data_6TKZ # _model_server_result.job_id ApBgXdpoM4p_YenC4gtdLA _model_server_result.datetime_utc '2024-12-12 13:45:45' _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 6tkz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 6TKZ # _exptl.entry_id 6TKZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 6TKZ _cell.length_a 97.17 _cell.length_b 97.17 _cell.length_c 312 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TKZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,C,D,E,F,G,H,I,J,K 1 1 A,B,C,D,E,F,G,H,I,J,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 E N N ? 3 F N N # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 6TKZ _atom_sites.fract_transf_matrix[1][1] 0.010291 _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] 0.010291 _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] 0.003205 _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 3 GDP C 1 201 201 GDP GDP . F 3 GDP D 1 201 201 GDP GDP . G 4 GOL A 1 2201 1 GOL GOL . H 5 HOH B 1 2201 213 HOH HOH . H 5 HOH B 2 2202 141 HOH HOH . H 5 HOH B 3 2203 34 HOH HOH . H 5 HOH B 4 2204 7 HOH HOH . H 5 HOH B 5 2205 167 HOH HOH . H 5 HOH B 6 2206 68 HOH HOH . H 5 HOH B 7 2207 162 HOH HOH . H 5 HOH B 8 2208 64 HOH HOH . H 5 HOH B 9 2209 236 HOH HOH . H 5 HOH B 10 2210 241 HOH HOH . H 5 HOH B 11 2211 20 HOH HOH . H 5 HOH B 12 2212 51 HOH HOH . H 5 HOH B 13 2213 40 HOH HOH . H 5 HOH B 14 2214 103 HOH HOH . H 5 HOH B 15 2215 27 HOH HOH . H 5 HOH B 16 2216 123 HOH HOH . H 5 HOH B 17 2217 12 HOH HOH . H 5 HOH B 18 2218 10 HOH HOH . H 5 HOH B 19 2219 9 HOH HOH . H 5 HOH B 20 2220 89 HOH HOH . H 5 HOH B 21 2221 216 HOH HOH . H 5 HOH B 22 2222 204 HOH HOH . H 5 HOH B 23 2223 84 HOH HOH . H 5 HOH B 24 2224 111 HOH HOH . H 5 HOH B 25 2225 156 HOH HOH . H 5 HOH B 26 2226 6 HOH HOH . H 5 HOH B 27 2227 186 HOH HOH . H 5 HOH B 28 2228 53 HOH HOH . H 5 HOH B 29 2229 109 HOH HOH . H 5 HOH B 30 2230 190 HOH HOH . H 5 HOH B 31 2231 201 HOH HOH . H 5 HOH B 32 2232 175 HOH HOH . H 5 HOH B 33 2233 194 HOH HOH . H 5 HOH B 34 2234 32 HOH HOH . H 5 HOH B 35 2235 15 HOH HOH . H 5 HOH B 36 2236 66 HOH HOH . H 5 HOH B 37 2237 102 HOH HOH . H 5 HOH B 38 2238 237 HOH HOH . H 5 HOH B 39 2239 159 HOH HOH . H 5 HOH B 40 2240 220 HOH HOH . H 5 HOH B 41 2241 54 HOH HOH . H 5 HOH B 42 2242 67 HOH HOH . H 5 HOH B 43 2243 92 HOH HOH . H 5 HOH B 44 2244 127 HOH HOH . H 5 HOH B 45 2245 18 HOH HOH . H 5 HOH B 46 2246 224 HOH HOH . H 5 HOH B 47 2247 121 HOH HOH . H 5 HOH B 48 2248 63 HOH HOH . H 5 HOH B 49 2249 17 HOH HOH . H 5 HOH B 50 2250 238 HOH HOH . H 5 HOH B 51 2251 93 HOH HOH . H 5 HOH B 52 2252 31 HOH HOH . H 5 HOH B 53 2253 126 HOH HOH . H 5 HOH B 54 2254 5 HOH HOH . H 5 HOH B 55 2255 118 HOH HOH . H 5 HOH B 56 2256 149 HOH HOH . H 5 HOH B 57 2257 113 HOH HOH . H 5 HOH B 58 2258 83 HOH HOH . H 5 HOH B 59 2259 11 HOH HOH . H 5 HOH B 60 2260 223 HOH HOH . H 5 HOH B 61 2261 37 HOH HOH . H 5 HOH B 62 2262 157 HOH HOH . H 5 HOH B 63 2263 217 HOH HOH . H 5 HOH B 64 2264 135 HOH HOH . H 5 HOH B 65 2265 229 HOH HOH . H 5 HOH B 66 2266 132 HOH HOH . H 5 HOH B 67 2267 214 HOH HOH . H 5 HOH B 68 2268 98 HOH HOH . H 5 HOH B 69 2269 119 HOH HOH . H 5 HOH B 70 2270 192 HOH HOH . H 5 HOH B 71 2271 55 HOH HOH . H 5 HOH B 72 2272 138 HOH HOH . H 5 HOH B 73 2273 80 HOH HOH . H 5 HOH B 74 2274 176 HOH HOH . H 5 HOH B 75 2275 146 HOH HOH . H 5 HOH B 76 2276 178 HOH HOH . H 5 HOH B 77 2277 203 HOH HOH . H 5 HOH B 78 2278 195 HOH HOH . H 5 HOH B 79 2279 212 HOH HOH . H 5 HOH B 80 2280 205 HOH HOH . H 5 HOH B 81 2281 193 HOH HOH . H 5 HOH B 82 2282 197 HOH HOH . H 5 HOH B 83 2283 191 HOH HOH . H 5 HOH B 84 2284 150 HOH HOH . H 5 HOH B 85 2285 144 HOH HOH . H 5 HOH B 86 2286 233 HOH HOH . H 5 HOH B 87 2287 235 HOH HOH . H 5 HOH B 88 2288 198 HOH HOH . H 5 HOH B 89 2289 163 HOH HOH . H 5 HOH B 90 2290 69 HOH HOH . H 5 HOH B 91 2291 185 HOH HOH . H 5 HOH B 92 2292 225 HOH HOH . H 5 HOH B 93 2293 188 HOH HOH . H 5 HOH B 94 2294 44 HOH HOH . H 5 HOH B 95 2295 202 HOH HOH . H 5 HOH B 96 2296 137 HOH HOH . I 5 HOH C 1 301 96 HOH HOH . I 5 HOH C 2 302 59 HOH HOH . I 5 HOH C 3 303 183 HOH HOH . I 5 HOH C 4 304 196 HOH HOH . I 5 HOH C 5 305 125 HOH HOH . I 5 HOH C 6 306 28 HOH HOH . I 5 HOH C 7 307 172 HOH HOH . I 5 HOH C 8 308 184 HOH HOH . I 5 HOH C 9 309 35 HOH HOH . I 5 HOH C 10 310 95 HOH HOH . I 5 HOH C 11 311 206 HOH HOH . I 5 HOH C 12 312 79 HOH HOH . I 5 HOH C 13 313 155 HOH HOH . I 5 HOH C 14 314 131 HOH HOH . I 5 HOH C 15 315 164 HOH HOH . I 5 HOH C 16 316 152 HOH HOH . I 5 HOH C 17 317 21 HOH HOH . I 5 HOH C 18 318 8 HOH HOH . I 5 HOH C 19 319 105 HOH HOH . I 5 HOH C 20 320 85 HOH HOH . I 5 HOH C 21 321 200 HOH HOH . I 5 HOH C 22 322 124 HOH HOH . I 5 HOH C 23 323 52 HOH HOH . I 5 HOH C 24 324 228 HOH HOH . I 5 HOH C 25 325 41 HOH HOH . I 5 HOH C 26 326 108 HOH HOH . I 5 HOH C 27 327 101 HOH HOH . I 5 HOH C 28 328 154 HOH HOH . I 5 HOH C 29 329 231 HOH HOH . J 5 HOH D 1 301 208 HOH HOH . J 5 HOH D 2 302 60 HOH HOH . J 5 HOH D 3 303 2 HOH HOH . J 5 HOH D 4 304 50 HOH HOH . J 5 HOH D 5 305 107 HOH HOH . J 5 HOH D 6 306 166 HOH HOH . J 5 HOH D 7 307 75 HOH HOH . J 5 HOH D 8 308 168 HOH HOH . J 5 HOH D 9 309 240 HOH HOH . J 5 HOH D 10 310 3 HOH HOH . J 5 HOH D 11 311 239 HOH HOH . J 5 HOH D 12 312 86 HOH HOH . J 5 HOH D 13 313 129 HOH HOH . J 5 HOH D 14 314 211 HOH HOH . J 5 HOH D 15 315 90 HOH HOH . J 5 HOH D 16 316 4 HOH HOH . J 5 HOH D 17 317 97 HOH HOH . J 5 HOH D 18 318 48 HOH HOH . J 5 HOH D 19 319 173 HOH HOH . J 5 HOH D 20 320 219 HOH HOH . J 5 HOH D 21 321 74 HOH HOH . J 5 HOH D 22 322 115 HOH HOH . J 5 HOH D 23 323 76 HOH HOH . J 5 HOH D 24 324 110 HOH HOH . J 5 HOH D 25 325 23 HOH HOH . J 5 HOH D 26 326 142 HOH HOH . J 5 HOH D 27 327 148 HOH HOH . J 5 HOH D 28 328 56 HOH HOH . J 5 HOH D 29 329 234 HOH HOH . J 5 HOH D 30 330 38 HOH HOH . J 5 HOH D 31 331 177 HOH HOH . J 5 HOH D 32 332 160 HOH HOH . J 5 HOH D 33 333 153 HOH HOH . J 5 HOH D 34 334 161 HOH HOH . J 5 HOH D 35 335 215 HOH HOH . J 5 HOH D 36 336 158 HOH HOH . K 5 HOH A 1 2301 82 HOH HOH . K 5 HOH A 2 2302 171 HOH HOH . K 5 HOH A 3 2303 47 HOH HOH . K 5 HOH A 4 2304 139 HOH HOH . K 5 HOH A 5 2305 77 HOH HOH . K 5 HOH A 6 2306 61 HOH HOH . K 5 HOH A 7 2307 91 HOH HOH . K 5 HOH A 8 2308 106 HOH HOH . K 5 HOH A 9 2309 87 HOH HOH . K 5 HOH A 10 2310 81 HOH HOH . K 5 HOH A 11 2311 114 HOH HOH . K 5 HOH A 12 2312 104 HOH HOH . K 5 HOH A 13 2313 65 HOH HOH . K 5 HOH A 14 2314 43 HOH HOH . K 5 HOH A 15 2315 134 HOH HOH . K 5 HOH A 16 2316 112 HOH HOH . K 5 HOH A 17 2317 36 HOH HOH . K 5 HOH A 18 2318 180 HOH HOH . K 5 HOH A 19 2319 145 HOH HOH . K 5 HOH A 20 2320 222 HOH HOH . K 5 HOH A 21 2321 33 HOH HOH . K 5 HOH A 22 2322 45 HOH HOH . K 5 HOH A 23 2323 26 HOH HOH . K 5 HOH A 24 2324 230 HOH HOH . K 5 HOH A 25 2325 187 HOH HOH . K 5 HOH A 26 2326 57 HOH HOH . K 5 HOH A 27 2327 100 HOH HOH . K 5 HOH A 28 2328 71 HOH HOH . K 5 HOH A 29 2329 218 HOH HOH . K 5 HOH A 30 2330 25 HOH HOH . K 5 HOH A 31 2331 117 HOH HOH . K 5 HOH A 32 2332 13 HOH HOH . K 5 HOH A 33 2333 46 HOH HOH . K 5 HOH A 34 2334 140 HOH HOH . K 5 HOH A 35 2335 116 HOH HOH . K 5 HOH A 36 2336 29 HOH HOH . K 5 HOH A 37 2337 88 HOH HOH . K 5 HOH A 38 2338 22 HOH HOH . K 5 HOH A 39 2339 16 HOH HOH . K 5 HOH A 40 2340 24 HOH HOH . K 5 HOH A 41 2341 120 HOH HOH . K 5 HOH A 42 2342 78 HOH HOH . K 5 HOH A 43 2343 14 HOH HOH . K 5 HOH A 44 2344 1 HOH HOH . K 5 HOH A 45 2345 73 HOH HOH . K 5 HOH A 46 2346 227 HOH HOH . K 5 HOH A 47 2347 70 HOH HOH . K 5 HOH A 48 2348 128 HOH HOH . K 5 HOH A 49 2349 133 HOH HOH . K 5 HOH A 50 2350 72 HOH HOH . K 5 HOH A 51 2351 122 HOH HOH . K 5 HOH A 52 2352 209 HOH HOH . K 5 HOH A 53 2353 179 HOH HOH . K 5 HOH A 54 2354 19 HOH HOH . K 5 HOH A 55 2355 42 HOH HOH . K 5 HOH A 56 2356 30 HOH HOH . K 5 HOH A 57 2357 49 HOH HOH . K 5 HOH A 58 2358 181 HOH HOH . K 5 HOH A 59 2359 151 HOH HOH . K 5 HOH A 60 2360 147 HOH HOH . K 5 HOH A 61 2361 136 HOH HOH . K 5 HOH A 62 2362 221 HOH HOH . K 5 HOH A 63 2363 170 HOH HOH . K 5 HOH A 64 2364 99 HOH HOH . K 5 HOH A 65 2365 182 HOH HOH . K 5 HOH A 66 2366 143 HOH HOH . K 5 HOH A 67 2367 174 HOH HOH . K 5 HOH A 68 2368 207 HOH HOH . K 5 HOH A 69 2369 39 HOH HOH . K 5 HOH A 70 2370 94 HOH HOH . K 5 HOH A 71 2371 232 HOH HOH . K 5 HOH A 72 2372 130 HOH HOH . K 5 HOH A 73 2373 62 HOH HOH . K 5 HOH A 74 2374 199 HOH HOH . K 5 HOH A 75 2375 226 HOH HOH . K 5 HOH A 76 2376 169 HOH HOH . K 5 HOH A 77 2377 189 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 P PB GDP . . . E 3 19.335 52.474 -35.376 1 92.99 ? PB GDP 201 C 1 HETATM 2 O O1B GDP . . . E 3 19.276 51.642 -36.63 1 101.63 ? O1B GDP 201 C 1 HETATM 3 O O2B GDP . . . E 3 18.214 53.493 -35.387 1 104.8 ? O2B GDP 201 C 1 HETATM 4 O O3B GDP . . . E 3 20.679 53.163 -35.34 1 89.41 ? O3B GDP 201 C 1 HETATM 5 O O3A GDP . . . E 3 19.145 51.543 -34.087 1 85.65 ? O3A GDP 201 C 1 HETATM 6 P PA GDP . . . E 3 17.962 50.449 -33.985 1 106.44 ? PA GDP 201 C 1 HETATM 7 O O1A GDP . . . E 3 17.267 50.24 -35.319 1 112.72 ? O1A GDP 201 C 1 HETATM 8 O O2A GDP . . . E 3 16.991 50.78 -32.875 1 89.62 ? O2A GDP 201 C 1 HETATM 9 O O5' GDP . . . E 3 18.741 49.128 -33.523 1 100.04 ? O5' GDP 201 C 1 HETATM 10 C C5' GDP . . . E 3 18.795 48.004 -34.394 1 101.32 ? C5' GDP 201 C 1 HETATM 11 C C4' GDP . . . E 3 18.733 46.725 -33.567 1 98.24 ? C4' GDP 201 C 1 HETATM 12 O O4' GDP . . . E 3 19.525 46.875 -32.389 1 96.17 ? O4' GDP 201 C 1 HETATM 13 C C3' GDP . . . E 3 17.32 46.366 -33.111 1 101.01 ? C3' GDP 201 C 1 HETATM 14 O O3' GDP . . . E 3 17.011 45.039 -33.553 1 95.79 ? O3' GDP 201 C 1 HETATM 15 C C2' GDP . . . E 3 17.346 46.423 -31.591 1 100.12 ? C2' GDP 201 C 1 HETATM 16 O O2' GDP . . . E 3 16.607 45.372 -30.95 1 93.66 ? O2' GDP 201 C 1 HETATM 17 C C1' GDP . . . E 3 18.825 46.323 -31.264 1 100.67 ? C1' GDP 201 C 1 HETATM 18 N N9 GDP . . . E 3 19.134 47.079 -30.027 1 102.87 ? N9 GDP 201 C 1 HETATM 19 C C8 GDP . . . E 3 18.959 48.4 -29.84 1 100.62 ? C8 GDP 201 C 1 HETATM 20 N N7 GDP . . . E 3 19.351 48.771 -28.595 1 101.38 ? N7 GDP 201 C 1 HETATM 21 C C5 GDP . . . E 3 19.795 47.671 -27.962 1 103.81 ? C5 GDP 201 C 1 HETATM 22 C C6 GDP . . . E 3 20.354 47.361 -26.623 1 105.95 ? C6 GDP 201 C 1 HETATM 23 O O6 GDP . . . E 3 20.513 48.256 -25.759 1 103.89 ? O6 GDP 201 C 1 HETATM 24 N N1 GDP . . . E 3 20.69 46.092 -26.364 1 106.62 ? N1 GDP 201 C 1 HETATM 25 C C2 GDP . . . E 3 20.537 45.112 -27.274 1 108.1 ? C2 GDP 201 C 1 HETATM 26 N N2 GDP . . . E 3 20.902 43.858 -26.924 1 112.69 ? N2 GDP 201 C 1 HETATM 27 N N3 GDP . . . E 3 20.033 45.321 -28.52 1 108.13 ? N3 GDP 201 C 1 HETATM 28 C C4 GDP . . . E 3 19.652 46.559 -28.914 1 106.08 ? C4 GDP 201 C 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 28 #