data_6T5U # _model_server_result.job_id Sv4vF5a0B278d3QFKPE73A _model_server_result.datetime_utc '2024-11-12 22:37:38' _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 6t5u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 6T5U # _exptl.entry_id 6T5U _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 78.47 _cell.angle_beta 85.59 _cell.angle_gamma 68.14 _cell.entry_id 6T5U _cell.length_a 33.597 _cell.length_b 41.084 _cell.length_c 65.192 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6T5U _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,D,E,I 1 1 B,F,G,H,J 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 ? 3 D N N ? 3 G 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 covale ? covale1 A SG CYS 13 A CYS 12 1_555 E C MKW . A MKW 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.695 ? covale ? covale2 B SG CYS 13 B CYS 12 1_555 H C MKW . B MKW 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.656 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc2 C MG MG . A MG 201 1_555 D O3B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc3 C MG MG . A MG 201 1_555 I O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc4 C MG MG . A MG 201 1_555 I O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc5 C MG MG . A MG 201 1_555 I O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc6 C MG MG . A MG 201 1_555 I O HOH . A HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc7 B OG SER 18 B SER 17 1_555 F MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc8 F MG MG . B MG 201 1_555 G O1B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc9 F MG MG . B MG 201 1_555 J O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc10 F MG MG . B MG 201 1_555 J O HOH . B HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc11 F MG MG . B MG 201 1_555 J O HOH . B HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc12 F MG MG . B MG 201 1_555 J O HOH . B HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? # _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 6T5U _atom_sites.fract_transf_matrix[1][1] 0.029765 _atom_sites.fract_transf_matrix[1][2] -0.011941 _atom_sites.fract_transf_matrix[1][3] -0.000087 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026226 _atom_sites.fract_transf_matrix[2][3] -0.004939 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015655 _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 1 201 201 MG MG . D 3 GDP A 1 202 206 GDP GDP . E 4 MKW A 1 203 1 MKW INH . F 2 MG B 1 201 201 MG MG . G 3 GDP B 1 202 206 GDP GDP . H 4 MKW B 1 203 2 MKW INH . I 5 HOH A 1 301 192 HOH HOH . I 5 HOH A 2 302 65 HOH HOH . I 5 HOH A 3 303 42 HOH HOH . I 5 HOH A 4 304 190 HOH HOH . I 5 HOH A 5 305 16 HOH HOH . I 5 HOH A 6 306 187 HOH HOH . I 5 HOH A 7 307 189 HOH HOH . I 5 HOH A 8 308 180 HOH HOH . I 5 HOH A 9 309 86 HOH HOH . I 5 HOH A 10 310 40 HOH HOH . I 5 HOH A 11 311 109 HOH HOH . I 5 HOH A 12 312 33 HOH HOH . I 5 HOH A 13 313 52 HOH HOH . I 5 HOH A 14 314 9 HOH HOH . I 5 HOH A 15 315 128 HOH HOH . I 5 HOH A 16 316 146 HOH HOH . I 5 HOH A 17 317 44 HOH HOH . I 5 HOH A 18 318 101 HOH HOH . I 5 HOH A 19 319 55 HOH HOH . I 5 HOH A 20 320 48 HOH HOH . I 5 HOH A 21 321 93 HOH HOH . I 5 HOH A 22 322 41 HOH HOH . I 5 HOH A 23 323 51 HOH HOH . I 5 HOH A 24 324 26 HOH HOH . I 5 HOH A 25 325 8 HOH HOH . I 5 HOH A 26 326 182 HOH HOH . I 5 HOH A 27 327 14 HOH HOH . I 5 HOH A 28 328 22 HOH HOH . I 5 HOH A 29 329 148 HOH HOH . I 5 HOH A 30 330 117 HOH HOH . I 5 HOH A 31 331 80 HOH HOH . I 5 HOH A 32 332 20 HOH HOH . I 5 HOH A 33 333 186 HOH HOH . I 5 HOH A 34 334 35 HOH HOH . I 5 HOH A 35 335 104 HOH HOH . I 5 HOH A 36 336 78 HOH HOH . I 5 HOH A 37 337 116 HOH HOH . I 5 HOH A 38 338 121 HOH HOH . I 5 HOH A 39 339 164 HOH HOH . I 5 HOH A 40 340 82 HOH HOH . I 5 HOH A 41 341 156 HOH HOH . I 5 HOH A 42 342 45 HOH HOH . I 5 HOH A 43 343 2 HOH HOH . I 5 HOH A 44 344 96 HOH HOH . I 5 HOH A 45 345 174 HOH HOH . I 5 HOH A 46 346 17 HOH HOH . I 5 HOH A 47 347 91 HOH HOH . I 5 HOH A 48 348 151 HOH HOH . I 5 HOH A 49 349 130 HOH HOH . I 5 HOH A 50 350 47 HOH HOH . I 5 HOH A 51 351 25 HOH HOH . I 5 HOH A 52 352 38 HOH HOH . I 5 HOH A 53 353 79 HOH HOH . I 5 HOH A 54 354 3 HOH HOH . I 5 HOH A 55 355 29 HOH HOH . I 5 HOH A 56 356 66 HOH HOH . I 5 HOH A 57 357 64 HOH HOH . I 5 HOH A 58 358 11 HOH HOH . I 5 HOH A 59 359 181 HOH HOH . I 5 HOH A 60 360 145 HOH HOH . I 5 HOH A 61 361 32 HOH HOH . I 5 HOH A 62 362 98 HOH HOH . I 5 HOH A 63 363 126 HOH HOH . I 5 HOH A 64 364 165 HOH HOH . I 5 HOH A 65 365 102 HOH HOH . I 5 HOH A 66 366 110 HOH HOH . I 5 HOH A 67 367 60 HOH HOH . I 5 HOH A 68 368 169 HOH HOH . I 5 HOH A 69 369 58 HOH HOH . I 5 HOH A 70 370 124 HOH HOH . I 5 HOH A 71 371 23 HOH HOH . I 5 HOH A 72 372 122 HOH HOH . I 5 HOH A 73 373 132 HOH HOH . I 5 HOH A 74 374 188 HOH HOH . I 5 HOH A 75 375 191 HOH HOH . I 5 HOH A 76 376 111 HOH HOH . I 5 HOH A 77 377 39 HOH HOH . I 5 HOH A 78 378 138 HOH HOH . I 5 HOH A 79 379 107 HOH HOH . I 5 HOH A 80 380 61 HOH HOH . I 5 HOH A 81 381 92 HOH HOH . I 5 HOH A 82 382 49 HOH HOH . I 5 HOH A 83 383 183 HOH HOH . I 5 HOH A 84 384 167 HOH HOH . I 5 HOH A 85 385 140 HOH HOH . I 5 HOH A 86 386 5 HOH HOH . I 5 HOH A 87 387 184 HOH HOH . I 5 HOH A 88 388 123 HOH HOH . I 5 HOH A 89 389 46 HOH HOH . I 5 HOH A 90 390 131 HOH HOH . I 5 HOH A 91 391 100 HOH HOH . I 5 HOH A 92 392 137 HOH HOH . I 5 HOH A 93 393 28 HOH HOH . I 5 HOH A 94 394 36 HOH HOH . I 5 HOH A 95 395 172 HOH HOH . I 5 HOH A 96 396 171 HOH HOH . I 5 HOH A 97 397 90 HOH HOH . I 5 HOH A 98 398 157 HOH HOH . I 5 HOH A 99 399 37 HOH HOH . I 5 HOH A 100 400 162 HOH HOH . I 5 HOH A 101 401 108 HOH HOH . I 5 HOH A 102 402 176 HOH HOH . I 5 HOH A 103 403 143 HOH HOH . I 5 HOH A 104 404 134 HOH HOH . I 5 HOH A 105 405 141 HOH HOH . I 5 HOH A 106 406 53 HOH HOH . J 5 HOH B 1 301 84 HOH HOH . J 5 HOH B 2 302 97 HOH HOH . J 5 HOH B 3 303 4 HOH HOH . J 5 HOH B 4 304 150 HOH HOH . J 5 HOH B 5 305 71 HOH HOH . J 5 HOH B 6 306 56 HOH HOH . J 5 HOH B 7 307 59 HOH HOH . J 5 HOH B 8 308 75 HOH HOH . J 5 HOH B 9 309 112 HOH HOH . J 5 HOH B 10 310 120 HOH HOH . J 5 HOH B 11 311 106 HOH HOH . J 5 HOH B 12 312 163 HOH HOH . J 5 HOH B 13 313 68 HOH HOH . J 5 HOH B 14 314 177 HOH HOH . J 5 HOH B 15 315 67 HOH HOH . J 5 HOH B 16 316 77 HOH HOH . J 5 HOH B 17 317 155 HOH HOH . J 5 HOH B 18 318 70 HOH HOH . J 5 HOH B 19 319 178 HOH HOH . J 5 HOH B 20 320 105 HOH HOH . J 5 HOH B 21 321 179 HOH HOH . J 5 HOH B 22 322 54 HOH HOH . J 5 HOH B 23 323 12 HOH HOH . J 5 HOH B 24 324 144 HOH HOH . J 5 HOH B 25 325 72 HOH HOH . J 5 HOH B 26 326 7 HOH HOH . J 5 HOH B 27 327 10 HOH HOH . J 5 HOH B 28 328 76 HOH HOH . J 5 HOH B 29 329 160 HOH HOH . J 5 HOH B 30 330 175 HOH HOH . J 5 HOH B 31 331 73 HOH HOH . J 5 HOH B 32 332 31 HOH HOH . J 5 HOH B 33 333 153 HOH HOH . J 5 HOH B 34 334 57 HOH HOH . J 5 HOH B 35 335 81 HOH HOH . J 5 HOH B 36 336 43 HOH HOH . J 5 HOH B 37 337 15 HOH HOH . J 5 HOH B 38 338 85 HOH HOH . J 5 HOH B 39 339 152 HOH HOH . J 5 HOH B 40 340 159 HOH HOH . J 5 HOH B 41 341 127 HOH HOH . J 5 HOH B 42 342 30 HOH HOH . J 5 HOH B 43 343 21 HOH HOH . J 5 HOH B 44 344 161 HOH HOH . J 5 HOH B 45 345 69 HOH HOH . J 5 HOH B 46 346 18 HOH HOH . J 5 HOH B 47 347 62 HOH HOH . J 5 HOH B 48 348 125 HOH HOH . J 5 HOH B 49 349 50 HOH HOH . J 5 HOH B 50 350 158 HOH HOH . J 5 HOH B 51 351 113 HOH HOH . J 5 HOH B 52 352 1 HOH HOH . J 5 HOH B 53 353 119 HOH HOH . J 5 HOH B 54 354 115 HOH HOH . J 5 HOH B 55 355 13 HOH HOH . J 5 HOH B 56 356 27 HOH HOH . J 5 HOH B 57 357 173 HOH HOH . J 5 HOH B 58 358 133 HOH HOH . J 5 HOH B 59 359 166 HOH HOH . J 5 HOH B 60 360 170 HOH HOH . J 5 HOH B 61 361 168 HOH HOH . J 5 HOH B 62 362 114 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 . . . D 3 10.019 5.516 0.72 1 19.75 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . D 3 8.755 5.413 -0.17 1 22.15 ? O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . D 3 11.286 5.648 -0.131 1 18.4 ? O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . D 3 9.772 6.435 1.876 1 19.21 ? O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . D 3 10.148 3.917 1.237 1 20.84 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . D 3 9.95 3.46 2.739 1 19.65 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . D 3 8.462 3.635 2.995 1 24.71 ? O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . D 3 10.83 3.819 3.83 1 23.86 ? O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . D 3 10.243 1.855 2.587 1 21.32 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . D 3 9.554 1.192 1.571 1 24.34 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . D 3 9.497 -0.287 2.046 1 25.67 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . D 3 10.808 -0.916 2.013 1 26.23 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . D 3 9.027 -0.518 3.447 1 26.79 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . D 3 8.306 -1.814 3.497 1 28.3 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . D 3 10.3 -0.661 4.24 1 26.31 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . D 3 10.349 -1.514 5.378 1 29.88 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . D 3 11.246 -1.296 3.263 1 24.84 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . D 3 12.67 -0.921 3.501 1 24.62 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . D 3 13.18 0.354 3.598 1 25.05 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . D 3 14.505 0.369 3.772 1 21.05 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . D 3 14.88 -0.987 3.86 1 20.69 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . D 3 16.14 -1.683 3.984 1 24.01 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . D 3 17.212 -1.106 4.166 1 18.63 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . D 3 16.188 -3.058 3.944 1 21.43 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . D 3 15.021 -3.714 3.773 1 24.72 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . D 3 15.082 -5.071 3.717 1 27.34 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . D 3 13.786 -3.154 3.614 1 22.88 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . D 3 13.668 -1.776 3.616 1 24.09 ? C4 GDP 202 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #