data_2AL7 # _model_server_result.job_id UFZCqGUNe95NCh7LjdTasQ _model_server_result.datetime_utc '2024-11-15 19:16:31' _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 2al7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 2AL7 # _exptl.entry_id 2AL7 _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 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 2AL7 _cell.length_a 41.732 _cell.length_b 62.393 _cell.length_c 63.796 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2AL7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 # _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 # 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 A OG1 THR 36 A THR 33 1_555 B MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc2 C O1B GDP . A GDP 201 1_555 B MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc3 B MG MG . A MG 202 1_555 D O HOH . A HOH 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc4 B MG MG . A MG 202 1_555 D O HOH . A HOH 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc5 B MG MG . A MG 202 1_555 D O HOH . A HOH 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc6 B MG MG . A MG 202 1_555 D O HOH . A HOH 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? # _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 2AL7 _atom_sites.fract_transf_matrix[1][1] 0.023962 _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] 0.016027 _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] 0.015675 _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 MG A 1 202 202 MG MG . C 3 GDP A 1 201 201 GDP GDP . D 4 HOH A 1 203 1 HOH HOH . D 4 HOH A 2 204 2 HOH HOH . D 4 HOH A 3 205 3 HOH HOH . D 4 HOH A 4 206 4 HOH HOH . D 4 HOH A 5 207 5 HOH HOH . D 4 HOH A 6 208 6 HOH HOH . D 4 HOH A 7 209 7 HOH HOH . D 4 HOH A 8 210 8 HOH HOH . D 4 HOH A 9 211 9 HOH HOH . D 4 HOH A 10 212 10 HOH HOH . D 4 HOH A 11 213 11 HOH HOH . D 4 HOH A 12 214 12 HOH HOH . D 4 HOH A 13 215 13 HOH HOH . D 4 HOH A 14 216 14 HOH HOH . D 4 HOH A 15 217 15 HOH HOH . D 4 HOH A 16 218 16 HOH HOH . D 4 HOH A 17 219 17 HOH HOH . D 4 HOH A 18 220 18 HOH HOH . D 4 HOH A 19 221 19 HOH HOH . D 4 HOH A 20 222 20 HOH HOH . D 4 HOH A 21 223 21 HOH HOH . D 4 HOH A 22 224 22 HOH HOH . D 4 HOH A 23 225 23 HOH HOH . D 4 HOH A 24 226 24 HOH HOH . D 4 HOH A 25 227 25 HOH HOH . D 4 HOH A 26 228 26 HOH HOH . D 4 HOH A 27 229 27 HOH HOH . D 4 HOH A 28 230 28 HOH HOH . D 4 HOH A 29 231 29 HOH HOH . D 4 HOH A 30 232 30 HOH HOH . D 4 HOH A 31 233 31 HOH HOH . D 4 HOH A 32 234 32 HOH HOH . D 4 HOH A 33 235 33 HOH HOH . D 4 HOH A 34 236 34 HOH HOH . D 4 HOH A 35 237 35 HOH HOH . D 4 HOH A 36 238 36 HOH HOH . D 4 HOH A 37 239 37 HOH HOH . D 4 HOH A 38 240 38 HOH HOH . D 4 HOH A 39 241 39 HOH HOH . D 4 HOH A 40 242 40 HOH HOH . D 4 HOH A 41 243 41 HOH HOH . D 4 HOH A 42 244 42 HOH HOH . D 4 HOH A 43 245 43 HOH HOH . D 4 HOH A 44 246 44 HOH HOH . D 4 HOH A 45 247 45 HOH HOH . D 4 HOH A 46 248 46 HOH HOH . D 4 HOH A 47 249 47 HOH HOH . D 4 HOH A 48 250 48 HOH HOH . D 4 HOH A 49 251 49 HOH HOH . D 4 HOH A 50 252 50 HOH HOH . D 4 HOH A 51 253 51 HOH HOH . D 4 HOH A 52 254 52 HOH HOH . D 4 HOH A 53 255 53 HOH HOH . D 4 HOH A 54 256 54 HOH HOH . D 4 HOH A 55 257 55 HOH HOH . D 4 HOH A 56 258 56 HOH HOH . D 4 HOH A 57 259 57 HOH HOH . D 4 HOH A 58 260 58 HOH HOH . D 4 HOH A 59 261 59 HOH HOH . D 4 HOH A 60 262 60 HOH HOH . D 4 HOH A 61 263 61 HOH HOH . D 4 HOH A 62 264 62 HOH HOH . D 4 HOH A 63 265 63 HOH HOH . D 4 HOH A 64 266 64 HOH HOH . D 4 HOH A 65 267 65 HOH HOH . D 4 HOH A 66 268 66 HOH HOH . D 4 HOH A 67 269 67 HOH HOH . D 4 HOH A 68 270 68 HOH HOH . D 4 HOH A 69 271 69 HOH HOH . D 4 HOH A 70 272 70 HOH HOH . D 4 HOH A 71 273 71 HOH HOH . D 4 HOH A 72 274 72 HOH HOH . D 4 HOH A 73 275 73 HOH HOH . D 4 HOH A 74 276 74 HOH HOH . D 4 HOH A 75 277 75 HOH HOH . D 4 HOH A 76 278 76 HOH HOH . D 4 HOH A 77 279 77 HOH HOH . D 4 HOH A 78 280 78 HOH HOH . D 4 HOH A 79 281 79 HOH HOH . D 4 HOH A 80 282 80 HOH HOH . D 4 HOH A 81 283 81 HOH HOH . D 4 HOH A 82 284 82 HOH HOH . D 4 HOH A 83 285 83 HOH HOH . D 4 HOH A 84 286 84 HOH HOH . D 4 HOH A 85 287 85 HOH HOH . D 4 HOH A 86 288 86 HOH HOH . D 4 HOH A 87 289 87 HOH HOH . D 4 HOH A 88 290 88 HOH HOH . D 4 HOH A 89 291 89 HOH HOH . D 4 HOH A 90 292 90 HOH HOH . D 4 HOH A 91 293 91 HOH HOH . D 4 HOH A 92 294 92 HOH HOH . D 4 HOH A 93 295 93 HOH HOH . D 4 HOH A 94 296 94 HOH HOH . D 4 HOH A 95 297 95 HOH HOH . D 4 HOH A 96 298 96 HOH HOH . D 4 HOH A 97 299 97 HOH HOH . D 4 HOH A 98 300 98 HOH HOH . D 4 HOH A 99 301 99 HOH HOH . D 4 HOH A 100 302 100 HOH HOH . D 4 HOH A 101 303 101 HOH HOH . D 4 HOH A 102 304 102 HOH HOH . D 4 HOH A 103 305 103 HOH HOH . D 4 HOH A 104 306 104 HOH HOH . D 4 HOH A 105 307 105 HOH HOH . D 4 HOH A 106 308 106 HOH HOH . D 4 HOH A 107 309 107 HOH HOH . D 4 HOH A 108 310 108 HOH HOH . D 4 HOH A 109 311 109 HOH HOH . D 4 HOH A 110 312 110 HOH HOH . D 4 HOH A 111 313 111 HOH HOH . D 4 HOH A 112 314 112 HOH HOH . D 4 HOH A 113 315 113 HOH HOH . D 4 HOH A 114 316 114 HOH HOH . D 4 HOH A 115 317 115 HOH HOH . D 4 HOH A 116 318 116 HOH HOH . D 4 HOH A 117 319 117 HOH HOH . D 4 HOH A 118 320 118 HOH HOH . D 4 HOH A 119 321 119 HOH HOH . D 4 HOH A 120 322 120 HOH HOH . D 4 HOH A 121 323 121 HOH HOH . D 4 HOH A 122 324 122 HOH HOH . D 4 HOH A 123 325 123 HOH HOH . D 4 HOH A 124 326 124 HOH HOH . D 4 HOH A 125 327 125 HOH HOH . D 4 HOH A 126 328 126 HOH HOH . D 4 HOH A 127 329 127 HOH HOH . D 4 HOH A 128 330 128 HOH HOH . D 4 HOH A 129 331 129 HOH HOH . D 4 HOH A 130 332 130 HOH HOH . D 4 HOH A 131 333 131 HOH HOH . D 4 HOH A 132 334 132 HOH HOH . D 4 HOH A 133 335 133 HOH HOH . D 4 HOH A 134 336 134 HOH HOH . D 4 HOH A 135 337 135 HOH HOH . D 4 HOH A 136 338 136 HOH HOH . D 4 HOH A 137 339 137 HOH HOH . D 4 HOH A 138 340 138 HOH HOH . D 4 HOH A 139 341 139 HOH HOH . D 4 HOH A 140 342 140 HOH HOH . D 4 HOH A 141 343 141 HOH HOH . D 4 HOH A 142 344 142 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 3 1.723 1.301 5.634 1 19.25 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 3 0.504 2.055 6.042 1 18.54 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 3 2.058 0.142 6.54 1 15.5 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 3 2.973 2.136 5.42 1 18.98 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 3 1.437 0.591 4.217 1 16.97 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 3 0.311 0.961 3.149 1 19.57 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 3 -1.071 0.552 3.516 1 19.17 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 3 0.566 2.393 2.789 1 19.8 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 3 0.769 -0.011 1.943 1 18.84 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 3 2.083 0.101 1.396 1 18.68 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 3 2.041 -0.419 -0.045 1 18.75 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 3 1.75 -1.814 -0.012 1 19.33 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 3 0.953 0.202 -0.905 1 21.3 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 3 1.468 0.306 -2.246 1 23.67 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 3 -0.144 -0.833 -0.874 1 19.66 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 3 -0.996 -0.747 -2.007 1 21.52 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 3 0.66 -2.132 -0.833 1 18.63 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 3 -0.089 -3.247 -0.235 1 19.19 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 3 -0.782 -3.241 0.926 1 18.46 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 3 -1.344 -4.446 1.163 1 17.15 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 3 -1.024 -5.249 0.118 1 18.51 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 3 -1.291 -6.64 -0.3 1 19.31 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 3 -1.982 -7.4 0.392 1 16.63 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 3 -0.739 -7.083 -1.46 1 17.88 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 3 0.003 -6.29 -2.252 1 19.66 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 3 0.503 -6.801 -3.401 1 18.23 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 3 0.279 -4.987 -1.947 1 18.11 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 3 -0.187 -4.448 -0.792 1 19.11 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #