data_7RP4 # _model_server_result.job_id Vb7JT7XUxRIKgssa2RC03A _model_server_result.datetime_utc '2024-10-15 14:28:01' _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 7rp4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":202}' # _entry.id 7RP4 # _exptl.entry_id 7RP4 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 88.97 _cell.angle_beta 84.94 _cell.angle_gamma 80.01 _cell.entry_id 7RP4 _cell.length_a 33.586 _cell.length_b 43.985 _cell.length_c 65.305 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RP4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 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,E,J 1 1 B,F,G,H,I,K 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 ? 3 D N N ? 3 G 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 covale ? covale1 A SG CYS 13 A CYS 12 1_555 C C MKZ . A MKZ 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? covale ? covale2 B SG CYS 13 B CYS 12 1_555 F C MKZ . B MKZ 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.824 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc2 D O2B GDP . A GDP 202 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc3 E MG MG . A MG 203 1_555 J O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc4 E MG MG . A MG 203 1_555 J O HOH . A HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc5 E MG MG . A MG 203 1_555 J O HOH . A HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc6 E MG MG . A MG 203 1_555 J O HOH . A HOH 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc7 B OG SER 18 B SER 17 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc8 G O1B GDP . B GDP 202 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc9 H MG MG . B MG 203 1_555 K O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc10 H MG MG . B MG 203 1_555 K O HOH . B HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc11 H MG MG . B MG 203 1_555 K O HOH . B HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc12 H MG MG . B MG 203 1_555 K O HOH . B HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? # _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 7RP4 _atom_sites.fract_transf_matrix[1][1] 0.029774 _atom_sites.fract_transf_matrix[1][2] -0.005244 _atom_sites.fract_transf_matrix[1][3] -0.002623 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023085 _atom_sites.fract_transf_matrix[2][3] -0.000063 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015373 _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 MKZ A 1 201 1 MKZ LIG . D 3 GDP A 1 202 3 GDP GDP . E 4 MG A 1 203 5 MG MG . F 2 MKZ B 1 201 2 MKZ LIG . G 3 GDP B 1 202 4 GDP GDP . H 4 MG B 1 203 6 MG MG . I 5 GOL B 1 204 1 GOL GOL . J 6 HOH A 1 301 115 HOH HOH . J 6 HOH A 2 302 51 HOH WAT . J 6 HOH A 3 303 114 HOH HOH . J 6 HOH A 4 304 78 HOH HOH . J 6 HOH A 5 305 161 HOH HOH . J 6 HOH A 6 306 143 HOH HOH . J 6 HOH A 7 307 81 HOH HOH . J 6 HOH A 8 308 71 HOH HOH . J 6 HOH A 9 309 80 HOH HOH . J 6 HOH A 10 310 58 HOH HOH . J 6 HOH A 11 311 25 HOH HOH . J 6 HOH A 12 312 2 HOH HOH . J 6 HOH A 13 313 134 HOH HOH . J 6 HOH A 14 314 137 HOH HOH . J 6 HOH A 15 315 17 HOH HOH . J 6 HOH A 16 316 11 HOH HOH . J 6 HOH A 17 317 13 HOH HOH . J 6 HOH A 18 318 52 HOH WAT . J 6 HOH A 19 319 119 HOH HOH . J 6 HOH A 20 320 23 HOH HOH . J 6 HOH A 21 321 52 HOH HOH . J 6 HOH A 22 322 36 HOH HOH . J 6 HOH A 23 323 53 HOH WAT . J 6 HOH A 24 324 65 HOH HOH . J 6 HOH A 25 325 6 HOH HOH . J 6 HOH A 26 326 10 HOH HOH . J 6 HOH A 27 327 151 HOH HOH . J 6 HOH A 28 328 69 HOH HOH . J 6 HOH A 29 329 42 HOH HOH . J 6 HOH A 30 330 93 HOH HOH . J 6 HOH A 31 331 16 HOH HOH . J 6 HOH A 32 332 122 HOH HOH . J 6 HOH A 33 333 54 HOH WAT . J 6 HOH A 34 334 85 HOH HOH . J 6 HOH A 35 335 127 HOH HOH . J 6 HOH A 36 336 63 HOH HOH . J 6 HOH A 37 337 120 HOH HOH . J 6 HOH A 38 338 147 HOH HOH . J 6 HOH A 39 339 64 HOH HOH . J 6 HOH A 40 340 110 HOH HOH . J 6 HOH A 41 341 123 HOH HOH . J 6 HOH A 42 342 61 HOH HOH . J 6 HOH A 43 343 88 HOH HOH . J 6 HOH A 44 344 89 HOH HOH . J 6 HOH A 45 345 5 HOH HOH . J 6 HOH A 46 346 155 HOH HOH . J 6 HOH A 47 347 39 HOH HOH . J 6 HOH A 48 348 138 HOH HOH . J 6 HOH A 49 349 26 HOH HOH . J 6 HOH A 50 350 86 HOH HOH . J 6 HOH A 51 351 107 HOH HOH . J 6 HOH A 52 352 100 HOH HOH . J 6 HOH A 53 353 9 HOH HOH . J 6 HOH A 54 354 90 HOH HOH . J 6 HOH A 55 355 156 HOH HOH . J 6 HOH A 56 356 96 HOH HOH . J 6 HOH A 57 357 159 HOH HOH . J 6 HOH A 58 358 144 HOH HOH . J 6 HOH A 59 359 98 HOH HOH . J 6 HOH A 60 360 148 HOH HOH . J 6 HOH A 61 361 54 HOH HOH . J 6 HOH A 62 362 35 HOH HOH . J 6 HOH A 63 363 132 HOH HOH . J 6 HOH A 64 364 130 HOH HOH . J 6 HOH A 65 365 24 HOH HOH . J 6 HOH A 66 366 125 HOH HOH . J 6 HOH A 67 367 152 HOH HOH . J 6 HOH A 68 368 53 HOH HOH . J 6 HOH A 69 369 158 HOH HOH . J 6 HOH A 70 370 111 HOH HOH . J 6 HOH A 71 371 106 HOH HOH . J 6 HOH A 72 372 128 HOH HOH . J 6 HOH A 73 373 50 HOH HOH . J 6 HOH A 74 374 149 HOH HOH . J 6 HOH A 75 375 94 HOH HOH . J 6 HOH A 76 376 157 HOH HOH . K 6 HOH B 1 301 97 HOH HOH . K 6 HOH B 2 302 34 HOH HOH . K 6 HOH B 3 303 61 HOH WAT . K 6 HOH B 4 304 99 HOH HOH . K 6 HOH B 5 305 8 HOH HOH . K 6 HOH B 6 306 59 HOH HOH . K 6 HOH B 7 307 41 HOH HOH . K 6 HOH B 8 308 84 HOH HOH . K 6 HOH B 9 309 49 HOH HOH . K 6 HOH B 10 310 79 HOH HOH . K 6 HOH B 11 311 64 HOH WAT . K 6 HOH B 12 312 124 HOH HOH . K 6 HOH B 13 313 51 HOH HOH . K 6 HOH B 14 314 4 HOH HOH . K 6 HOH B 15 315 12 HOH HOH . K 6 HOH B 16 316 62 HOH WAT . K 6 HOH B 17 317 60 HOH HOH . K 6 HOH B 18 318 63 HOH WAT . K 6 HOH B 19 319 91 HOH HOH . K 6 HOH B 20 320 103 HOH HOH . K 6 HOH B 21 321 43 HOH HOH . K 6 HOH B 22 322 31 HOH HOH . K 6 HOH B 23 323 27 HOH HOH . K 6 HOH B 24 324 145 HOH HOH . K 6 HOH B 25 325 75 HOH HOH . K 6 HOH B 26 326 3 HOH HOH . K 6 HOH B 27 327 109 HOH HOH . K 6 HOH B 28 328 29 HOH HOH . K 6 HOH B 29 329 40 HOH HOH . K 6 HOH B 30 330 37 HOH HOH . K 6 HOH B 31 331 14 HOH HOH . K 6 HOH B 32 332 48 HOH HOH . K 6 HOH B 33 333 73 HOH HOH . K 6 HOH B 34 334 95 HOH HOH . K 6 HOH B 35 335 44 HOH HOH . K 6 HOH B 36 336 56 HOH HOH . K 6 HOH B 37 337 72 HOH HOH . K 6 HOH B 38 338 15 HOH HOH . K 6 HOH B 39 339 7 HOH HOH . K 6 HOH B 40 340 153 HOH HOH . K 6 HOH B 41 341 55 HOH HOH . K 6 HOH B 42 342 68 HOH HOH . K 6 HOH B 43 343 82 HOH HOH . K 6 HOH B 44 344 70 HOH HOH . K 6 HOH B 45 345 116 HOH HOH . K 6 HOH B 46 346 141 HOH HOH . K 6 HOH B 47 347 62 HOH HOH . K 6 HOH B 48 348 135 HOH HOH . K 6 HOH B 49 349 142 HOH HOH . K 6 HOH B 50 350 113 HOH HOH . K 6 HOH B 51 351 101 HOH HOH . K 6 HOH B 52 352 118 HOH HOH . K 6 HOH B 53 353 22 HOH HOH . K 6 HOH B 54 354 30 HOH HOH . K 6 HOH B 55 355 108 HOH HOH . K 6 HOH B 56 356 126 HOH HOH . K 6 HOH B 57 357 87 HOH HOH . K 6 HOH B 58 358 133 HOH HOH . K 6 HOH B 59 359 139 HOH HOH . K 6 HOH B 60 360 45 HOH HOH . K 6 HOH B 61 361 160 HOH HOH . K 6 HOH B 62 362 140 HOH HOH . K 6 HOH B 63 363 121 HOH HOH . K 6 HOH B 64 364 129 HOH HOH . K 6 HOH B 65 365 154 HOH HOH . K 6 HOH B 66 366 32 HOH HOH . K 6 HOH B 67 367 18 HOH HOH . K 6 HOH B 68 368 66 HOH HOH . K 6 HOH B 69 369 104 HOH HOH . K 6 HOH B 70 370 131 HOH HOH . K 6 HOH B 71 371 83 HOH HOH . K 6 HOH B 72 372 150 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 . . . G 3 35.495 2.13 -19.939 1 35.52 ? PB GDP 202 B 1 HETATM 2 O O1B GDP . . . G 3 35.622 2.846 -21.262 1 42.02 ? O1B GDP 202 B 1 HETATM 3 O O2B GDP . . . G 3 34.49 2.838 -19.06 1 36.95 ? O2B GDP 202 B 1 HETATM 4 O O3B GDP . . . G 3 36.835 2.115 -19.246 1 34.75 ? O3B GDP 202 B 1 HETATM 5 O O3A GDP . . . G 3 34.991 0.619 -20.173 1 33.96 ? O3A GDP 202 B 1 HETATM 6 P PA GDP . . . G 3 35.499 -0.262 -21.422 1 33.49 ? PA GDP 202 B 1 HETATM 7 O O1A GDP . . . G 3 34.645 0.012 -22.635 1 32.83 ? O1A GDP 202 B 1 HETATM 8 O O2A GDP . . . G 3 36.957 -0.014 -21.72 1 31.46 ? O2A GDP 202 B 1 HETATM 9 O O5' GDP . . . G 3 35.255 -1.766 -20.903 1 39.08 ? O5' GDP 202 B 1 HETATM 10 C C5' GDP . . . G 3 36.292 -2.475 -20.227 1 41.62 ? C5' GDP 202 B 1 HETATM 11 C C4' GDP . . . G 3 36.038 -3.973 -20.33 1 42.27 ? C4' GDP 202 B 1 HETATM 12 O O4' GDP . . . G 3 34.666 -4.264 -20.055 1 40.11 ? O4' GDP 202 B 1 HETATM 13 C C3' GDP . . . G 3 36.336 -4.47 -21.733 1 43.46 ? C3' GDP 202 B 1 HETATM 14 O O3' GDP . . . G 3 37.378 -5.447 -21.677 1 47.47 ? O3' GDP 202 B 1 HETATM 15 C C2' GDP . . . G 3 35.058 -5.106 -22.236 1 41.88 ? C2' GDP 202 B 1 HETATM 16 O O2' GDP . . . G 3 35.326 -6.41 -22.762 1 43.9 ? O2' GDP 202 B 1 HETATM 17 C C1' GDP . . . G 3 34.148 -5.185 -21.02 1 40.16 ? C1' GDP 202 B 1 HETATM 18 N N9 GDP . . . G 3 32.75 -4.825 -21.37 1 37.26 ? N9 GDP 202 B 1 HETATM 19 C C8 GDP . . . G 3 32.281 -3.585 -21.608 1 34.97 ? C8 GDP 202 B 1 HETATM 20 N N7 GDP . . . G 3 30.953 -3.611 -21.89 1 34.62 ? N7 GDP 202 B 1 HETATM 21 C C5 GDP . . . G 3 30.551 -4.894 -21.827 1 35.97 ? C5 GDP 202 B 1 HETATM 22 C C6 GDP . . . G 3 29.278 -5.63 -22.012 1 37.32 ? C6 GDP 202 B 1 HETATM 23 O O6 GDP . . . G 3 28.222 -5.03 -22.306 1 38.12 ? O6 GDP 202 B 1 HETATM 24 N N1 GDP . . . G 3 29.295 -6.961 -21.855 1 38.07 ? N1 GDP 202 B 1 HETATM 25 C C2 GDP . . . G 3 30.417 -7.635 -21.538 1 37.95 ? C2 GDP 202 B 1 HETATM 26 N N2 GDP . . . G 3 30.353 -8.981 -21.398 1 39.66 ? N2 GDP 202 B 1 HETATM 27 N N3 GDP . . . G 3 31.614 -7.026 -21.352 1 37.26 ? N3 GDP 202 B 1 HETATM 28 C C4 GDP . . . G 3 31.739 -5.686 -21.481 1 36.81 ? C4 GDP 202 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #