data_1Y3A # _model_server_result.job_id fIxLajdXB1rCmZIhhMpimA _model_server_result.datetime_utc '2025-07-20 10:44:38' _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 1y3a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":358}' # _entry.id 1Y3A # _exptl.entry_id 1Y3A _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.75 _cell.angle_gamma 90 _cell.entry_id 1Y3A _cell.length_a 72.943 _cell.length_b 112.785 _cell.length_c 109.49 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y3A _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 dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I,M,Q 1 1 B,F,J,N,R 2 1 C,G,K,O,S 3 1 D,H,L,P,T 4 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 I N N ? 3 J N N ? 3 K N N ? 3 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 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 1Y3A _atom_sites.fract_transf_matrix[1][1] 0.013709 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000899 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008866 _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] 0.009153 _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 I 3 GDP A 1 355 355 GDP GDP . J 3 GDP B 1 356 356 GDP GDP . K 3 GDP C 1 357 357 GDP GDP . L 3 GDP D 1 358 358 GDP GDP . M 4 HOH A 1 356 2 HOH HOH . M 4 HOH A 2 357 6 HOH HOH . M 4 HOH A 3 358 8 HOH HOH . M 4 HOH A 4 359 12 HOH HOH . M 4 HOH A 5 360 13 HOH HOH . M 4 HOH A 6 361 14 HOH HOH . M 4 HOH A 7 362 17 HOH HOH . M 4 HOH A 8 363 24 HOH HOH . M 4 HOH A 9 364 29 HOH HOH . M 4 HOH A 10 365 36 HOH HOH . M 4 HOH A 11 366 39 HOH HOH . M 4 HOH A 12 367 44 HOH HOH . M 4 HOH A 13 368 46 HOH HOH . M 4 HOH A 14 369 47 HOH HOH . M 4 HOH A 15 370 48 HOH HOH . M 4 HOH A 16 371 51 HOH HOH . M 4 HOH A 17 372 52 HOH HOH . M 4 HOH A 18 373 53 HOH HOH . M 4 HOH A 19 374 55 HOH HOH . M 4 HOH A 20 375 57 HOH HOH . M 4 HOH A 21 376 59 HOH HOH . M 4 HOH A 22 377 62 HOH HOH . M 4 HOH A 23 378 65 HOH HOH . M 4 HOH A 24 379 66 HOH HOH . M 4 HOH A 25 380 69 HOH HOH . M 4 HOH A 26 381 70 HOH HOH . M 4 HOH A 27 382 72 HOH HOH . M 4 HOH A 28 383 74 HOH HOH . M 4 HOH A 29 384 77 HOH HOH . M 4 HOH A 30 385 80 HOH HOH . M 4 HOH A 31 386 83 HOH HOH . M 4 HOH A 32 387 85 HOH HOH . M 4 HOH A 33 388 86 HOH HOH . M 4 HOH A 34 389 94 HOH HOH . M 4 HOH A 35 390 99 HOH HOH . M 4 HOH A 36 391 100 HOH HOH . M 4 HOH A 37 392 101 HOH HOH . M 4 HOH A 38 393 103 HOH HOH . M 4 HOH A 39 394 104 HOH HOH . M 4 HOH A 40 395 107 HOH HOH . M 4 HOH A 41 396 114 HOH HOH . M 4 HOH A 42 397 119 HOH HOH . M 4 HOH A 43 398 121 HOH HOH . M 4 HOH A 44 399 122 HOH HOH . M 4 HOH A 45 400 128 HOH HOH . M 4 HOH A 46 401 130 HOH HOH . N 4 HOH B 1 357 9 HOH HOH . N 4 HOH B 2 358 10 HOH HOH . N 4 HOH B 3 359 19 HOH HOH . N 4 HOH B 4 360 20 HOH HOH . N 4 HOH B 5 361 21 HOH HOH . N 4 HOH B 6 362 22 HOH HOH . N 4 HOH B 7 363 27 HOH HOH . N 4 HOH B 8 364 50 HOH HOH . N 4 HOH B 9 365 56 HOH HOH . N 4 HOH B 10 366 61 HOH HOH . N 4 HOH B 11 367 64 HOH HOH . N 4 HOH B 12 368 76 HOH HOH . N 4 HOH B 13 369 78 HOH HOH . N 4 HOH B 14 370 82 HOH HOH . N 4 HOH B 15 371 90 HOH HOH . N 4 HOH B 16 372 92 HOH HOH . N 4 HOH B 17 373 105 HOH HOH . N 4 HOH B 18 374 108 HOH HOH . N 4 HOH B 19 375 109 HOH HOH . N 4 HOH B 20 376 111 HOH HOH . N 4 HOH B 21 377 113 HOH HOH . N 4 HOH B 22 378 115 HOH HOH . N 4 HOH B 23 379 116 HOH HOH . N 4 HOH B 24 380 120 HOH HOH . N 4 HOH B 25 381 123 HOH HOH . N 4 HOH B 26 382 126 HOH HOH . N 4 HOH B 27 383 132 HOH HOH . N 4 HOH B 28 384 134 HOH HOH . N 4 HOH B 29 385 136 HOH HOH . O 4 HOH C 1 358 5 HOH HOH . O 4 HOH C 2 359 7 HOH HOH . O 4 HOH C 3 360 16 HOH HOH . O 4 HOH C 4 361 25 HOH HOH . O 4 HOH C 5 362 26 HOH HOH . O 4 HOH C 6 363 28 HOH HOH . O 4 HOH C 7 364 31 HOH HOH . O 4 HOH C 8 365 34 HOH HOH . O 4 HOH C 9 366 35 HOH HOH . O 4 HOH C 10 367 37 HOH HOH . O 4 HOH C 11 368 38 HOH HOH . O 4 HOH C 12 369 43 HOH HOH . O 4 HOH C 13 370 54 HOH HOH . O 4 HOH C 14 371 58 HOH HOH . O 4 HOH C 15 372 67 HOH HOH . O 4 HOH C 16 373 68 HOH HOH . O 4 HOH C 17 374 71 HOH HOH . O 4 HOH C 18 375 75 HOH HOH . O 4 HOH C 19 376 79 HOH HOH . O 4 HOH C 20 377 87 HOH HOH . O 4 HOH C 21 378 88 HOH HOH . O 4 HOH C 22 379 91 HOH HOH . O 4 HOH C 23 380 96 HOH HOH . O 4 HOH C 24 381 102 HOH HOH . O 4 HOH C 25 382 117 HOH HOH . O 4 HOH C 26 383 118 HOH HOH . O 4 HOH C 27 384 124 HOH HOH . O 4 HOH C 28 385 129 HOH HOH . O 4 HOH C 29 386 131 HOH HOH . O 4 HOH C 30 387 135 HOH HOH . P 4 HOH D 1 359 1 HOH HOH . P 4 HOH D 2 360 3 HOH HOH . P 4 HOH D 3 361 4 HOH HOH . P 4 HOH D 4 362 11 HOH HOH . P 4 HOH D 5 363 15 HOH HOH . P 4 HOH D 6 364 18 HOH HOH . P 4 HOH D 7 365 23 HOH HOH . P 4 HOH D 8 366 30 HOH HOH . P 4 HOH D 9 367 32 HOH HOH . P 4 HOH D 10 368 33 HOH HOH . P 4 HOH D 11 369 41 HOH HOH . P 4 HOH D 12 370 42 HOH HOH . P 4 HOH D 13 371 45 HOH HOH . P 4 HOH D 14 372 49 HOH HOH . P 4 HOH D 15 373 84 HOH HOH . P 4 HOH D 16 374 89 HOH HOH . P 4 HOH D 17 375 93 HOH HOH . P 4 HOH D 18 376 95 HOH HOH . P 4 HOH D 19 377 97 HOH HOH . P 4 HOH D 20 378 98 HOH HOH . P 4 HOH D 21 379 106 HOH HOH . P 4 HOH D 22 380 110 HOH HOH . P 4 HOH D 23 381 112 HOH HOH . P 4 HOH D 24 382 125 HOH HOH . P 4 HOH D 25 383 127 HOH HOH . Q 4 HOH E 1 40 40 HOH HOH . Q 4 HOH E 2 133 133 HOH HOH . R 4 HOH F 1 81 81 HOH HOH . S 4 HOH G 1 60 60 HOH HOH . S 4 HOH G 2 63 63 HOH HOH . T 4 HOH H 1 73 73 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 . . . L 3 12.968 57.007 55.137 1 50.9 ? PB GDP 358 D 1 HETATM 2 O O1B GDP . . . L 3 13.047 55.994 56.177 1 53.76 ? O1B GDP 358 D 1 HETATM 3 O O2B GDP . . . L 3 14.204 57.208 54.319 1 52.18 ? O2B GDP 358 D 1 HETATM 4 O O3B GDP . . . L 3 11.967 56.759 54.026 1 56.58 ? O3B GDP 358 D 1 HETATM 5 O O3A GDP . . . L 3 12.923 58.474 55.993 1 55.49 ? O3A GDP 358 D 1 HETATM 6 P PA GDP . . . L 3 11.73 58.894 57.059 1 56.25 ? PA GDP 358 D 1 HETATM 7 O O1A GDP . . . L 3 12.356 60.146 57.609 1 59.2 ? O1A GDP 358 D 1 HETATM 8 O O2A GDP . . . L 3 10.44 58.273 57.375 1 55.31 ? O2A GDP 358 D 1 HETATM 9 O O5' GDP . . . L 3 11.143 59.977 56.037 1 48.24 ? O5' GDP 358 D 1 HETATM 10 C C5' GDP . . . L 3 10.248 60.016 54.942 1 40.7 ? C5' GDP 358 D 1 HETATM 11 C C4' GDP . . . L 3 9.753 61.535 54.976 1 36.2 ? C4' GDP 358 D 1 HETATM 12 O O4' GDP . . . L 3 8.324 61.741 54.653 1 34.15 ? O4' GDP 358 D 1 HETATM 13 C C3' GDP . . . L 3 9.792 62.232 56.397 1 35.33 ? C3' GDP 358 D 1 HETATM 14 O O3' GDP . . . L 3 9.924 63.655 56.143 1 35.96 ? O3' GDP 358 D 1 HETATM 15 C C2' GDP . . . L 3 8.415 61.907 57.016 1 33.27 ? C2' GDP 358 D 1 HETATM 16 O O2' GDP . . . L 3 8 62.82 58.023 1 28.7 ? O2' GDP 358 D 1 HETATM 17 C C1' GDP . . . L 3 7.508 61.957 55.815 1 32.06 ? C1' GDP 358 D 1 HETATM 18 N N9 GDP . . . L 3 6.499 60.85 55.803 1 32.24 ? N9 GDP 358 D 1 HETATM 19 C C8 GDP . . . L 3 6.63 59.499 55.966 1 32.78 ? C8 GDP 358 D 1 HETATM 20 N N7 GDP . . . L 3 5.514 58.848 55.874 1 32.12 ? N7 GDP 358 D 1 HETATM 21 C C5 GDP . . . L 3 4.56 59.804 55.629 1 33.68 ? C5 GDP 358 D 1 HETATM 22 C C6 GDP . . . L 3 3.15 59.707 55.431 1 33.9 ? C6 GDP 358 D 1 HETATM 23 O O6 GDP . . . L 3 2.458 58.663 55.426 1 36.86 ? O6 GDP 358 D 1 HETATM 24 N N1 GDP . . . L 3 2.551 60.98 55.211 1 33.79 ? N1 GDP 358 D 1 HETATM 25 C C2 GDP . . . L 3 3.224 62.191 55.195 1 35.69 ? C2 GDP 358 D 1 HETATM 26 N N2 GDP . . . L 3 2.474 63.271 54.975 1 36.43 ? N2 GDP 358 D 1 HETATM 27 N N3 GDP . . . L 3 4.572 62.3 55.383 1 34.11 ? N3 GDP 358 D 1 HETATM 28 C C4 GDP . . . L 3 5.141 61.081 55.593 1 33.13 ? C4 GDP 358 D 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #