data_1FQK # _model_server_result.job_id CzaJVjbTMGpQWodq4_yyIQ _model_server_result.datetime_utc '2024-11-25 02:03:43' _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 1fqk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":361}' # _entry.id 1FQK # _exptl.entry_id 1FQK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 1FQK _cell.length_a 96.785 _cell.length_b 115.073 _cell.length_c 136.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1FQK _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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 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,B,E,F,G,K,L 1 1 C,D,H,I,J,M,N 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 ? 5 G N N ? 5 J 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 metalc ? metalc1 A OG SER 18 A SER 43 1_555 E MG MG . A MG 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc2 A OG1 THR 152 A THR 177 1_555 E MG MG . A MG 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc3 E MG MG . A MG 352 1_555 G O2B GDP . A GDP 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc4 E MG MG . A MG 352 1_555 F F4 ALF . A ALF 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.128 ? metalc ? metalc5 E MG MG . A MG 352 1_555 F F1 ALF . A ALF 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc6 E MG MG . A MG 352 1_555 F AL ALF . A ALF 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.66 ? metalc ? metalc7 E MG MG . A MG 352 1_555 K O HOH . A HOH 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc8 E MG MG . A MG 352 1_555 K O HOH . A HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc9 G O3B GDP . A GDP 360 1_555 F AL ALF . A ALF 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc10 G O2B GDP . A GDP 360 1_555 F AL ALF . A ALF 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.305 ? metalc ? metalc11 F AL ALF . A ALF 362 1_555 K O HOH . A HOH 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc12 C OG SER 18 C SER 43 1_555 H MG MG . C MG 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc13 C OG1 THR 152 C THR 177 1_555 H MG MG . C MG 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc14 H MG MG . C MG 352 1_555 J O2B GDP . C GDP 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc15 H MG MG . C MG 352 1_555 I F1 ALF . C ALF 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc16 H MG MG . C MG 352 1_555 M O HOH . C HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc17 H MG MG . C MG 352 1_555 M O HOH . C HOH 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc18 J O2B GDP . C GDP 361 1_555 I AL ALF . C ALF 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.287 ? metalc ? metalc19 J O3B GDP . C GDP 361 1_555 I AL ALF . C ALF 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.834 ? metalc ? metalc20 I AL ALF . C ALF 363 1_555 M O HOH . C HOH 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 1FQK _atom_sites.fract_transf_matrix[1][1] 0.010332 _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] 0.00869 _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] 0.007328 _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 E 3 MG A 1 352 352 MG MG . F 4 ALF A 1 362 355 ALF ALF . G 5 GDP A 1 360 351 GDP GDP . H 3 MG C 1 352 352 MG MG . I 4 ALF C 1 363 355 ALF ALF . J 5 GDP C 1 361 351 GDP GDP . K 6 HOH A 1 363 1 HOH HOH . K 6 HOH A 2 364 2 HOH HOH . K 6 HOH A 3 365 3 HOH HOH . K 6 HOH A 4 366 8 HOH HOH . K 6 HOH A 5 367 13 HOH HOH . K 6 HOH A 6 368 15 HOH HOH . K 6 HOH A 7 369 16 HOH HOH . K 6 HOH A 8 370 19 HOH HOH . K 6 HOH A 9 371 20 HOH HOH . K 6 HOH A 10 372 21 HOH HOH . K 6 HOH A 11 373 23 HOH HOH . K 6 HOH A 12 374 24 HOH HOH . K 6 HOH A 13 375 28 HOH HOH . K 6 HOH A 14 376 38 HOH HOH . K 6 HOH A 15 377 39 HOH HOH . K 6 HOH A 16 378 40 HOH HOH . K 6 HOH A 17 379 44 HOH HOH . K 6 HOH A 18 380 46 HOH HOH . K 6 HOH A 19 381 48 HOH HOH . K 6 HOH A 20 382 49 HOH HOH . K 6 HOH A 21 383 50 HOH HOH . K 6 HOH A 22 384 51 HOH HOH . K 6 HOH A 23 385 55 HOH HOH . K 6 HOH A 24 386 62 HOH HOH . K 6 HOH A 25 387 63 HOH HOH . K 6 HOH A 26 388 64 HOH HOH . K 6 HOH A 27 389 65 HOH HOH . K 6 HOH A 28 390 67 HOH HOH . K 6 HOH A 29 391 68 HOH HOH . K 6 HOH A 30 392 69 HOH HOH . K 6 HOH A 31 393 70 HOH HOH . K 6 HOH A 32 394 73 HOH HOH . K 6 HOH A 33 395 75 HOH HOH . K 6 HOH A 34 396 79 HOH HOH . K 6 HOH A 35 397 80 HOH HOH . K 6 HOH A 36 398 81 HOH HOH . K 6 HOH A 37 399 82 HOH HOH . K 6 HOH A 38 400 85 HOH HOH . K 6 HOH A 39 401 89 HOH HOH . K 6 HOH A 40 402 90 HOH HOH . K 6 HOH A 41 403 94 HOH HOH . K 6 HOH A 42 404 97 HOH HOH . K 6 HOH A 43 405 98 HOH HOH . K 6 HOH A 44 406 109 HOH HOH . K 6 HOH A 45 407 112 HOH HOH . K 6 HOH A 46 408 114 HOH HOH . K 6 HOH A 47 409 116 HOH HOH . L 6 HOH B 1 14 14 HOH HOH . L 6 HOH B 2 18 18 HOH HOH . L 6 HOH B 3 33 33 HOH HOH . L 6 HOH B 4 34 34 HOH HOH . L 6 HOH B 5 35 35 HOH HOH . L 6 HOH B 6 60 60 HOH HOH . L 6 HOH B 7 87 87 HOH HOH . L 6 HOH B 8 99 99 HOH HOH . L 6 HOH B 9 102 102 HOH HOH . L 6 HOH B 10 110 110 HOH HOH . M 6 HOH C 1 364 4 HOH HOH . M 6 HOH C 2 365 5 HOH HOH . M 6 HOH C 3 366 6 HOH HOH . M 6 HOH C 4 367 9 HOH HOH . M 6 HOH C 5 368 12 HOH HOH . M 6 HOH C 6 369 22 HOH HOH . M 6 HOH C 7 370 25 HOH HOH . M 6 HOH C 8 371 26 HOH HOH . M 6 HOH C 9 372 27 HOH HOH . M 6 HOH C 10 373 29 HOH HOH . M 6 HOH C 11 374 30 HOH HOH . M 6 HOH C 12 375 32 HOH HOH . M 6 HOH C 13 376 37 HOH HOH . M 6 HOH C 14 377 41 HOH HOH . M 6 HOH C 15 378 42 HOH HOH . M 6 HOH C 16 379 52 HOH HOH . M 6 HOH C 17 380 53 HOH HOH . M 6 HOH C 18 381 54 HOH HOH . M 6 HOH C 19 382 56 HOH HOH . M 6 HOH C 20 383 58 HOH HOH . M 6 HOH C 21 384 59 HOH HOH . M 6 HOH C 22 385 61 HOH HOH . M 6 HOH C 23 386 66 HOH HOH . M 6 HOH C 24 387 72 HOH HOH . M 6 HOH C 25 388 74 HOH HOH . M 6 HOH C 26 389 76 HOH HOH . M 6 HOH C 27 390 78 HOH HOH . M 6 HOH C 28 391 83 HOH HOH . M 6 HOH C 29 392 86 HOH HOH . M 6 HOH C 30 393 88 HOH HOH . M 6 HOH C 31 394 91 HOH HOH . M 6 HOH C 32 395 92 HOH HOH . M 6 HOH C 33 396 93 HOH HOH . M 6 HOH C 34 397 95 HOH HOH . M 6 HOH C 35 398 100 HOH HOH . M 6 HOH C 36 399 103 HOH HOH . M 6 HOH C 37 400 104 HOH HOH . M 6 HOH C 38 401 105 HOH HOH . M 6 HOH C 39 402 106 HOH HOH . M 6 HOH C 40 403 107 HOH HOH . M 6 HOH C 41 404 108 HOH HOH . M 6 HOH C 42 405 113 HOH HOH . M 6 HOH C 43 406 115 HOH HOH . N 6 HOH D 1 7 7 HOH HOH . N 6 HOH D 2 10 10 HOH HOH . N 6 HOH D 3 11 11 HOH HOH . N 6 HOH D 4 17 17 HOH HOH . N 6 HOH D 5 31 31 HOH HOH . N 6 HOH D 6 36 36 HOH HOH . N 6 HOH D 7 43 43 HOH HOH . N 6 HOH D 8 45 45 HOH HOH . N 6 HOH D 9 47 47 HOH HOH . N 6 HOH D 10 57 57 HOH HOH . N 6 HOH D 11 71 71 HOH HOH . N 6 HOH D 12 77 77 HOH HOH . N 6 HOH D 13 84 84 HOH HOH . N 6 HOH D 14 96 96 HOH HOH . N 6 HOH D 15 101 101 HOH HOH . N 6 HOH D 16 111 111 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 5 10.495 4.335 148.608 1 61.05 ? PB GDP 361 C 1 HETATM 2 O O1B GDP . . . J 5 10.202 4.147 150.042 1 67.19 ? O1B GDP 361 C 1 HETATM 3 O O2B GDP . . . J 5 9.791 3.513 147.726 1 55.69 ? O2B GDP 361 C 1 HETATM 4 O O3B GDP . . . J 5 10.417 5.916 148.416 1 65.99 ? O3B GDP 361 C 1 HETATM 5 O O3A GDP . . . J 5 11.993 3.963 148.336 1 58.33 ? O3A GDP 361 C 1 HETATM 6 P PA GDP . . . J 5 12.66 2.825 147.333 1 50.19 ? PA GDP 361 C 1 HETATM 7 O O1A GDP . . . J 5 12.349 1.473 147.885 1 57.97 ? O1A GDP 361 C 1 HETATM 8 O O2A GDP . . . J 5 12.143 3.049 145.934 1 56.66 ? O2A GDP 361 C 1 HETATM 9 O O5' GDP . . . J 5 14.141 3.164 147.585 1 53.69 ? O5' GDP 361 C 1 HETATM 10 C C5' GDP . . . J 5 14.806 4.199 146.777 1 52.58 ? C5' GDP 361 C 1 HETATM 11 C C4' GDP . . . J 5 16.13 3.829 146.284 1 51.46 ? C4' GDP 361 C 1 HETATM 12 O O4' GDP . . . J 5 17.027 3.679 147.472 1 50.62 ? O4' GDP 361 C 1 HETATM 13 C C3' GDP . . . J 5 16.205 2.398 145.656 1 51.77 ? C3' GDP 361 C 1 HETATM 14 O O3' GDP . . . J 5 17.254 2.525 144.638 1 52.05 ? O3' GDP 361 C 1 HETATM 15 C C2' GDP . . . J 5 16.688 1.398 146.756 1 53.06 ? C2' GDP 361 C 1 HETATM 16 O O2' GDP . . . J 5 17.388 0.199 146.336 1 54.6 ? O2' GDP 361 C 1 HETATM 17 C C1' GDP . . . J 5 17.607 2.296 147.64 1 52.35 ? C1' GDP 361 C 1 HETATM 18 N N9 GDP . . . J 5 17.619 2.019 149.121 1 49.6 ? N9 GDP 361 C 1 HETATM 19 C C8 GDP . . . J 5 16.317 1.98 149.868 1 52.47 ? C8 GDP 361 C 1 HETATM 20 N N7 GDP . . . J 5 16.948 1.723 151.116 1 49.96 ? N7 GDP 361 C 1 HETATM 21 C C5 GDP . . . J 5 18.276 1.613 151.21 1 52.74 ? C5 GDP 361 C 1 HETATM 22 C C6 GDP . . . J 5 19.384 1.393 152.072 1 54.62 ? C6 GDP 361 C 1 HETATM 23 O O6 GDP . . . J 5 19.103 1.203 153.376 1 55.79 ? O6 GDP 361 C 1 HETATM 24 N N1 GDP . . . J 5 20.671 1.365 151.679 1 53.47 ? N1 GDP 361 C 1 HETATM 25 C C2 GDP . . . J 5 20.967 1.586 150.234 1 49.69 ? C2 GDP 361 C 1 HETATM 26 N N2 GDP . . . J 5 22.281 1.522 150.055 1 52.57 ? N2 GDP 361 C 1 HETATM 27 N N3 GDP . . . J 5 20.021 1.792 149.426 1 53.21 ? N3 GDP 361 C 1 HETATM 28 C C4 GDP . . . J 5 18.746 1.81 149.853 1 49.73 ? C4 GDP 361 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #