data_3TK1 # _model_server_result.job_id 3j5BzcDdGm5h0bZ-uT3ONg _model_server_result.datetime_utc '2024-11-28 03:19:07' _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 3tk1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":327}' # _entry.id 3TK1 # _exptl.entry_id 3TK1 _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 3TK1 _cell.length_a 42.38 _cell.length_b 106.43 _cell.length_c 134.04 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TK1 _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 PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 # 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 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 3TK1 _atom_sites.fract_transf_matrix[1][1] 0.023596 _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] 0.009396 _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] 0.00746 _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 1 327 1 GDP GDP . D 2 GDP B 1 327 2 GDP GDP . E 3 CL B 1 328 1 CL CL . F 4 HOH A 1 328 2 HOH HOH . F 4 HOH A 2 329 6 HOH HOH . F 4 HOH A 3 330 11 HOH HOH . F 4 HOH A 4 331 24 HOH HOH . F 4 HOH A 5 332 25 HOH HOH . F 4 HOH A 6 333 27 HOH HOH . F 4 HOH A 7 334 28 HOH HOH . F 4 HOH A 8 335 29 HOH HOH . F 4 HOH A 9 336 30 HOH HOH . F 4 HOH A 10 337 43 HOH HOH . F 4 HOH A 11 338 44 HOH HOH . F 4 HOH A 12 339 52 HOH HOH . F 4 HOH A 13 340 53 HOH HOH . F 4 HOH A 14 341 61 HOH HOH . F 4 HOH A 15 342 74 HOH HOH . F 4 HOH A 16 343 75 HOH HOH . F 4 HOH A 17 344 76 HOH HOH . F 4 HOH A 18 345 77 HOH HOH . F 4 HOH A 19 346 78 HOH HOH . F 4 HOH A 20 347 79 HOH HOH . F 4 HOH A 21 348 80 HOH HOH . F 4 HOH A 22 349 81 HOH HOH . F 4 HOH A 23 350 82 HOH HOH . F 4 HOH A 24 351 83 HOH HOH . F 4 HOH A 25 352 98 HOH HOH . F 4 HOH A 26 353 99 HOH HOH . F 4 HOH A 27 354 100 HOH HOH . G 4 HOH B 1 329 1 HOH HOH . G 4 HOH B 2 330 3 HOH HOH . G 4 HOH B 3 331 4 HOH HOH . G 4 HOH B 4 332 5 HOH HOH . G 4 HOH B 5 333 7 HOH HOH . G 4 HOH B 6 334 8 HOH HOH . G 4 HOH B 7 335 9 HOH HOH . G 4 HOH B 8 336 10 HOH HOH . G 4 HOH B 9 337 12 HOH HOH . G 4 HOH B 10 338 13 HOH HOH . G 4 HOH B 11 339 14 HOH HOH . G 4 HOH B 12 340 15 HOH HOH . G 4 HOH B 13 341 16 HOH HOH . G 4 HOH B 14 342 17 HOH HOH . G 4 HOH B 15 343 18 HOH HOH . G 4 HOH B 16 344 19 HOH HOH . G 4 HOH B 17 345 20 HOH HOH . G 4 HOH B 18 346 21 HOH HOH . G 4 HOH B 19 347 22 HOH HOH . G 4 HOH B 20 348 23 HOH HOH . G 4 HOH B 21 349 26 HOH HOH . G 4 HOH B 22 350 31 HOH HOH . G 4 HOH B 23 351 32 HOH HOH . G 4 HOH B 24 352 33 HOH HOH . G 4 HOH B 25 353 34 HOH HOH . G 4 HOH B 26 354 35 HOH HOH . G 4 HOH B 27 355 36 HOH HOH . G 4 HOH B 28 356 37 HOH HOH . G 4 HOH B 29 357 38 HOH HOH . G 4 HOH B 30 358 39 HOH HOH . G 4 HOH B 31 359 40 HOH HOH . G 4 HOH B 32 360 41 HOH HOH . G 4 HOH B 33 361 42 HOH HOH . G 4 HOH B 34 362 45 HOH HOH . G 4 HOH B 35 363 46 HOH HOH . G 4 HOH B 36 364 47 HOH HOH . G 4 HOH B 37 365 48 HOH HOH . G 4 HOH B 38 366 49 HOH HOH . G 4 HOH B 39 367 50 HOH HOH . G 4 HOH B 40 368 51 HOH HOH . G 4 HOH B 41 369 54 HOH HOH . G 4 HOH B 42 370 55 HOH HOH . G 4 HOH B 43 371 56 HOH HOH . G 4 HOH B 44 372 57 HOH HOH . G 4 HOH B 45 373 58 HOH HOH . G 4 HOH B 46 374 59 HOH HOH . G 4 HOH B 47 375 60 HOH HOH . G 4 HOH B 48 376 62 HOH HOH . G 4 HOH B 49 377 63 HOH HOH . G 4 HOH B 50 378 64 HOH HOH . G 4 HOH B 51 379 65 HOH HOH . G 4 HOH B 52 380 66 HOH HOH . G 4 HOH B 53 381 67 HOH HOH . G 4 HOH B 54 382 68 HOH HOH . G 4 HOH B 55 383 69 HOH HOH . G 4 HOH B 56 384 70 HOH HOH . G 4 HOH B 57 385 71 HOH HOH . G 4 HOH B 58 386 72 HOH HOH . G 4 HOH B 59 387 73 HOH HOH . G 4 HOH B 60 388 84 HOH HOH . G 4 HOH B 61 389 85 HOH HOH . G 4 HOH B 62 390 86 HOH HOH . G 4 HOH B 63 391 87 HOH HOH . G 4 HOH B 64 392 88 HOH HOH . G 4 HOH B 65 393 89 HOH HOH . G 4 HOH B 66 394 90 HOH HOH . G 4 HOH B 67 395 91 HOH HOH . G 4 HOH B 68 396 92 HOH HOH . G 4 HOH B 69 397 93 HOH HOH . G 4 HOH B 70 398 94 HOH HOH . G 4 HOH B 71 399 95 HOH HOH . G 4 HOH B 72 400 96 HOH HOH . G 4 HOH B 73 401 97 HOH HOH . G 4 HOH B 74 402 101 HOH HOH . G 4 HOH B 75 403 102 HOH HOH . G 4 HOH B 76 404 103 HOH HOH . G 4 HOH B 77 405 104 HOH HOH . G 4 HOH B 78 406 105 HOH HOH . G 4 HOH B 79 407 106 HOH HOH . G 4 HOH B 80 408 107 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 2 -43.628 -15.136 -5.335 1 21.09 ? PB GDP 327 B 1 HETATM 2 O O1B GDP . . . D 2 -44.483 -14.734 -6.494 1 23.07 ? O1B GDP 327 B 1 HETATM 3 O O2B GDP . . . D 2 -44.099 -14.714 -3.939 1 19.01 ? O2B GDP 327 B 1 HETATM 4 O O3B GDP . . . D 2 -42.157 -14.962 -5.654 1 21.41 ? O3B GDP 327 B 1 HETATM 5 O O3A GDP . . . D 2 -43.76 -16.754 -5.19 1 20.63 ? O3A GDP 327 B 1 HETATM 6 P PA GDP . . . D 2 -44.901 -17.531 -4.353 1 19.88 ? PA GDP 327 B 1 HETATM 7 O O1A GDP . . . D 2 -46.263 -17.022 -4.684 1 21.45 ? O1A GDP 327 B 1 HETATM 8 O O2A GDP . . . D 2 -44.479 -17.715 -2.909 1 21.61 ? O2A GDP 327 B 1 HETATM 9 O O5' GDP . . . D 2 -44.719 -18.98 -5.08 1 23.13 ? O5' GDP 327 B 1 HETATM 10 C C5' GDP . . . D 2 -44.989 -19.166 -6.486 1 22.71 ? C5' GDP 327 B 1 HETATM 11 C C4' GDP . . . D 2 -45.427 -20.593 -6.791 1 24.48 ? C4' GDP 327 B 1 HETATM 12 O O4' GDP . . . D 2 -44.353 -21.56 -6.599 1 27.29 ? O4' GDP 327 B 1 HETATM 13 C C3' GDP . . . D 2 -46.555 -21.043 -5.885 1 25.48 ? C3' GDP 327 B 1 HETATM 14 O O3' GDP . . . D 2 -47.366 -22.011 -6.542 1 26.8 ? O3' GDP 327 B 1 HETATM 15 C C2' GDP . . . D 2 -45.825 -21.73 -4.768 1 26.3 ? C2' GDP 327 B 1 HETATM 16 O O2' GDP . . . D 2 -46.605 -22.687 -4.102 1 27.05 ? O2' GDP 327 B 1 HETATM 17 C C1' GDP . . . D 2 -44.659 -22.402 -5.469 1 26.91 ? C1' GDP 327 B 1 HETATM 18 N N9 GDP . . . D 2 -43.54 -22.553 -4.501 1 30 ? N9 GDP 327 B 1 HETATM 19 C C8 GDP . . . D 2 -43.093 -21.633 -3.58 1 30.94 ? C8 GDP 327 B 1 HETATM 20 N N7 GDP . . . D 2 -42.063 -22.133 -2.855 1 30.71 ? N7 GDP 327 B 1 HETATM 21 C C5 GDP . . . D 2 -41.831 -23.374 -3.304 1 29.37 ? C5 GDP 327 B 1 HETATM 22 C C6 GDP . . . D 2 -40.872 -24.441 -2.969 1 29.82 ? C6 GDP 327 B 1 HETATM 23 O O6 GDP . . . D 2 -40.034 -24.254 -2.051 1 28.76 ? O6 GDP 327 B 1 HETATM 24 N N1 GDP . . . D 2 -40.964 -25.597 -3.662 1 28.34 ? N1 GDP 327 B 1 HETATM 25 C C2 GDP . . . D 2 -41.888 -25.783 -4.636 1 28.64 ? C2 GDP 327 B 1 HETATM 26 N N2 GDP . . . D 2 -41.917 -26.957 -5.305 1 29.9 ? N2 GDP 327 B 1 HETATM 27 N N3 GDP . . . D 2 -42.778 -24.845 -5.027 1 27.42 ? N3 GDP 327 B 1 HETATM 28 C C4 GDP . . . D 2 -42.8 -23.655 -4.387 1 30.15 ? C4 GDP 327 B 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #