data_3N5C # _model_server_result.job_id ohYNqGDjNefeEjkaLg6PoA _model_server_result.datetime_utc '2024-10-19 15:38:22' _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 3n5c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":200}' # _entry.id 3N5C # _exptl.entry_id 3N5C _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 3N5C _cell.length_a 38.47 _cell.length_b 49.72 _cell.length_c 143.07 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3N5C _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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,D,E,H 1 1 B,F,G,I 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 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 3N5C _atom_sites.fract_transf_matrix[1][1] 0.025994 _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] 0.020113 _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] 0.00699 _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 1 200 200 GDP GDP . D 3 CL A 1 1 1 CL CL . E 3 CL A 1 180 180 CL CL . F 2 GDP B 1 200 200 GDP GDP . G 3 CL B 1 2 2 CL CL . H 4 HOH A 1 2 2 HOH HOH . H 4 HOH A 2 3 3 HOH HOH . H 4 HOH A 3 4 4 HOH HOH . H 4 HOH A 4 5 5 HOH HOH . H 4 HOH A 5 8 8 HOH HOH . H 4 HOH A 6 10 10 HOH HOH . H 4 HOH A 7 12 12 HOH HOH . H 4 HOH A 8 176 176 HOH HOH . H 4 HOH A 9 177 177 HOH HOH . H 4 HOH A 10 178 16 HOH HOH . H 4 HOH A 11 179 18 HOH HOH . H 4 HOH A 12 181 19 HOH HOH . H 4 HOH A 13 182 20 HOH HOH . H 4 HOH A 14 183 21 HOH HOH . H 4 HOH A 15 184 22 HOH HOH . H 4 HOH A 16 185 24 HOH HOH . H 4 HOH A 17 186 25 HOH HOH . H 4 HOH A 18 187 27 HOH HOH . H 4 HOH A 19 188 28 HOH HOH . H 4 HOH A 20 189 30 HOH HOH . H 4 HOH A 21 190 31 HOH HOH . H 4 HOH A 22 191 33 HOH HOH . H 4 HOH A 23 192 35 HOH HOH . H 4 HOH A 24 193 37 HOH HOH . H 4 HOH A 25 194 194 HOH HOH . H 4 HOH A 26 195 38 HOH HOH . H 4 HOH A 27 196 44 HOH HOH . H 4 HOH A 28 197 45 HOH HOH . H 4 HOH A 29 198 48 HOH HOH . H 4 HOH A 30 199 49 HOH HOH . H 4 HOH A 31 201 50 HOH HOH . H 4 HOH A 32 202 54 HOH HOH . H 4 HOH A 33 203 203 HOH HOH . H 4 HOH A 34 204 56 HOH HOH . H 4 HOH A 35 205 57 HOH HOH . H 4 HOH A 36 206 58 HOH HOH . H 4 HOH A 37 207 207 HOH HOH . H 4 HOH A 38 208 62 HOH HOH . H 4 HOH A 39 209 66 HOH HOH . H 4 HOH A 40 210 210 HOH HOH . H 4 HOH A 41 211 68 HOH HOH . H 4 HOH A 42 212 69 HOH HOH . H 4 HOH A 43 213 70 HOH HOH . H 4 HOH A 44 214 73 HOH HOH . H 4 HOH A 45 215 75 HOH HOH . H 4 HOH A 46 216 77 HOH HOH . H 4 HOH A 47 217 78 HOH HOH . H 4 HOH A 48 218 79 HOH HOH . H 4 HOH A 49 219 83 HOH HOH . H 4 HOH A 50 220 85 HOH HOH . H 4 HOH A 51 221 86 HOH HOH . H 4 HOH A 52 222 88 HOH HOH . H 4 HOH A 53 223 89 HOH HOH . H 4 HOH A 54 224 94 HOH HOH . H 4 HOH A 55 225 97 HOH HOH . H 4 HOH A 56 226 98 HOH HOH . H 4 HOH A 57 227 111 HOH HOH . H 4 HOH A 58 228 112 HOH HOH . H 4 HOH A 59 229 113 HOH HOH . H 4 HOH A 60 230 126 HOH HOH . H 4 HOH A 61 231 129 HOH HOH . H 4 HOH A 62 232 134 HOH HOH . H 4 HOH A 63 233 137 HOH HOH . H 4 HOH A 64 234 138 HOH HOH . H 4 HOH A 65 235 140 HOH HOH . H 4 HOH A 66 236 144 HOH HOH . H 4 HOH A 67 237 145 HOH HOH . H 4 HOH A 68 238 150 HOH HOH . H 4 HOH A 69 239 151 HOH HOH . H 4 HOH A 70 240 163 HOH HOH . H 4 HOH A 71 241 167 HOH HOH . H 4 HOH A 72 242 170 HOH HOH . H 4 HOH A 73 243 173 HOH HOH . H 4 HOH A 74 244 1 HOH HOH . H 4 HOH A 75 245 100 HOH HOH . H 4 HOH A 76 301 301 HOH HOH . H 4 HOH A 77 302 302 HOH HOH . H 4 HOH A 78 303 303 HOH HOH . H 4 HOH A 79 304 304 HOH HOH . H 4 HOH A 80 308 308 HOH HOH . H 4 HOH A 81 401 401 HOH HOH . H 4 HOH A 82 402 402 HOH HOH . H 4 HOH A 83 405 405 HOH HOH . H 4 HOH A 84 500 500 HOH HOH . H 4 HOH A 85 501 501 HOH HOH . H 4 HOH A 86 502 502 HOH HOH . H 4 HOH A 87 504 504 HOH HOH . H 4 HOH A 88 505 505 HOH HOH . H 4 HOH A 89 506 506 HOH HOH . H 4 HOH A 90 507 507 HOH HOH . I 4 HOH B 1 6 6 HOH HOH . I 4 HOH B 2 7 7 HOH HOH . I 4 HOH B 3 9 9 HOH HOH . I 4 HOH B 4 11 11 HOH HOH . I 4 HOH B 5 13 13 HOH HOH . I 4 HOH B 6 176 14 HOH HOH . I 4 HOH B 7 177 15 HOH HOH . I 4 HOH B 8 178 17 HOH HOH . I 4 HOH B 9 179 23 HOH HOH . I 4 HOH B 10 180 26 HOH HOH . I 4 HOH B 11 181 29 HOH HOH . I 4 HOH B 12 182 182 HOH HOH . I 4 HOH B 13 183 32 HOH HOH . I 4 HOH B 14 184 34 HOH HOH . I 4 HOH B 15 185 36 HOH HOH . I 4 HOH B 16 186 39 HOH HOH . I 4 HOH B 17 187 40 HOH HOH . I 4 HOH B 18 188 41 HOH HOH . I 4 HOH B 19 189 42 HOH HOH . I 4 HOH B 20 190 190 HOH HOH . I 4 HOH B 21 191 191 HOH HOH . I 4 HOH B 22 192 43 HOH HOH . I 4 HOH B 23 193 51 HOH HOH . I 4 HOH B 24 194 52 HOH HOH . I 4 HOH B 25 195 53 HOH HOH . I 4 HOH B 26 196 55 HOH HOH . I 4 HOH B 27 197 59 HOH HOH . I 4 HOH B 28 198 198 HOH HOH . I 4 HOH B 29 199 60 HOH HOH . I 4 HOH B 30 201 201 HOH HOH . I 4 HOH B 31 202 202 HOH HOH . I 4 HOH B 32 203 61 HOH HOH . I 4 HOH B 33 204 204 HOH HOH . I 4 HOH B 34 205 63 HOH HOH . I 4 HOH B 35 206 206 HOH HOH . I 4 HOH B 36 207 64 HOH HOH . I 4 HOH B 37 208 71 HOH HOH . I 4 HOH B 38 209 209 HOH HOH . I 4 HOH B 39 210 72 HOH HOH . I 4 HOH B 40 211 76 HOH HOH . I 4 HOH B 41 212 80 HOH HOH . I 4 HOH B 42 213 81 HOH HOH . I 4 HOH B 43 214 82 HOH HOH . I 4 HOH B 44 215 84 HOH HOH . I 4 HOH B 45 216 87 HOH HOH . I 4 HOH B 46 217 91 HOH HOH . I 4 HOH B 47 218 92 HOH HOH . I 4 HOH B 48 219 95 HOH HOH . I 4 HOH B 49 220 96 HOH HOH . I 4 HOH B 50 221 99 HOH HOH . I 4 HOH B 51 222 104 HOH HOH . I 4 HOH B 52 223 105 HOH HOH . I 4 HOH B 53 224 107 HOH HOH . I 4 HOH B 54 225 108 HOH HOH . I 4 HOH B 55 226 109 HOH HOH . I 4 HOH B 56 227 110 HOH HOH . I 4 HOH B 57 228 114 HOH HOH . I 4 HOH B 58 229 115 HOH HOH . I 4 HOH B 59 230 116 HOH HOH . I 4 HOH B 60 231 117 HOH HOH . I 4 HOH B 61 232 118 HOH HOH . I 4 HOH B 62 233 124 HOH HOH . I 4 HOH B 63 234 128 HOH HOH . I 4 HOH B 64 235 131 HOH HOH . I 4 HOH B 65 236 132 HOH HOH . I 4 HOH B 66 237 139 HOH HOH . I 4 HOH B 67 238 141 HOH HOH . I 4 HOH B 68 239 143 HOH HOH . I 4 HOH B 69 240 146 HOH HOH . I 4 HOH B 70 241 152 HOH HOH . I 4 HOH B 71 242 153 HOH HOH . I 4 HOH B 72 243 166 HOH HOH . I 4 HOH B 73 244 168 HOH HOH . I 4 HOH B 74 245 169 HOH HOH . I 4 HOH B 75 246 172 HOH HOH . I 4 HOH B 76 247 175 HOH HOH . I 4 HOH B 77 306 306 HOH HOH . I 4 HOH B 78 400 400 HOH HOH . I 4 HOH B 79 403 403 HOH HOH . I 4 HOH B 80 404 404 HOH HOH . I 4 HOH B 81 408 408 HOH HOH . I 4 HOH B 82 503 503 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 . . . F 2 15.094 17.163 7.116 1 22.92 ? PB GDP 200 B 1 HETATM 2 O O1B GDP . . . F 2 15.323 15.731 6.73 1 24.7 ? O1B GDP 200 B 1 HETATM 3 O O2B GDP . . . F 2 13.552 17.601 6.999 1 24.23 ? O2B GDP 200 B 1 HETATM 4 O O3B GDP . . . F 2 15.612 17.419 8.573 1 24.6 ? O3B GDP 200 B 1 HETATM 5 O O3A GDP . . . F 2 15.877 18.054 6.057 1 26.61 ? O3A GDP 200 B 1 HETATM 6 P PA GDP . . . F 2 17.308 18.853 6.232 1 26.28 ? PA GDP 200 B 1 HETATM 7 O O1A GDP . . . F 2 17.283 20.046 7.126 1 27.52 ? O1A GDP 200 B 1 HETATM 8 O O2A GDP . . . F 2 18.416 17.867 6.626 1 28.4 ? O2A GDP 200 B 1 HETATM 9 O O5' GDP . . . F 2 17.453 19.512 4.773 1 27.1 ? O5' GDP 200 B 1 HETATM 10 C C5' GDP . . . F 2 17.61 18.54 3.727 1 27.03 ? C5' GDP 200 B 1 HETATM 11 C C4' GDP . . . F 2 18.59 19.107 2.706 1 28.07 ? C4' GDP 200 B 1 HETATM 12 O O4' GDP . . . F 2 18.01 20.308 2.117 1 27.72 ? O4' GDP 200 B 1 HETATM 13 C C3' GDP . . . F 2 19.955 19.576 3.341 1 29.13 ? C3' GDP 200 B 1 HETATM 14 O O3' GDP . . . F 2 20.994 19.439 2.36 1 33.46 ? O3' GDP 200 B 1 HETATM 15 C C2' GDP . . . F 2 19.73 21.102 3.504 1 29.49 ? C2' GDP 200 B 1 HETATM 16 O O2' GDP . . . F 2 20.927 21.894 3.424 1 31.72 ? O2' GDP 200 B 1 HETATM 17 C C1' GDP . . . F 2 18.869 21.442 2.278 1 27.67 ? C1' GDP 200 B 1 HETATM 18 N N9 GDP . . . F 2 18.001 22.588 2.552 1 26.66 ? N9 GDP 200 B 1 HETATM 19 C C8 GDP . . . F 2 17.17 22.804 3.637 1 26.45 ? C8 GDP 200 B 1 HETATM 20 N N7 GDP . . . F 2 16.497 23.919 3.494 1 26.58 ? N7 GDP 200 B 1 HETATM 21 C C5 GDP . . . F 2 16.832 24.455 2.299 1 25.5 ? C5 GDP 200 B 1 HETATM 22 C C6 GDP . . . F 2 16.424 25.628 1.56 1 26.63 ? C6 GDP 200 B 1 HETATM 23 O O6 GDP . . . F 2 15.612 26.449 1.979 1 26.69 ? O6 GDP 200 B 1 HETATM 24 N N1 GDP . . . F 2 16.981 25.817 0.36 1 26.34 ? N1 GDP 200 B 1 HETATM 25 C C2 GDP . . . F 2 17.934 24.947 -0.197 1 26.58 ? C2 GDP 200 B 1 HETATM 26 N N2 GDP . . . F 2 18.459 25.258 -1.437 1 28.71 ? N2 GDP 200 B 1 HETATM 27 N N3 GDP . . . F 2 18.304 23.841 0.422 1 26.8 ? N3 GDP 200 B 1 HETATM 28 C C4 GDP . . . F 2 17.799 23.588 1.683 1 26.23 ? C4 GDP 200 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #