 123 HOH HOH . L 4 HOH C 39 3299 124 HOH HOH . L 4 HOH C 40 3300 126 HOH HOH . L 4 HOH C 41 3301 134 HOH HOH . L 4 HOH C 42 3302 136 HOH HOH . L 4 HOH C 43 3303 137 HOH HOH . L 4 HOH C 44 3304 140 HOH HOH . L 4 HOH C 45 3305 142 HOH HOH . L 4 HOH C 46 3306 151 HOH HOH . L 4 HOH C 47 3307 152 HOH HOH . L 4 HOH C 48 3308 155 HOH HOH . L 4 HOH C 49 3309 157 HOH HOH . L 4 HOH C 50 3310 158 HOH HOH . L 4 HOH C 51 3311 164 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 . . . G 3 69.595 110.062 36.338 1 54.84 ? CS MTA 2260 B 1 HETATM 2 S S5' MTA . . . G 3 70.515 110.196 34.776 1 55.89 ? S5' MTA 2260 B 1 HETATM 3 C C5' MTA . . . G 3 69.251 110.94 33.722 1 52.47 ? C5' MTA 2260 B 1 HETATM 4 C C4' MTA . . . G 3 69.137 110.051 32.479 1 50.74 ? C4' MTA 2260 B 1 HETATM 5 O O4' MTA . . . G 3 68.385 108.832 32.816 1 49.84 ? O4' MTA 2260 B 1 HETATM 6 C C2' MTA . . . G 3 66.965 110.063 31.428 1 49.17 ? C2' MTA 2260 B 1 HETATM 7 O O2' MTA . . . G 3 66.534 109.518 30.17 1 47.59 ? O2' MTA 2260 B 1 HETATM 8 C C3' MTA . . . G 3 68.42 110.722 31.341 1 49.94 ? C3' MTA 2260 B 1 HETATM 9 O O3' MTA . . . G 3 69.141 110.401 30.068 1 50.2 ? O3' MTA 2260 B 1 HETATM 10 C C1' MTA . . . G 3 66.975 108.944 32.537 1 48.77 ? C1' MTA 2260 B 1 HETATM 11 N N9 MTA . . . G 3 66.244 109.269 33.944 1 47.86 ? N9 MTA 2260 B 1 HETATM 12 C C8 MTA . . . G 3 66.303 108.428 35.062 1 47.42 ? C8 MTA 2260 B 1 HETATM 13 N N7 MTA . . . G 3 65.648 108.867 36.127 1 46.99 ? N7 MTA 2260 B 1 HETATM 14 C C5 MTA . . . G 3 65.114 110.067 35.716 1 46.91 ? C5 MTA 2260 B 1 HETATM 15 C C6 MTA . . . G 3 64.297 111.075 36.36 1 46.45 ? C6 MTA 2260 B 1 HETATM 16 N N6 MTA . . . G 3 63.899 110.952 37.627 1 46.13 ? N6 MTA 2260 B 1 HETATM 17 N N1 MTA . . . G 3 63.929 112.212 35.602 1 46.11 ? N1 MTA 2260 B 1 HETATM 18 C C2 MTA . . . G 3 64.334 112.349 34.302 1 45.84 ? C2 MTA 2260 B 1 HETATM 19 N N3 MTA . . . G 3 65.105 111.46 33.607 1 46.37 ? N3 MTA 2260 B 1 HETATM 20 C C4 MTA . . . G 3 65.463 110.34 34.366 1 46.99 ? C4 MTA 2260 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 20 #