data_3EMT # _model_server_result.job_id 39cKaz8WraCkKNVYMzDFBg _model_server_result.datetime_utc '2024-11-16 21:53:24' _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 3emt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 3EMT # _exptl.entry_id 3EMT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYGUANOSINE-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 120 _cell.entry_id 3EMT _cell.length_a 70.212 _cell.length_b 70.212 _cell.length_c 104.668 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EMT _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 70.212 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 35.106 60.805376 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 F 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 D O2B DGI . A DGI 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc2 D O2A DGI . A DGI 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc3 C MG MG . A MG 202 1_555 G O HOH . A HOH 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc4 F O1A DGI . B DGI 201 1_555 E MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc5 F O2B DGI . B DGI 201 1_555 E MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc6 E MG MG . B MG 202 1_555 H O HOH . B HOH 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id DGI _chem_comp.mon_nstd_flag n _chem_comp.name "2'-DEOXYGUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'dna 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 O1B PB DGI doub 83 n n PB O2B DGI sing 84 n n PB O3B DGI sing 85 n n PB O3A DGI sing 86 n n O2B HOB2 DGI sing 87 n n O3B HOB3 DGI sing 88 n n O3A PA DGI sing 89 n n PA O1A DGI doub 90 n n PA O2A DGI sing 91 n n PA O5' DGI sing 92 n n O2A HOA2 DGI sing 93 n n O5' C5' DGI sing 94 n n C5' C4' DGI sing 95 n n C5' H5' DGI sing 96 n n C5' "H5''" DGI sing 97 n n C4' O4' DGI sing 98 n n C4' C3' DGI sing 99 n n C4' H4' DGI sing 100 n n O4' C1' DGI sing 101 n n C3' O3' DGI sing 102 n n C3' C2' DGI sing 103 n n C3' H3' DGI sing 104 n n O3' HO3' DGI sing 105 n n C2' C1' DGI sing 106 n n C2' H2' DGI sing 107 n n C2' "H2''" DGI sing 108 n n C1' N9 DGI sing 109 n n C1' H1' DGI sing 110 n n N9 C8 DGI sing 111 n y N9 C4 DGI sing 112 n y C8 N7 DGI doub 113 n y C8 H8 DGI sing 114 n n N7 C5 DGI sing 115 n y C5 C4 DGI doub 116 n y C5 C6 DGI sing 117 n n C4 N3 DGI sing 118 n n N3 C2 DGI doub 119 n n C2 N2 DGI sing 120 n n C2 N1 DGI sing 121 n n N2 HN21 DGI sing 122 n n N2 HN22 DGI sing 123 n n N1 C6 DGI sing 124 n n N1 HN1 DGI sing 125 n n C6 O6 DGI doub 126 n n # _atom_sites.entry_id 3EMT _atom_sites.fract_transf_matrix[1][1] 0.014242 _atom_sites.fract_transf_matrix[1][2] 0.008223 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016446 _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] 0.009554 _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 MG A 1 202 202 MG MG . D 3 DGI A 1 201 201 DGI DGI . E 2 MG B 1 202 202 MG MG . F 3 DGI B 1 201 201 DGI DGI . G 4 HOH A 1 203 1 HOH HOH . G 4 HOH A 2 204 4 HOH HOH . G 4 HOH A 3 205 6 HOH HOH . G 4 HOH A 4 206 8 HOH HOH . G 4 HOH A 5 207 9 HOH HOH . G 4 HOH A 6 208 10 HOH HOH . G 4 HOH A 7 209 11 HOH HOH . G 4 HOH A 8 210 12 HOH HOH . G 4 HOH A 9 211 13 HOH HOH . G 4 HOH A 10 212 16 HOH HOH . G 4 HOH A 11 213 17 HOH HOH . G 4 HOH A 12 214 21 HOH HOH . G 4 HOH A 13 215 22 HOH HOH . G 4 HOH A 14 216 23 HOH HOH . G 4 HOH A 15 217 24 HOH HOH . G 4 HOH A 16 218 25 HOH HOH . G 4 HOH A 17 219 28 HOH HOH . G 4 HOH A 18 220 31 HOH HOH . G 4 HOH A 19 221 32 HOH HOH . G 4 HOH A 20 222 34 HOH HOH . G 4 HOH A 21 223 35 HOH HOH . G 4 HOH A 22 224 36 HOH HOH . G 4 HOH A 23 225 40 HOH HOH . G 4 HOH A 24 226 45 HOH HOH . G 4 HOH A 25 227 46 HOH HOH . G 4 HOH A 26 228 49 HOH HOH . G 4 HOH A 27 229 50 HOH HOH . G 4 HOH A 28 230 51 HOH HOH . G 4 HOH A 29 231 54 HOH HOH . G 4 HOH A 30 232 57 HOH HOH . G 4 HOH A 31 233 59 HOH HOH . G 4 HOH A 32 234 61 HOH HOH . G 4 HOH A 33 235 65 HOH HOH . G 4 HOH A 34 236 67 HOH HOH . G 4 HOH A 35 237 70 HOH HOH . G 4 HOH A 36 238 73 HOH HOH . G 4 HOH A 37 239 75 HOH HOH . G 4 HOH A 38 240 80 HOH HOH . G 4 HOH A 39 241 81 HOH HOH . G 4 HOH A 40 242 83 HOH HOH . G 4 HOH A 41 243 86 HOH HOH . G 4 HOH A 42 244 89 HOH HOH . G 4 HOH A 43 245 90 HOH HOH . G 4 HOH A 44 246 102 HOH HOH . G 4 HOH A 45 247 103 HOH HOH . G 4 HOH A 46 248 105 HOH HOH . G 4 HOH A 47 249 112 HOH HOH . G 4 HOH A 48 250 115 HOH HOH . G 4 HOH A 49 251 116 HOH HOH . G 4 HOH A 50 252 122 HOH HOH . G 4 HOH A 51 253 123 HOH HOH . G 4 HOH A 52 254 124 HOH HOH . G 4 HOH A 53 255 129 HOH HOH . G 4 HOH A 54 256 134 HOH HOH . G 4 HOH A 55 257 139 HOH HOH . G 4 HOH A 56 258 141 HOH HOH . G 4 HOH A 57 259 145 HOH HOH . G 4 HOH A 58 260 148 HOH HOH . G 4 HOH A 59 261 149 HOH HOH . G 4 HOH A 60 262 150 HOH HOH . G 4 HOH A 61 263 151 HOH HOH . G 4 HOH A 62 264 163 HOH HOH . G 4 HOH A 63 265 173 HOH HOH . G 4 HOH A 64 266 181 HOH HOH . G 4 HOH A 65 267 183 HOH HOH . G 4 HOH A 66 268 186 HOH HOH . G 4 HOH A 67 269 202 HOH HOH . G 4 HOH A 68 270 214 HOH HOH . G 4 HOH A 69 271 227 HOH HOH . G 4 HOH A 70 272 241 HOH HOH . G 4 HOH A 71 273 265 HOH HOH . G 4 HOH A 72 274 272 HOH HOH . G 4 HOH A 73 275 292 HOH HOH . G 4 HOH A 74 276 308 HOH HOH . G 4 HOH A 75 277 309 HOH HOH . G 4 HOH A 76 278 315 HOH HOH . G 4 HOH A 77 279 318 HOH HOH . G 4 HOH A 78 280 320 HOH HOH . G 4 HOH A 79 281 323 HOH HOH . G 4 HOH A 80 282 332 HOH HOH . G 4 HOH A 81 283 334 HOH HOH . G 4 HOH A 82 284 337 HOH HOH . G 4 HOH A 83 285 339 HOH HOH . G 4 HOH A 84 286 342 HOH HOH . G 4 HOH A 85 287 347 HOH HOH . G 4 HOH A 86 288 351 HOH HOH . G 4 HOH A 87 289 355 HOH HOH . G 4 HOH A 88 290 359 HOH HOH . H 4 HOH B 1 203 2 HOH HOH . H 4 HOH B 2 204 3 HOH HOH . H 4 HOH B 3 205 5 HOH HOH . H 4 HOH B 4 206 7 HOH HOH . H 4 HOH B 5 207 14 HOH HOH . H 4 HOH B 6 208 15 HOH HOH . H 4 HOH B 7 209 18 HOH HOH . H 4 HOH B 8 210 19 HOH HOH . H 4 HOH B 9 211 20 HOH HOH . H 4 HOH B 10 212 26 HOH HOH . H 4 HOH B 11 213 27 HOH HOH . H 4 HOH B 12 214 29 HOH HOH . H 4 HOH B 13 215 30 HOH HOH . H 4 HOH B 14 216 33 HOH HOH . H 4 HOH B 15 217 38 HOH HOH . H 4 HOH B 16 218 41 HOH HOH . H 4 HOH B 17 219 43 HOH HOH . H 4 HOH B 18 220 47 HOH HOH . H 4 HOH B 19 221 52 HOH HOH . H 4 HOH B 20 222 56 HOH HOH . H 4 HOH B 21 223 58 HOH HOH . H 4 HOH B 22 224 60 HOH HOH . H 4 HOH B 23 225 63 HOH HOH . H 4 HOH B 24 226 64 HOH HOH . H 4 HOH B 25 227 68 HOH HOH . H 4 HOH B 26 228 69 HOH HOH . H 4 HOH B 27 229 71 HOH HOH . H 4 HOH B 28 230 77 HOH HOH . H 4 HOH B 29 231 78 HOH HOH . H 4 HOH B 30 232 79 HOH HOH . H 4 HOH B 31 233 82 HOH HOH . H 4 HOH B 32 234 84 HOH HOH . H 4 HOH B 33 235 87 HOH HOH . H 4 HOH B 34 236 88 HOH HOH . H 4 HOH B 35 237 92 HOH HOH . H 4 HOH B 36 238 93 HOH HOH . H 4 HOH B 37 239 96 HOH HOH . H 4 HOH B 38 240 98 HOH HOH . H 4 HOH B 39 241 99 HOH HOH . H 4 HOH B 40 242 104 HOH HOH . H 4 HOH B 41 243 106 HOH HOH . H 4 HOH B 42 244 109 HOH HOH . H 4 HOH B 43 245 111 HOH HOH . H 4 HOH B 44 246 114 HOH HOH . H 4 HOH B 45 247 118 HOH HOH . H 4 HOH B 46 248 120 HOH HOH . H 4 HOH B 47 249 125 HOH HOH . H 4 HOH B 48 250 133 HOH HOH . H 4 HOH B 49 251 137 HOH HOH . H 4 HOH B 50 252 140 HOH HOH . H 4 HOH B 51 253 146 HOH HOH . H 4 HOH B 52 254 153 HOH HOH . H 4 HOH B 53 255 154 HOH HOH . H 4 HOH B 54 256 155 HOH HOH . H 4 HOH B 55 257 160 HOH HOH . H 4 HOH B 56 258 176 HOH HOH . H 4 HOH B 57 259 177 HOH HOH . H 4 HOH B 58 260 187 HOH HOH . H 4 HOH B 59 261 188 HOH HOH . H 4 HOH B 60 262 191 HOH HOH . H 4 HOH B 61 263 194 HOH HOH . H 4 HOH B 62 264 198 HOH HOH . H 4 HOH B 63 265 212 HOH HOH . H 4 HOH B 64 266 213 HOH HOH . H 4 HOH B 65 267 215 HOH HOH . H 4 HOH B 66 268 223 HOH HOH . H 4 HOH B 67 269 232 HOH HOH . H 4 HOH B 68 270 234 HOH HOH . H 4 HOH B 69 271 244 HOH HOH . H 4 HOH B 70 272 257 HOH HOH . H 4 HOH B 71 273 261 HOH HOH . H 4 HOH B 72 274 264 HOH HOH . H 4 HOH B 73 275 273 HOH HOH . H 4 HOH B 74 276 283 HOH HOH . H 4 HOH B 75 277 290 HOH HOH . H 4 HOH B 76 278 302 HOH HOH . H 4 HOH B 77 279 303 HOH HOH . H 4 HOH B 78 280 310 HOH HOH . H 4 HOH B 79 281 311 HOH HOH . H 4 HOH B 80 282 313 HOH HOH . H 4 HOH B 81 283 317 HOH HOH . H 4 HOH B 82 284 319 HOH HOH . H 4 HOH B 83 285 321 HOH HOH . H 4 HOH B 84 286 322 HOH HOH . H 4 HOH B 85 287 324 HOH HOH . H 4 HOH B 86 288 325 HOH HOH . H 4 HOH B 87 289 326 HOH HOH . H 4 HOH B 88 290 327 HOH HOH . H 4 HOH B 89 291 328 HOH HOH . H 4 HOH B 90 292 331 HOH HOH . H 4 HOH B 91 293 336 HOH HOH . H 4 HOH B 92 294 350 HOH HOH . H 4 HOH B 93 295 357 HOH HOH . H 4 HOH B 94 296 361 HOH HOH . H 4 HOH B 95 297 362 HOH HOH . H 4 HOH B 96 298 363 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 O O1B DGI . . . F 3 52.713 27.253 -5.992 1 11.64 ? O1B DGI 201 B 1 HETATM 2 P PB DGI . . . F 3 52.302 26.712 -7.404 1 14.33 ? PB DGI 201 B 1 HETATM 3 O O2B DGI . . . F 3 53.016 25.176 -7.821 1 15.9 ? O2B DGI 201 B 1 HETATM 4 O O3B DGI . . . F 3 50.581 26.569 -7.583 1 13.58 ? O3B DGI 201 B 1 HETATM 5 O O3A DGI . . . F 3 52.631 27.83 -8.539 1 12.56 ? O3A DGI 201 B 1 HETATM 6 P PA DGI . . . F 3 53.964 28.174 -9.396 1 14.87 ? PA DGI 201 B 1 HETATM 7 O O1A DGI . . . F 3 55.042 27.032 -9.444 1 18.68 ? O1A DGI 201 B 1 HETATM 8 O O2A DGI . . . F 3 53.365 28.606 -10.995 1 21.26 ? O2A DGI 201 B 1 HETATM 9 O O5' DGI . . . F 3 54.534 29.498 -8.71 1 13.64 ? O5' DGI 201 B 1 HETATM 10 C C5' DGI . . . F 3 55.365 29.388 -7.556 1 13.62 ? C5' DGI 201 B 1 HETATM 11 C C4' DGI . . . F 3 54.98 30.493 -6.589 1 14.13 ? C4' DGI 201 B 1 HETATM 12 O O4' DGI . . . F 3 55.276 31.791 -7.132 1 15.6 ? O4' DGI 201 B 1 HETATM 13 C C3' DGI . . . F 3 53.487 30.506 -6.303 1 14.28 ? C3' DGI 201 B 1 HETATM 14 O O3' DGI . . . F 3 53.146 29.664 -5.191 1 14.21 ? O3' DGI 201 B 1 HETATM 15 C C2' DGI . . . F 3 53.218 31.961 -5.984 1 15.52 ? C2' DGI 201 B 1 HETATM 16 C C1' DGI . . . F 3 54.226 32.719 -6.834 1 14.8 ? C1' DGI 201 B 1 HETATM 17 N N9 DGI . . . F 3 53.553 33.149 -8.084 1 16.47 ? N9 DGI 201 B 1 HETATM 18 C C8 DGI . . . F 3 53.353 32.385 -9.163 1 16.47 ? C8 DGI 201 B 1 HETATM 19 N N7 DGI . . . F 3 52.707 33.117 -10.099 1 20.13 ? N7 DGI 201 B 1 HETATM 20 C C5 DGI . . . F 3 52.51 34.35 -9.601 1 17.35 ? C5 DGI 201 B 1 HETATM 21 C C4 DGI . . . F 3 53.049 34.372 -8.329 1 16.35 ? C4 DGI 201 B 1 HETATM 22 N N3 DGI . . . F 3 52.982 35.493 -7.6 1 20.28 ? N3 DGI 201 B 1 HETATM 23 C C2 DGI . . . F 3 52.4 36.595 -8.123 1 18.23 ? C2 DGI 201 B 1 HETATM 24 N N2 DGI . . . F 3 52.338 37.724 -7.384 1 25.3 ? N2 DGI 201 B 1 HETATM 25 N N1 DGI . . . F 3 51.874 36.594 -9.357 1 20.94 ? N1 DGI 201 B 1 HETATM 26 C C6 DGI . . . F 3 51.913 35.498 -10.115 1 22.05 ? C6 DGI 201 B 1 HETATM 27 O O6 DGI . . . F 3 51.422 35.502 -11.271 1 24.95 ? O6 DGI 201 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #