data_5VQ1 # _model_server_result.job_id JKARXaXKD2HVspxVgo9uUQ _model_server_result.datetime_utc '2024-11-01 18:22:30' _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 5vq1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5VQ1 # _exptl.entry_id 5VQ1 _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 5VQ1 _cell.length_a 93.862 _cell.length_b 93.862 _cell.length_c 120.498 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VQ1 _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,H 1 1 B,E,F,G,I 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc2 C O3B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc3 D MG MG . A MG 202 1_555 H O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc4 D MG MG . A MG 202 1_555 H O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc5 D MG MG . A MG 202 1_555 H O HOH . A HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc6 D MG MG . A MG 202 1_555 H O HOH . A HOH 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc7 B OG SER 18 B SER 17 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc8 E O2B GDP . B GDP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc9 F MG MG . B MG 202 1_555 I O HOH . B HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc10 F MG MG . B MG 202 1_555 I O HOH . B HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc11 F MG MG . B MG 202 1_555 I O HOH . B HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc12 F MG MG . B MG 202 1_555 I O HOH . B HOH 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? # _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 5VQ1 _atom_sites.fract_transf_matrix[1][1] 0.010654 _atom_sites.fract_transf_matrix[1][2] 0.006151 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012302 _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] 0.008299 _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 PG4 B 1 203 1 PG4 PG4 . H 5 HOH A 1 301 34 HOH HOH . H 5 HOH A 2 302 35 HOH HOH . H 5 HOH A 3 303 77 HOH HOH . H 5 HOH A 4 304 70 HOH HOH . H 5 HOH A 5 305 126 HOH HOH . H 5 HOH A 6 306 124 HOH HOH . H 5 HOH A 7 307 2 HOH HOH . H 5 HOH A 8 308 130 HOH HOH . H 5 HOH A 9 309 84 HOH HOH . H 5 HOH A 10 310 28 HOH HOH . H 5 HOH A 11 311 102 HOH HOH . H 5 HOH A 12 312 1 HOH HOH . H 5 HOH A 13 313 86 HOH HOH . H 5 HOH A 14 314 94 HOH HOH . H 5 HOH A 15 315 107 HOH HOH . H 5 HOH A 16 316 131 HOH HOH . H 5 HOH A 17 317 125 HOH HOH . H 5 HOH A 18 318 57 HOH HOH . H 5 HOH A 19 319 52 HOH HOH . H 5 HOH A 20 320 41 HOH HOH . H 5 HOH A 21 321 49 HOH HOH . H 5 HOH A 22 322 128 HOH HOH . H 5 HOH A 23 323 117 HOH HOH . H 5 HOH A 24 324 3 HOH HOH . H 5 HOH A 25 325 91 HOH HOH . H 5 HOH A 26 326 7 HOH HOH . H 5 HOH A 27 327 87 HOH HOH . H 5 HOH A 28 328 13 HOH HOH . H 5 HOH A 29 329 50 HOH HOH . H 5 HOH A 30 330 123 HOH HOH . H 5 HOH A 31 331 105 HOH HOH . H 5 HOH A 32 332 137 HOH HOH . H 5 HOH A 33 333 25 HOH HOH . H 5 HOH A 34 334 76 HOH HOH . H 5 HOH A 35 335 115 HOH HOH . H 5 HOH A 36 336 121 HOH HOH . H 5 HOH A 37 337 85 HOH HOH . H 5 HOH A 38 338 60 HOH HOH . H 5 HOH A 39 339 11 HOH HOH . H 5 HOH A 40 340 71 HOH HOH . H 5 HOH A 41 341 15 HOH HOH . H 5 HOH A 42 342 62 HOH HOH . H 5 HOH A 43 343 80 HOH HOH . H 5 HOH A 44 344 106 HOH HOH . H 5 HOH A 45 345 78 HOH HOH . H 5 HOH A 46 346 113 HOH HOH . H 5 HOH A 47 347 38 HOH HOH . H 5 HOH A 48 348 24 HOH HOH . H 5 HOH A 49 349 16 HOH HOH . H 5 HOH A 50 350 31 HOH HOH . H 5 HOH A 51 351 21 HOH HOH . H 5 HOH A 52 352 64 HOH HOH . H 5 HOH A 53 353 144 HOH HOH . H 5 HOH A 54 354 42 HOH HOH . H 5 HOH A 55 355 88 HOH HOH . H 5 HOH A 56 356 45 HOH HOH . H 5 HOH A 57 357 145 HOH HOH . H 5 HOH A 58 358 22 HOH HOH . H 5 HOH A 59 359 133 HOH HOH . H 5 HOH A 60 360 116 HOH HOH . H 5 HOH A 61 361 73 HOH HOH . H 5 HOH A 62 362 14 HOH HOH . H 5 HOH A 63 363 104 HOH HOH . H 5 HOH A 64 364 33 HOH HOH . H 5 HOH A 65 365 67 HOH HOH . H 5 HOH A 66 366 51 HOH HOH . H 5 HOH A 67 367 103 HOH HOH . H 5 HOH A 68 368 79 HOH HOH . H 5 HOH A 69 369 54 HOH HOH . H 5 HOH A 70 370 122 HOH HOH . H 5 HOH A 71 371 114 HOH HOH . H 5 HOH A 72 372 17 HOH HOH . H 5 HOH A 73 373 111 HOH HOH . H 5 HOH A 74 374 118 HOH HOH . H 5 HOH A 75 375 132 HOH HOH . H 5 HOH A 76 376 95 HOH HOH . H 5 HOH A 77 377 127 HOH HOH . H 5 HOH A 78 378 109 HOH HOH . H 5 HOH A 79 379 110 HOH HOH . I 5 HOH B 1 301 141 HOH HOH . I 5 HOH B 2 302 46 HOH HOH . I 5 HOH B 3 303 142 HOH HOH . I 5 HOH B 4 304 129 HOH HOH . I 5 HOH B 5 305 82 HOH HOH . I 5 HOH B 6 306 36 HOH HOH . I 5 HOH B 7 307 6 HOH HOH . I 5 HOH B 8 308 97 HOH HOH . I 5 HOH B 9 309 99 HOH HOH . I 5 HOH B 10 310 134 HOH HOH . I 5 HOH B 11 311 138 HOH HOH . I 5 HOH B 12 312 43 HOH HOH . I 5 HOH B 13 313 58 HOH HOH . I 5 HOH B 14 314 47 HOH HOH . I 5 HOH B 15 315 4 HOH HOH . I 5 HOH B 16 316 135 HOH HOH . I 5 HOH B 17 317 40 HOH HOH . I 5 HOH B 18 318 119 HOH HOH . I 5 HOH B 19 319 9 HOH HOH . I 5 HOH B 20 320 8 HOH HOH . I 5 HOH B 21 321 136 HOH HOH . I 5 HOH B 22 322 72 HOH HOH . I 5 HOH B 23 323 10 HOH HOH . I 5 HOH B 24 324 5 HOH HOH . I 5 HOH B 25 325 92 HOH HOH . I 5 HOH B 26 326 100 HOH HOH . I 5 HOH B 27 327 147 HOH HOH . I 5 HOH B 28 328 93 HOH HOH . I 5 HOH B 29 329 61 HOH HOH . I 5 HOH B 30 330 63 HOH HOH . I 5 HOH B 31 331 12 HOH HOH . I 5 HOH B 32 332 55 HOH HOH . I 5 HOH B 33 333 69 HOH HOH . I 5 HOH B 34 334 39 HOH HOH . I 5 HOH B 35 335 89 HOH HOH . I 5 HOH B 36 336 66 HOH HOH . I 5 HOH B 37 337 48 HOH HOH . I 5 HOH B 38 338 32 HOH HOH . I 5 HOH B 39 339 143 HOH HOH . I 5 HOH B 40 340 140 HOH HOH . I 5 HOH B 41 341 26 HOH HOH . I 5 HOH B 42 342 27 HOH HOH . I 5 HOH B 43 343 37 HOH HOH . I 5 HOH B 44 344 83 HOH HOH . I 5 HOH B 45 345 53 HOH HOH . I 5 HOH B 46 346 30 HOH HOH . I 5 HOH B 47 347 23 HOH HOH . I 5 HOH B 48 348 139 HOH HOH . I 5 HOH B 49 349 68 HOH HOH . I 5 HOH B 50 350 59 HOH HOH . I 5 HOH B 51 351 98 HOH HOH . I 5 HOH B 52 352 112 HOH HOH . I 5 HOH B 53 353 29 HOH HOH . I 5 HOH B 54 354 74 HOH HOH . I 5 HOH B 55 355 90 HOH HOH . I 5 HOH B 56 356 44 HOH HOH . I 5 HOH B 57 357 56 HOH HOH . I 5 HOH B 58 358 75 HOH HOH . I 5 HOH B 59 359 65 HOH HOH . I 5 HOH B 60 360 81 HOH HOH . I 5 HOH B 61 361 101 HOH HOH . I 5 HOH B 62 362 148 HOH HOH . I 5 HOH B 63 363 20 HOH HOH . I 5 HOH B 64 364 146 HOH HOH . I 5 HOH B 65 365 120 HOH HOH . I 5 HOH B 66 366 96 HOH HOH . I 5 HOH B 67 367 108 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 16.147 0.254 18.665 1 20.62 ? PB GDP 201 B 1 HETATM 2 O O1B GDP . . . E 2 15.653 1.179 17.554 1 19.63 ? O1B GDP 201 B 1 HETATM 3 O O2B GDP . . . E 2 17.553 0.511 19.111 1 22.47 ? O2B GDP 201 B 1 HETATM 4 O O3B GDP . . . E 2 15.082 0.156 19.716 1 19.52 ? O3B GDP 201 B 1 HETATM 5 O O3A GDP . . . E 2 16.196 -1.18 17.937 1 19.68 ? O3A GDP 201 B 1 HETATM 6 P PA GDP . . . E 2 17.293 -2.375 18.016 1 21.01 ? PA GDP 201 B 1 HETATM 7 O O1A GDP . . . E 2 18.62 -2.116 17.362 1 20.64 ? O1A GDP 201 B 1 HETATM 8 O O2A GDP . . . E 2 17.274 -2.831 19.442 1 25.36 ? O2A GDP 201 B 1 HETATM 9 O O5' GDP . . . E 2 16.704 -3.515 17.088 1 21.18 ? O5' GDP 201 B 1 HETATM 10 C C5' GDP . . . E 2 15.374 -3.968 17.39 1 22.48 ? C5' GDP 201 B 1 HETATM 11 C C4' GDP . . . E 2 15.236 -5.385 16.856 1 21.26 ? C4' GDP 201 B 1 HETATM 12 O O4' GDP . . . E 2 15.276 -5.414 15.418 1 19.09 ? O4' GDP 201 B 1 HETATM 13 C C3' GDP . . . E 2 16.371 -6.305 17.313 1 22.43 ? C3' GDP 201 B 1 HETATM 14 O O3' GDP . . . E 2 15.85 -7.641 17.392 1 24.33 ? O3' GDP 201 B 1 HETATM 15 C C2' GDP . . . E 2 17.334 -6.296 16.161 1 24.28 ? C2' GDP 201 B 1 HETATM 16 O O2' GDP . . . E 2 18.094 -7.486 16.051 1 25.98 ? O2' GDP 201 B 1 HETATM 17 C C1' GDP . . . E 2 16.372 -6.211 14.975 1 20.63 ? C1' GDP 201 B 1 HETATM 18 N N9 GDP . . . E 2 16.99 -5.492 13.841 1 16.98 ? N9 GDP 201 B 1 HETATM 19 C C8 GDP . . . E 2 17.589 -4.275 13.907 1 16.89 ? C8 GDP 201 B 1 HETATM 20 N N7 GDP . . . E 2 17.958 -3.846 12.69 1 17.68 ? N7 GDP 201 B 1 HETATM 21 C C5 GDP . . . E 2 17.667 -4.865 11.83 1 16.21 ? C5 GDP 201 B 1 HETATM 22 C C6 GDP . . . E 2 17.882 -5.145 10.417 1 19.04 ? C6 GDP 201 B 1 HETATM 23 O O6 GDP . . . E 2 18.392 -4.301 9.632 1 18.19 ? O6 GDP 201 B 1 HETATM 24 N N1 GDP . . . E 2 17.438 -6.317 9.931 1 17.46 ? N1 GDP 201 B 1 HETATM 25 C C2 GDP . . . E 2 16.849 -7.259 10.699 1 16.63 ? C2 GDP 201 B 1 HETATM 26 N N2 GDP . . . E 2 16.458 -8.397 10.098 1 16.86 ? N2 GDP 201 B 1 HETATM 27 N N3 GDP . . . E 2 16.638 -7.065 11.997 1 16.87 ? N3 GDP 201 B 1 HETATM 28 C C4 GDP . . . E 2 17.066 -5.948 12.603 1 18.32 ? C4 GDP 201 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #