data_6IY1 # _model_server_result.job_id G7qyZ4aHPlwQXBx7Ov4_Lg _model_server_result.datetime_utc '2024-11-06 00:09:09' _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 6iy1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":201}' # _entry.id 6IY1 # _exptl.entry_id 6IY1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 98.46 _cell.angle_gamma 90 _cell.entry_id 6IY1 _cell.length_a 52.606 _cell.length_b 150.762 _cell.length_c 60.125 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IY1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 PISA monomeric 1 author_and_software_defined_assembly 5 PISA monomeric 1 author_and_software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,M 1 1 B,H,N 2 1 C,I,O 3 1 D,J,P 4 1 E,K,Q 5 1 F,L,R 6 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 ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L 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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 6IY1 _atom_sites.fract_transf_matrix[1][1] 0.019009 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002826 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006633 _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] 0.016815 _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 G 4 GDP A 1 201 201 GDP GDP . H 4 GDP B 1 201 201 GDP GDP . I 4 GDP C 1 201 201 GDP GDP . J 4 GDP D 1 201 201 GDP GDP . K 4 GDP E 1 201 201 GDP GDP . L 4 GDP F 1 201 201 GDP GDP . M 5 HOH A 1 301 103 HOH HOH . M 5 HOH A 2 302 201 HOH HOH . M 5 HOH A 3 303 104 HOH HOH . M 5 HOH A 4 304 175 HOH HOH . M 5 HOH A 5 305 21 HOH HOH . M 5 HOH A 6 306 58 HOH HOH . M 5 HOH A 7 307 36 HOH HOH . M 5 HOH A 8 308 43 HOH HOH . M 5 HOH A 9 309 152 HOH HOH . M 5 HOH A 10 310 166 HOH HOH . M 5 HOH A 11 311 23 HOH HOH . M 5 HOH A 12 312 29 HOH HOH . M 5 HOH A 13 313 31 HOH HOH . M 5 HOH A 14 314 60 HOH HOH . M 5 HOH A 15 315 70 HOH HOH . M 5 HOH A 16 316 96 HOH HOH . M 5 HOH A 17 317 55 HOH HOH . M 5 HOH A 18 318 50 HOH HOH . M 5 HOH A 19 319 138 HOH HOH . M 5 HOH A 20 320 37 HOH HOH . M 5 HOH A 21 321 76 HOH HOH . M 5 HOH A 22 322 182 HOH HOH . M 5 HOH A 23 323 168 HOH HOH . M 5 HOH A 24 324 116 HOH HOH . M 5 HOH A 25 325 137 HOH HOH . M 5 HOH A 26 326 206 HOH HOH . M 5 HOH A 27 327 207 HOH HOH . M 5 HOH A 28 328 170 HOH HOH . M 5 HOH A 29 329 176 HOH HOH . M 5 HOH A 30 330 211 HOH HOH . M 5 HOH A 31 331 75 HOH HOH . M 5 HOH A 32 332 183 HOH HOH . M 5 HOH A 33 333 205 HOH HOH . M 5 HOH A 34 334 52 HOH HOH . M 5 HOH A 35 335 197 HOH HOH . M 5 HOH A 36 336 14 HOH HOH . N 5 HOH B 1 301 214 HOH HOH . N 5 HOH B 2 302 10 HOH HOH . N 5 HOH B 3 303 67 HOH HOH . N 5 HOH B 4 304 173 HOH HOH . N 5 HOH B 5 305 195 HOH HOH . N 5 HOH B 6 306 1 HOH HOH . N 5 HOH B 7 307 174 HOH HOH . N 5 HOH B 8 308 101 HOH HOH . N 5 HOH B 9 309 99 HOH HOH . N 5 HOH B 10 310 22 HOH HOH . N 5 HOH B 11 311 77 HOH HOH . N 5 HOH B 12 312 40 HOH HOH . N 5 HOH B 13 313 198 HOH HOH . N 5 HOH B 14 314 140 HOH HOH . N 5 HOH B 15 315 102 HOH HOH . N 5 HOH B 16 316 123 HOH HOH . N 5 HOH B 17 317 28 HOH HOH . N 5 HOH B 18 318 90 HOH HOH . N 5 HOH B 19 319 95 HOH HOH . N 5 HOH B 20 320 162 HOH HOH . N 5 HOH B 21 321 39 HOH HOH . N 5 HOH B 22 322 15 HOH HOH . N 5 HOH B 23 323 86 HOH HOH . N 5 HOH B 24 324 63 HOH HOH . N 5 HOH B 25 325 208 HOH HOH . N 5 HOH B 26 326 204 HOH HOH . N 5 HOH B 27 327 41 HOH HOH . N 5 HOH B 28 328 18 HOH HOH . N 5 HOH B 29 329 110 HOH HOH . N 5 HOH B 30 330 150 HOH HOH . N 5 HOH B 31 331 192 HOH HOH . N 5 HOH B 32 332 147 HOH HOH . N 5 HOH B 33 333 135 HOH HOH . N 5 HOH B 34 334 122 HOH HOH . N 5 HOH B 35 335 106 HOH HOH . N 5 HOH B 36 336 130 HOH HOH . N 5 HOH B 37 337 81 HOH HOH . N 5 HOH B 38 338 163 HOH HOH . N 5 HOH B 39 339 164 HOH HOH . O 5 HOH C 1 301 66 HOH HOH . O 5 HOH C 2 302 74 HOH HOH . O 5 HOH C 3 303 161 HOH HOH . O 5 HOH C 4 304 91 HOH HOH . O 5 HOH C 5 305 69 HOH HOH . O 5 HOH C 6 306 200 HOH HOH . O 5 HOH C 7 307 154 HOH HOH . O 5 HOH C 8 308 185 HOH HOH . O 5 HOH C 9 309 25 HOH HOH . O 5 HOH C 10 310 129 HOH HOH . O 5 HOH C 11 311 24 HOH HOH . O 5 HOH C 12 312 85 HOH HOH . O 5 HOH C 13 313 145 HOH HOH . O 5 HOH C 14 314 186 HOH HOH . O 5 HOH C 15 315 209 HOH HOH . O 5 HOH C 16 316 94 HOH HOH . O 5 HOH C 17 317 169 HOH HOH . O 5 HOH C 18 318 143 HOH HOH . O 5 HOH C 19 319 12 HOH HOH . O 5 HOH C 20 320 11 HOH HOH . O 5 HOH C 21 321 189 HOH HOH . O 5 HOH C 22 322 165 HOH HOH . O 5 HOH C 23 323 117 HOH HOH . O 5 HOH C 24 324 112 HOH HOH . O 5 HOH C 25 325 167 HOH HOH . O 5 HOH C 26 326 20 HOH HOH . O 5 HOH C 27 327 72 HOH HOH . O 5 HOH C 28 328 56 HOH HOH . O 5 HOH C 29 329 9 HOH HOH . O 5 HOH C 30 330 48 HOH HOH . O 5 HOH C 31 331 126 HOH HOH . O 5 HOH C 32 332 188 HOH HOH . O 5 HOH C 33 333 187 HOH HOH . O 5 HOH C 34 334 42 HOH HOH . O 5 HOH C 35 335 121 HOH HOH . O 5 HOH C 36 336 212 HOH HOH . O 5 HOH C 37 337 57 HOH HOH . O 5 HOH C 38 338 105 HOH HOH . O 5 HOH C 39 339 80 HOH HOH . O 5 HOH C 40 340 79 HOH HOH . O 5 HOH C 41 341 38 HOH HOH . O 5 HOH C 42 342 132 HOH HOH . O 5 HOH C 43 343 213 HOH HOH . P 5 HOH D 1 301 196 HOH HOH . P 5 HOH D 2 302 155 HOH HOH . P 5 HOH D 3 303 46 HOH HOH . P 5 HOH D 4 304 32 HOH HOH . P 5 HOH D 5 305 171 HOH HOH . P 5 HOH D 6 306 7 HOH HOH . P 5 HOH D 7 307 44 HOH HOH . P 5 HOH D 8 308 73 HOH HOH . P 5 HOH D 9 309 5 HOH HOH . P 5 HOH D 10 310 114 HOH HOH . P 5 HOH D 11 311 191 HOH HOH . P 5 HOH D 12 312 139 HOH HOH . P 5 HOH D 13 313 203 HOH HOH . P 5 HOH D 14 314 8 HOH HOH . P 5 HOH D 15 315 30 HOH HOH . P 5 HOH D 16 316 119 HOH HOH . P 5 HOH D 17 317 190 HOH HOH . P 5 HOH D 18 318 179 HOH HOH . P 5 HOH D 19 319 109 HOH HOH . P 5 HOH D 20 320 142 HOH HOH . P 5 HOH D 21 321 148 HOH HOH . P 5 HOH D 22 322 134 HOH HOH . P 5 HOH D 23 323 127 HOH HOH . P 5 HOH D 24 324 13 HOH HOH . P 5 HOH D 25 325 68 HOH HOH . P 5 HOH D 26 326 118 HOH HOH . P 5 HOH D 27 327 131 HOH HOH . P 5 HOH D 28 328 97 HOH HOH . P 5 HOH D 29 329 53 HOH HOH . P 5 HOH D 30 330 180 HOH HOH . Q 5 HOH E 1 301 172 HOH HOH . Q 5 HOH E 2 302 181 HOH HOH . Q 5 HOH E 3 303 158 HOH HOH . Q 5 HOH E 4 304 128 HOH HOH . Q 5 HOH E 5 305 159 HOH HOH . Q 5 HOH E 6 306 107 HOH HOH . Q 5 HOH E 7 307 193 HOH HOH . Q 5 HOH E 8 308 34 HOH HOH . Q 5 HOH E 9 309 65 HOH HOH . Q 5 HOH E 10 310 144 HOH HOH . Q 5 HOH E 11 311 64 HOH HOH . Q 5 HOH E 12 312 47 HOH HOH . Q 5 HOH E 13 313 89 HOH HOH . Q 5 HOH E 14 314 100 HOH HOH . Q 5 HOH E 15 315 141 HOH HOH . Q 5 HOH E 16 316 83 HOH HOH . Q 5 HOH E 17 317 71 HOH HOH . Q 5 HOH E 18 318 35 HOH HOH . Q 5 HOH E 19 319 93 HOH HOH . Q 5 HOH E 20 320 160 HOH HOH . Q 5 HOH E 21 321 17 HOH HOH . Q 5 HOH E 22 322 6 HOH HOH . Q 5 HOH E 23 323 27 HOH HOH . Q 5 HOH E 24 324 51 HOH HOH . Q 5 HOH E 25 325 33 HOH HOH . R 5 HOH F 1 301 87 HOH HOH . R 5 HOH F 2 302 4 HOH HOH . R 5 HOH F 3 303 120 HOH HOH . R 5 HOH F 4 304 92 HOH HOH . R 5 HOH F 5 305 78 HOH HOH . R 5 HOH F 6 306 16 HOH HOH . R 5 HOH F 7 307 62 HOH HOH . R 5 HOH F 8 308 115 HOH HOH . R 5 HOH F 9 309 108 HOH HOH . R 5 HOH F 10 310 125 HOH HOH . R 5 HOH F 11 311 45 HOH HOH . R 5 HOH F 12 312 177 HOH HOH . R 5 HOH F 13 313 199 HOH HOH . R 5 HOH F 14 314 54 HOH HOH . R 5 HOH F 15 315 156 HOH HOH . R 5 HOH F 16 316 19 HOH HOH . R 5 HOH F 17 317 61 HOH HOH . R 5 HOH F 18 318 84 HOH HOH . R 5 HOH F 19 319 149 HOH HOH . R 5 HOH F 20 320 210 HOH HOH . R 5 HOH F 21 321 124 HOH HOH . R 5 HOH F 22 322 136 HOH HOH . R 5 HOH F 23 323 146 HOH HOH . R 5 HOH F 24 324 184 HOH HOH . R 5 HOH F 25 325 26 HOH HOH . R 5 HOH F 26 326 2 HOH HOH . R 5 HOH F 27 327 59 HOH HOH . R 5 HOH F 28 328 153 HOH HOH . R 5 HOH F 29 329 178 HOH HOH . R 5 HOH F 30 330 49 HOH HOH . R 5 HOH F 31 331 111 HOH HOH . R 5 HOH F 32 332 113 HOH HOH . R 5 HOH F 33 333 98 HOH HOH . R 5 HOH F 34 334 82 HOH HOH . R 5 HOH F 35 335 202 HOH HOH . R 5 HOH F 36 336 88 HOH HOH . R 5 HOH F 37 337 194 HOH HOH . R 5 HOH F 38 338 157 HOH HOH . R 5 HOH F 39 339 3 HOH HOH . R 5 HOH F 40 340 151 HOH HOH . R 5 HOH F 41 341 133 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 . . . J 4 -31.366 32.453 18.425 1 22.41 ? PB GDP 201 D 1 HETATM 2 O O1B GDP . . . J 4 -31.532 32.715 16.963 1 20.79 ? O1B GDP 201 D 1 HETATM 3 O O2B GDP . . . J 4 -32.045 33.468 19.288 1 22.81 ? O2B GDP 201 D 1 HETATM 4 O O3B GDP . . . J 4 -29.981 32.099 18.86 1 20.53 ? O3B GDP 201 D 1 HETATM 5 O O3A GDP . . . J 4 -32.239 31.132 18.68 1 22.01 ? O3A GDP 201 D 1 HETATM 6 P PA GDP . . . J 4 -31.827 29.913 19.64 1 24.17 ? PA GDP 201 D 1 HETATM 7 O O1A GDP . . . J 4 -30.717 29.133 19.011 1 23.25 ? O1A GDP 201 D 1 HETATM 8 O O2A GDP . . . J 4 -31.686 30.428 21.034 1 24.43 ? O2A GDP 201 D 1 HETATM 9 O O5' GDP . . . J 4 -33.141 29.004 19.563 1 24.01 ? O5' GDP 201 D 1 HETATM 10 C C5' GDP . . . J 4 -34.378 29.444 20.11 1 22.33 ? C5' GDP 201 D 1 HETATM 11 C C4' GDP . . . J 4 -35.265 28.243 20.382 1 21.23 ? C4' GDP 201 D 1 HETATM 12 O O4' GDP . . . J 4 -35.492 27.507 19.185 1 19.3 ? O4' GDP 201 D 1 HETATM 13 C C3' GDP . . . J 4 -34.575 27.321 21.368 1 20.95 ? C3' GDP 201 D 1 HETATM 14 O O3' GDP . . . J 4 -35.56 26.862 22.285 1 21.01 ? O3' GDP 201 D 1 HETATM 15 C C2' GDP . . . J 4 -34.065 26.174 20.53 1 20.19 ? C2' GDP 201 D 1 HETATM 16 O O2' GDP . . . J 4 -34.099 24.935 21.233 1 21.8 ? O2' GDP 201 D 1 HETATM 17 C C1' GDP . . . J 4 -35.027 26.174 19.361 1 19.42 ? C1' GDP 201 D 1 HETATM 18 N N9 GDP . . . J 4 -34.396 25.664 18.128 1 19.74 ? N9 GDP 201 D 1 HETATM 19 C C8 GDP . . . J 4 -33.197 25.974 17.623 1 18.23 ? C8 GDP 201 D 1 HETATM 20 N N7 GDP . . . J 4 -32.972 25.298 16.475 1 17.47 ? N7 GDP 201 D 1 HETATM 21 C C5 GDP . . . J 4 -34.045 24.534 16.238 1 17.61 ? C5 GDP 201 D 1 HETATM 22 C C6 GDP . . . J 4 -34.474 23.572 15.202 1 17.37 ? C6 GDP 201 D 1 HETATM 23 O O6 GDP . . . J 4 -33.741 23.305 14.237 1 16.46 ? O6 GDP 201 D 1 HETATM 24 N N1 GDP . . . J 4 -35.674 23 15.35 1 18.01 ? N1 GDP 201 D 1 HETATM 25 C C2 GDP . . . J 4 -36.489 23.268 16.385 1 17.86 ? C2 GDP 201 D 1 HETATM 26 N N2 GDP . . . J 4 -37.688 22.653 16.462 1 18.19 ? N2 GDP 201 D 1 HETATM 27 N N3 GDP . . . J 4 -36.161 24.136 17.366 1 17.76 ? N3 GDP 201 D 1 HETATM 28 C C4 GDP . . . J 4 -34.978 24.779 17.338 1 18.63 ? C4 GDP 201 D 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 38 _model_server_stats.element_count 28 #