data_5W22 # _model_server_result.job_id BksQMxweNGm8mhmglT-wCg _model_server_result.datetime_utc '2024-11-25 15:57:35' _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 5w22 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5W22 # _exptl.entry_id 5W22 _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 120 _cell.entry_id 5W22 _cell.length_a 93.177 _cell.length_b 93.177 _cell.length_c 118.431 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W22 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 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 ? 2 C N N ? 2 E 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 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc2 C O3B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc3 D MG MG . A MG 202 1_555 G O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc4 D MG MG . A MG 202 1_555 G O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc5 D MG MG . A MG 202 1_555 G O HOH . A HOH 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc6 D MG MG . A MG 202 1_555 G O HOH . A HOH 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc7 B OG SER 18 B SER 17 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc8 E O2B GDP . B GDP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc9 F MG MG . B MG 202 1_555 H O HOH . B HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc10 F MG MG . B MG 202 1_555 H O HOH . B HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc11 F MG MG . B MG 202 1_555 H O HOH . B HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc12 F MG MG . B MG 202 1_555 H O HOH . B HOH 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? # _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 5W22 _atom_sites.fract_transf_matrix[1][1] 0.010732 _atom_sites.fract_transf_matrix[1][2] 0.006196 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012393 _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] 0.008444 _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 1 201 1 GDP GDP . D 3 MG A 1 202 1 MG MG . E 2 GDP B 1 201 2 GDP GDP . F 3 MG B 1 202 2 MG MG . G 4 HOH A 1 301 96 HOH HOH . G 4 HOH A 2 302 54 HOH HOH . G 4 HOH A 3 303 68 HOH HOH . G 4 HOH A 4 304 145 HOH HOH . G 4 HOH A 5 305 84 HOH HOH . G 4 HOH A 6 306 43 HOH HOH . G 4 HOH A 7 307 46 HOH HOH . G 4 HOH A 8 308 93 HOH HOH . G 4 HOH A 9 309 81 HOH HOH . G 4 HOH A 10 310 99 HOH HOH . G 4 HOH A 11 311 35 HOH HOH . G 4 HOH A 12 312 149 HOH HOH . G 4 HOH A 13 313 47 HOH HOH . G 4 HOH A 14 314 48 HOH HOH . G 4 HOH A 15 315 23 HOH HOH . G 4 HOH A 16 316 28 HOH HOH . G 4 HOH A 17 317 79 HOH HOH . G 4 HOH A 18 318 27 HOH HOH . G 4 HOH A 19 319 94 HOH HOH . G 4 HOH A 20 320 38 HOH HOH . G 4 HOH A 21 321 59 HOH HOH . G 4 HOH A 22 322 90 HOH HOH . G 4 HOH A 23 323 89 HOH HOH . G 4 HOH A 24 324 80 HOH HOH . G 4 HOH A 25 325 21 HOH HOH . G 4 HOH A 26 326 49 HOH HOH . G 4 HOH A 27 327 1 HOH HOH . G 4 HOH A 28 328 147 HOH HOH . G 4 HOH A 29 329 78 HOH HOH . G 4 HOH A 30 330 87 HOH HOH . G 4 HOH A 31 331 20 HOH HOH . G 4 HOH A 32 332 69 HOH HOH . G 4 HOH A 33 333 153 HOH HOH . G 4 HOH A 34 334 104 HOH HOH . G 4 HOH A 35 335 3 HOH HOH . G 4 HOH A 36 336 83 HOH HOH . G 4 HOH A 37 337 44 HOH HOH . G 4 HOH A 38 338 91 HOH HOH . G 4 HOH A 39 339 7 HOH HOH . G 4 HOH A 40 340 25 HOH HOH . G 4 HOH A 41 341 71 HOH HOH . G 4 HOH A 42 342 150 HOH HOH . G 4 HOH A 43 343 103 HOH HOH . G 4 HOH A 44 344 30 HOH HOH . G 4 HOH A 45 345 138 HOH HOH . G 4 HOH A 46 346 42 HOH HOH . G 4 HOH A 47 347 13 HOH HOH . G 4 HOH A 48 348 72 HOH HOH . G 4 HOH A 49 349 97 HOH HOH . G 4 HOH A 50 350 5 HOH HOH . G 4 HOH A 51 351 152 HOH HOH . G 4 HOH A 52 352 88 HOH HOH . G 4 HOH A 53 353 151 HOH HOH . G 4 HOH A 54 354 148 HOH HOH . G 4 HOH A 55 355 142 HOH HOH . G 4 HOH A 56 356 155 HOH HOH . G 4 HOH A 57 357 140 HOH HOH . G 4 HOH A 58 358 154 HOH HOH . G 4 HOH A 59 359 141 HOH HOH . G 4 HOH A 60 360 67 HOH HOH . G 4 HOH A 61 361 158 HOH HOH . G 4 HOH A 62 362 86 HOH HOH . G 4 HOH A 63 363 12 HOH HOH . G 4 HOH A 64 364 41 HOH HOH . G 4 HOH A 65 365 77 HOH HOH . G 4 HOH A 66 366 144 HOH HOH . G 4 HOH A 67 367 139 HOH HOH . G 4 HOH A 68 368 33 HOH HOH . G 4 HOH A 69 369 85 HOH HOH . G 4 HOH A 70 370 65 HOH HOH . G 4 HOH A 71 371 157 HOH HOH . G 4 HOH A 72 372 146 HOH HOH . G 4 HOH A 73 373 143 HOH HOH . G 4 HOH A 74 374 39 HOH HOH . G 4 HOH A 75 375 137 HOH HOH . G 4 HOH A 76 376 95 HOH HOH . G 4 HOH A 77 377 32 HOH HOH . G 4 HOH A 78 378 156 HOH HOH . G 4 HOH A 79 379 98 HOH HOH . G 4 HOH A 80 380 92 HOH HOH . G 4 HOH A 81 381 102 HOH HOH . H 4 HOH B 1 301 131 HOH HOH . H 4 HOH B 2 302 100 HOH HOH . H 4 HOH B 3 303 53 HOH HOH . H 4 HOH B 4 304 82 HOH HOH . H 4 HOH B 5 305 19 HOH HOH . H 4 HOH B 6 306 122 HOH HOH . H 4 HOH B 7 307 73 HOH HOH . H 4 HOH B 8 308 36 HOH HOH . H 4 HOH B 9 309 29 HOH HOH . H 4 HOH B 10 310 66 HOH HOH . H 4 HOH B 11 311 112 HOH HOH . H 4 HOH B 12 312 40 HOH HOH . H 4 HOH B 13 313 31 HOH HOH . H 4 HOH B 14 314 34 HOH HOH . H 4 HOH B 15 315 126 HOH HOH . H 4 HOH B 16 316 123 HOH HOH . H 4 HOH B 17 317 37 HOH HOH . H 4 HOH B 18 318 134 HOH HOH . H 4 HOH B 19 319 52 HOH HOH . H 4 HOH B 20 320 127 HOH HOH . H 4 HOH B 21 321 55 HOH HOH . H 4 HOH B 22 322 70 HOH HOH . H 4 HOH B 23 323 107 HOH HOH . H 4 HOH B 24 324 14 HOH HOH . H 4 HOH B 25 325 129 HOH HOH . H 4 HOH B 26 326 26 HOH HOH . H 4 HOH B 27 327 64 HOH HOH . H 4 HOH B 28 328 22 HOH HOH . H 4 HOH B 29 329 50 HOH HOH . H 4 HOH B 30 330 4 HOH HOH . H 4 HOH B 31 331 130 HOH HOH . H 4 HOH B 32 332 159 HOH HOH . H 4 HOH B 33 333 56 HOH HOH . H 4 HOH B 34 334 2 HOH HOH . H 4 HOH B 35 335 132 HOH HOH . H 4 HOH B 36 336 110 HOH HOH . H 4 HOH B 37 337 8 HOH HOH . H 4 HOH B 38 338 115 HOH HOH . H 4 HOH B 39 339 105 HOH HOH . H 4 HOH B 40 340 9 HOH HOH . H 4 HOH B 41 341 119 HOH HOH . H 4 HOH B 42 342 10 HOH HOH . H 4 HOH B 43 343 109 HOH HOH . H 4 HOH B 44 344 135 HOH HOH . H 4 HOH B 45 345 118 HOH HOH . H 4 HOH B 46 346 6 HOH HOH . H 4 HOH B 47 347 57 HOH HOH . H 4 HOH B 48 348 74 HOH HOH . H 4 HOH B 49 349 113 HOH HOH . H 4 HOH B 50 350 128 HOH HOH . H 4 HOH B 51 351 76 HOH HOH . H 4 HOH B 52 352 117 HOH HOH . H 4 HOH B 53 353 11 HOH HOH . H 4 HOH B 54 354 116 HOH HOH . H 4 HOH B 55 355 60 HOH HOH . H 4 HOH B 56 356 63 HOH HOH . H 4 HOH B 57 357 45 HOH HOH . H 4 HOH B 58 358 106 HOH HOH . H 4 HOH B 59 359 124 HOH HOH . H 4 HOH B 60 360 114 HOH HOH . H 4 HOH B 61 361 62 HOH HOH . H 4 HOH B 62 362 125 HOH HOH . H 4 HOH B 63 363 160 HOH HOH . H 4 HOH B 64 364 58 HOH HOH . H 4 HOH B 65 365 136 HOH HOH . H 4 HOH B 66 366 18 HOH HOH . H 4 HOH B 67 367 15 HOH HOH . H 4 HOH B 68 368 16 HOH HOH . H 4 HOH B 69 369 108 HOH HOH . H 4 HOH B 70 370 120 HOH HOH . H 4 HOH B 71 371 111 HOH HOH . H 4 HOH B 72 372 61 HOH HOH . H 4 HOH B 73 373 133 HOH HOH . H 4 HOH B 74 374 121 HOH HOH . H 4 HOH B 75 375 101 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 . . . E 2 16.189 0.819 30.654 1 14.18 ? PB GDP 201 B 1 HETATM 2 O O1B GDP . . . E 2 15.719 1.747 29.551 1 13.32 ? O1B GDP 201 B 1 HETATM 3 O O2B GDP . . . E 2 17.562 1.136 31.158 1 14.16 ? O2B GDP 201 B 1 HETATM 4 O O3B GDP . . . E 2 15.066 0.68 31.665 1 13.57 ? O3B GDP 201 B 1 HETATM 5 O O3A GDP . . . E 2 16.293 -0.593 29.895 1 14.54 ? O3A GDP 201 B 1 HETATM 6 P PA GDP . . . E 2 17.382 -1.768 29.992 1 15.1 ? PA GDP 201 B 1 HETATM 7 O O1A GDP . . . E 2 18.635 -1.311 29.301 1 18.01 ? O1A GDP 201 B 1 HETATM 8 O O2A GDP . . . E 2 17.45 -2.175 31.441 1 17.65 ? O2A GDP 201 B 1 HETATM 9 O O5' GDP . . . E 2 16.77 -2.889 29.031 1 16.61 ? O5' GDP 201 B 1 HETATM 10 C C5' GDP . . . E 2 15.454 -3.415 29.252 1 18.18 ? C5' GDP 201 B 1 HETATM 11 C C4' GDP . . . E 2 15.38 -4.842 28.749 1 17.92 ? C4' GDP 201 B 1 HETATM 12 O O4' GDP . . . E 2 15.436 -4.851 27.319 1 16.21 ? O4' GDP 201 B 1 HETATM 13 C C3' GDP . . . E 2 16.552 -5.693 29.225 1 19.5 ? C3' GDP 201 B 1 HETATM 14 O O3' GDP . . . E 2 16.115 -7.028 29.445 1 22.72 ? O3' GDP 201 B 1 HETATM 15 C C2' GDP . . . E 2 17.469 -5.743 28.031 1 19.42 ? C2' GDP 201 B 1 HETATM 16 O O2' GDP . . . E 2 18.124 -6.992 27.939 1 22.67 ? O2' GDP 201 B 1 HETATM 17 C C1' GDP . . . E 2 16.521 -5.617 26.849 1 16.63 ? C1' GDP 201 B 1 HETATM 18 N N9 GDP . . . E 2 17.103 -4.879 25.732 1 14.62 ? N9 GDP 201 B 1 HETATM 19 C C8 GDP . . . E 2 17.63 -3.633 25.76 1 13.43 ? C8 GDP 201 B 1 HETATM 20 N N7 GDP . . . E 2 18.052 -3.274 24.537 1 13.48 ? N7 GDP 201 B 1 HETATM 21 C C5 GDP . . . E 2 17.804 -4.295 23.694 1 12.85 ? C5 GDP 201 B 1 HETATM 22 C C6 GDP . . . E 2 17.956 -4.569 22.266 1 13.52 ? C6 GDP 201 B 1 HETATM 23 O O6 GDP . . . E 2 18.445 -3.751 21.488 1 12.44 ? O6 GDP 201 B 1 HETATM 24 N N1 GDP . . . E 2 17.581 -5.773 21.807 1 14.15 ? N1 GDP 201 B 1 HETATM 25 C C2 GDP . . . E 2 17.015 -6.7 22.608 1 13.8 ? C2 GDP 201 B 1 HETATM 26 N N2 GDP . . . E 2 16.651 -7.888 22.088 1 14.44 ? N2 GDP 201 B 1 HETATM 27 N N3 GDP . . . E 2 16.838 -6.514 23.923 1 14.39 ? N3 GDP 201 B 1 HETATM 28 C C4 GDP . . . E 2 17.187 -5.346 24.494 1 14.24 ? C4 GDP 201 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #