data_1Z6Y # _model_server_result.job_id dhK4xCKCHxyS-M14iLSP-Q _model_server_result.datetime_utc '2024-11-24 15:51:28' _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 1z6y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":180}' # _entry.id 1Z6Y # _exptl.entry_id 1Z6Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 112.96 _cell.angle_beta 97.69 _cell.angle_gamma 90 _cell.entry_id 1Z6Y _cell.length_a 38.657 _cell.length_b 48.775 _cell.length_c 55.905 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z6Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,C,E 1 1 B,D,F 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 C N N ? 2 D 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 1Z6Y _atom_sites.fract_transf_matrix[1][1] 0.025869 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0038 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020502 _atom_sites.fract_transf_matrix[2][3] 0.008779 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.019635 _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 GDP A 1 180 1 GDP GDP . D 2 GDP B 1 180 2 GDP GDP . E 3 HOH A 1 201 201 HOH HOH . E 3 HOH A 2 206 206 HOH HOH . E 3 HOH A 3 207 207 HOH HOH . E 3 HOH A 4 209 209 HOH HOH . E 3 HOH A 5 212 212 HOH HOH . E 3 HOH A 6 213 213 HOH HOH . E 3 HOH A 7 216 216 HOH HOH . E 3 HOH A 8 217 217 HOH HOH . E 3 HOH A 9 220 220 HOH HOH . E 3 HOH A 10 221 221 HOH HOH . E 3 HOH A 11 222 222 HOH HOH . E 3 HOH A 12 223 223 HOH HOH . E 3 HOH A 13 224 224 HOH HOH . E 3 HOH A 14 226 226 HOH HOH . E 3 HOH A 15 228 228 HOH HOH . E 3 HOH A 16 229 229 HOH HOH . E 3 HOH A 17 232 232 HOH HOH . E 3 HOH A 18 234 234 HOH HOH . E 3 HOH A 19 239 239 HOH HOH . E 3 HOH A 20 243 243 HOH HOH . E 3 HOH A 21 245 245 HOH HOH . E 3 HOH A 22 246 246 HOH HOH . E 3 HOH A 23 248 248 HOH HOH . E 3 HOH A 24 249 249 HOH HOH . E 3 HOH A 25 252 252 HOH HOH . E 3 HOH A 26 253 253 HOH HOH . E 3 HOH A 27 257 257 HOH HOH . E 3 HOH A 28 258 258 HOH HOH . E 3 HOH A 29 259 259 HOH HOH . E 3 HOH A 30 262 262 HOH HOH . E 3 HOH A 31 263 263 HOH HOH . E 3 HOH A 32 264 264 HOH HOH . E 3 HOH A 33 265 265 HOH HOH . E 3 HOH A 34 266 266 HOH HOH . E 3 HOH A 35 267 267 HOH HOH . E 3 HOH A 36 271 271 HOH HOH . E 3 HOH A 37 272 272 HOH HOH . E 3 HOH A 38 273 273 HOH HOH . E 3 HOH A 39 277 277 HOH HOH . E 3 HOH A 40 279 279 HOH HOH . E 3 HOH A 41 280 280 HOH HOH . E 3 HOH A 42 281 281 HOH HOH . E 3 HOH A 43 282 282 HOH HOH . E 3 HOH A 44 285 285 HOH HOH . E 3 HOH A 45 287 287 HOH HOH . E 3 HOH A 46 288 288 HOH HOH . E 3 HOH A 47 290 290 HOH HOH . E 3 HOH A 48 291 291 HOH HOH . E 3 HOH A 49 293 293 HOH HOH . E 3 HOH A 50 294 294 HOH HOH . E 3 HOH A 51 295 295 HOH HOH . E 3 HOH A 52 296 296 HOH HOH . E 3 HOH A 53 299 299 HOH HOH . E 3 HOH A 54 300 300 HOH HOH . E 3 HOH A 55 301 301 HOH HOH . E 3 HOH A 56 303 303 HOH HOH . E 3 HOH A 57 304 304 HOH HOH . E 3 HOH A 58 305 305 HOH HOH . E 3 HOH A 59 306 306 HOH HOH . E 3 HOH A 60 307 307 HOH HOH . E 3 HOH A 61 308 308 HOH HOH . E 3 HOH A 62 313 313 HOH HOH . E 3 HOH A 63 314 314 HOH HOH . E 3 HOH A 64 315 315 HOH HOH . E 3 HOH A 65 316 316 HOH HOH . E 3 HOH A 66 317 317 HOH HOH . E 3 HOH A 67 326 326 HOH HOH . E 3 HOH A 68 327 327 HOH HOH . E 3 HOH A 69 328 328 HOH HOH . E 3 HOH A 70 331 331 HOH HOH . E 3 HOH A 71 333 333 HOH HOH . E 3 HOH A 72 335 335 HOH HOH . E 3 HOH A 73 336 336 HOH HOH . F 3 HOH B 1 202 202 HOH HOH . F 3 HOH B 2 203 203 HOH HOH . F 3 HOH B 3 204 204 HOH HOH . F 3 HOH B 4 205 205 HOH HOH . F 3 HOH B 5 208 208 HOH HOH . F 3 HOH B 6 210 210 HOH HOH . F 3 HOH B 7 211 211 HOH HOH . F 3 HOH B 8 214 214 HOH HOH . F 3 HOH B 9 215 215 HOH HOH . F 3 HOH B 10 218 218 HOH HOH . F 3 HOH B 11 219 219 HOH HOH . F 3 HOH B 12 225 225 HOH HOH . F 3 HOH B 13 227 227 HOH HOH . F 3 HOH B 14 230 230 HOH HOH . F 3 HOH B 15 231 231 HOH HOH . F 3 HOH B 16 233 233 HOH HOH . F 3 HOH B 17 235 235 HOH HOH . F 3 HOH B 18 236 236 HOH HOH . F 3 HOH B 19 238 238 HOH HOH . F 3 HOH B 20 240 240 HOH HOH . F 3 HOH B 21 241 241 HOH HOH . F 3 HOH B 22 242 242 HOH HOH . F 3 HOH B 23 244 244 HOH HOH . F 3 HOH B 24 247 247 HOH HOH . F 3 HOH B 25 250 250 HOH HOH . F 3 HOH B 26 251 251 HOH HOH . F 3 HOH B 27 254 254 HOH HOH . F 3 HOH B 28 255 255 HOH HOH . F 3 HOH B 29 256 256 HOH HOH . F 3 HOH B 30 260 260 HOH HOH . F 3 HOH B 31 261 261 HOH HOH . F 3 HOH B 32 268 268 HOH HOH . F 3 HOH B 33 269 269 HOH HOH . F 3 HOH B 34 270 270 HOH HOH . F 3 HOH B 35 274 274 HOH HOH . F 3 HOH B 36 275 275 HOH HOH . F 3 HOH B 37 276 276 HOH HOH . F 3 HOH B 38 278 278 HOH HOH . F 3 HOH B 39 283 283 HOH HOH . F 3 HOH B 40 284 284 HOH HOH . F 3 HOH B 41 286 286 HOH HOH . F 3 HOH B 42 289 289 HOH HOH . F 3 HOH B 43 292 292 HOH HOH . F 3 HOH B 44 297 297 HOH HOH . F 3 HOH B 45 298 298 HOH HOH . F 3 HOH B 46 302 302 HOH HOH . F 3 HOH B 47 309 309 HOH HOH . F 3 HOH B 48 310 310 HOH HOH . F 3 HOH B 49 311 311 HOH HOH . F 3 HOH B 50 312 312 HOH HOH . F 3 HOH B 51 318 318 HOH HOH . F 3 HOH B 52 319 319 HOH HOH . F 3 HOH B 53 320 320 HOH HOH . F 3 HOH B 54 321 321 HOH HOH . F 3 HOH B 55 322 322 HOH HOH . F 3 HOH B 56 323 323 HOH HOH . F 3 HOH B 57 324 324 HOH HOH . F 3 HOH B 58 325 325 HOH HOH . F 3 HOH B 59 329 329 HOH HOH . F 3 HOH B 60 330 330 HOH HOH . F 3 HOH B 61 332 332 HOH HOH . F 3 HOH B 62 334 334 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 . . . C 2 15.675 -28.288 8.796 1 11.28 ? PB GDP 180 A 1 HETATM 2 O O1B GDP . . . C 2 16.406 -29.25 7.893 1 13.21 ? O1B GDP 180 A 1 HETATM 3 O O2B GDP . . . C 2 16.493 -27.88 9.997 1 11.96 ? O2B GDP 180 A 1 HETATM 4 O O3B GDP . . . C 2 15.379 -27.036 8.014 1 13.41 ? O3B GDP 180 A 1 HETATM 5 O O3A GDP . . . C 2 14.251 -28.833 9.245 1 11.88 ? O3A GDP 180 A 1 HETATM 6 P PA GDP . . . C 2 13.705 -30.314 9.382 1 11.02 ? PA GDP 180 A 1 HETATM 7 O O1A GDP . . . C 2 13.417 -30.879 8.006 1 12.99 ? O1A GDP 180 A 1 HETATM 8 O O2A GDP . . . C 2 14.469 -31.161 10.341 1 12.65 ? O2A GDP 180 A 1 HETATM 9 O O5' GDP . . . C 2 12.263 -30.062 10.05 1 13.26 ? O5' GDP 180 A 1 HETATM 10 C C5' GDP . . . C 2 12.274 -29.786 11.434 1 14.88 ? C5' GDP 180 A 1 HETATM 11 C C4' GDP . . . C 2 11.068 -30.427 12.107 1 17.15 ? C4' GDP 180 A 1 HETATM 12 O O4' GDP . . . C 2 9.813 -29.942 11.617 1 16.28 ? O4' GDP 180 A 1 HETATM 13 C C3' GDP . . . C 2 11.091 -31.918 11.91 1 16.53 ? C3' GDP 180 A 1 HETATM 14 O O3' GDP . . . C 2 10.768 -32.366 13.225 1 17.91 ? O3' GDP 180 A 1 HETATM 15 C C2' GDP . . . C 2 9.941 -32.247 11.002 1 19.18 ? C2' GDP 180 A 1 HETATM 16 O O2' GDP . . . C 2 9.351 -33.462 11.514 1 22.88 ? O2' GDP 180 A 1 HETATM 17 C C1' GDP . . . C 2 9.023 -31.008 11.122 1 16.71 ? C1' GDP 180 A 1 HETATM 18 N N9 GDP . . . C 2 8.443 -30.645 9.806 1 15.37 ? N9 GDP 180 A 1 HETATM 19 C C8 GDP . . . C 2 9.028 -30.546 8.596 1 12.28 ? C8 GDP 180 A 1 HETATM 20 N N7 GDP . . . C 2 8.109 -30.221 7.644 1 13.21 ? N7 GDP 180 A 1 HETATM 21 C C5 GDP . . . C 2 6.891 -30.112 8.251 1 13.34 ? C5 GDP 180 A 1 HETATM 22 C C6 GDP . . . C 2 5.483 -29.81 7.868 1 13.12 ? C6 GDP 180 A 1 HETATM 23 O O6 GDP . . . C 2 5.145 -29.536 6.669 1 10.27 ? O6 GDP 180 A 1 HETATM 24 N N1 GDP . . . C 2 4.566 -29.811 8.875 1 13.36 ? N1 GDP 180 A 1 HETATM 25 C C2 GDP . . . C 2 4.877 -30.086 10.165 1 13.88 ? C2 GDP 180 A 1 HETATM 26 N N2 GDP . . . C 2 3.94 -30.147 11.141 1 14.9 ? N2 GDP 180 A 1 HETATM 27 N N3 GDP . . . C 2 6.136 -30.363 10.565 1 15.03 ? N3 GDP 180 A 1 HETATM 28 C C4 GDP . . . C 2 7.145 -30.384 9.668 1 14.7 ? C4 GDP 180 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 213 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #