data_7Q9U # _model_server_result.job_id zL0UDEcbEtc2FwJjWH_AaQ _model_server_result.datetime_utc '2024-11-22 21:07:00' _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 7q9u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":202}' # _entry.id 7Q9U # _exptl.entry_id 7Q9U _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 82.771 _cell.angle_beta 81.709 _cell.angle_gamma 68.447 _cell.entry_id 7Q9U _cell.length_a 51.086 _cell.length_b 57.925 _cell.length_c 78.913 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Q9U _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_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,F,Q 1 1 B,G,H,I,R 2 1 C,J,K,L,S 3 1 D,M,N,O,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 E N N ? 3 H 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 C ILE 184 AAA ILE 184 1_555 A N CMT 185 AAA CMT 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.267 ? covale ? covale2 A SG CMT 185 AAA CMT 185 1_555 F C1 FAR . AAA FAR 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.622 ? covale ? covale3 B C ILE 184 BBB ILE 184 1_555 B N CMT 185 BBB CMT 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.264 ? covale ? covale4 B SG CMT 185 BBB CMT 185 1_555 I C1 FAR . BBB FAR 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? # _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 148 n n PB O2B GDP sing 149 n n PB O3B GDP sing 150 n n PB O3A GDP sing 151 n n O2B HOB2 GDP sing 152 n n O3B HOB3 GDP sing 153 n n O3A PA GDP sing 154 n n PA O1A GDP doub 155 n n PA O2A GDP sing 156 n n PA O5' GDP sing 157 n n O2A HOA2 GDP sing 158 n n O5' C5' GDP sing 159 n n C5' C4' GDP sing 160 n n C5' H5' GDP sing 161 n n C5' "H5''" GDP sing 162 n n C4' O4' GDP sing 163 n n C4' C3' GDP sing 164 n n C4' H4' GDP sing 165 n n O4' C1' GDP sing 166 n n C3' O3' GDP sing 167 n n C3' C2' GDP sing 168 n n C3' H3' GDP sing 169 n n O3' HO3' GDP sing 170 n n C2' O2' GDP sing 171 n n C2' C1' GDP sing 172 n n C2' H2' GDP sing 173 n n O2' HO2' GDP sing 174 n n C1' N9 GDP sing 175 n n C1' H1' GDP sing 176 n n N9 C8 GDP sing 177 n y N9 C4 GDP sing 178 n y C8 N7 GDP doub 179 n y C8 H8 GDP sing 180 n n N7 C5 GDP sing 181 n y C5 C6 GDP sing 182 n n C5 C4 GDP doub 183 n y C6 O6 GDP doub 184 n n C6 N1 GDP sing 185 n n N1 C2 GDP sing 186 n n N1 HN1 GDP sing 187 n n C2 N2 GDP sing 188 n n C2 N3 GDP doub 189 n n N2 HN21 GDP sing 190 n n N2 HN22 GDP sing 191 n n N3 C4 GDP sing 192 n n # _atom_sites.entry_id 7Q9U _atom_sites.fract_transf_matrix[1][1] 0.019575 _atom_sites.fract_transf_matrix[1][2] -0.007732 _atom_sites.fract_transf_matrix[1][3] -0.002247 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018562 _atom_sites.fract_transf_matrix[2][3] -0.001474 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012846 _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 GDP AAA 1 201 2 GDP GDP . F 4 FAR AAA 1 202 1 FAR FAR . G 5 SO4 BBB 1 201 201 SO4 SO4 . H 3 GDP BBB 1 202 1 GDP GDP . I 4 FAR BBB 1 203 2 FAR FAR . J 5 SO4 DDD 1 201 201 SO4 SO4 . K 6 EDO DDD 1 202 301 EDO EDO . L 6 EDO DDD 1 203 401 EDO EDO . M 5 SO4 CCC 1 201 201 SO4 SO4 . N 6 EDO CCC 1 202 301 EDO EDO . O 6 EDO CCC 1 203 401 EDO EDO . P 6 EDO CCC 1 204 501 EDO EDO . Q 7 HOH AAA 1 301 92 HOH HOH . Q 7 HOH AAA 2 302 13 HOH HOH . Q 7 HOH AAA 3 303 146 HOH HOH . Q 7 HOH AAA 4 304 105 HOH HOH . Q 7 HOH AAA 5 305 139 HOH HOH . Q 7 HOH AAA 6 306 34 HOH HOH . Q 7 HOH AAA 7 307 103 HOH HOH . Q 7 HOH AAA 8 308 61 HOH HOH . Q 7 HOH AAA 9 309 9 HOH HOH . Q 7 HOH AAA 10 310 47 HOH HOH . Q 7 HOH AAA 11 311 84 HOH HOH . Q 7 HOH AAA 12 312 72 HOH HOH . Q 7 HOH AAA 13 313 113 HOH HOH . Q 7 HOH AAA 14 314 80 HOH HOH . Q 7 HOH AAA 15 315 18 HOH HOH . Q 7 HOH AAA 16 316 11 HOH HOH . Q 7 HOH AAA 17 317 77 HOH HOH . Q 7 HOH AAA 18 318 101 HOH HOH . Q 7 HOH AAA 19 319 65 HOH HOH . Q 7 HOH AAA 20 320 12 HOH HOH . Q 7 HOH AAA 21 321 143 HOH HOH . Q 7 HOH AAA 22 322 123 HOH HOH . Q 7 HOH AAA 23 323 148 HOH HOH . Q 7 HOH AAA 24 324 57 HOH HOH . Q 7 HOH AAA 25 325 120 HOH HOH . Q 7 HOH AAA 26 326 131 HOH HOH . Q 7 HOH AAA 27 327 22 HOH HOH . Q 7 HOH AAA 28 328 132 HOH HOH . Q 7 HOH AAA 29 329 108 HOH HOH . Q 7 HOH AAA 30 330 157 HOH HOH . Q 7 HOH AAA 31 331 154 HOH HOH . Q 7 HOH AAA 32 332 19 HOH HOH . R 7 HOH BBB 1 301 136 HOH HOH . R 7 HOH BBB 2 302 128 HOH HOH . R 7 HOH BBB 3 303 155 HOH HOH . R 7 HOH BBB 4 304 38 HOH HOH . R 7 HOH BBB 5 305 42 HOH HOH . R 7 HOH BBB 6 306 121 HOH HOH . R 7 HOH BBB 7 307 127 HOH HOH . R 7 HOH BBB 8 308 5 HOH HOH . R 7 HOH BBB 9 309 55 HOH HOH . R 7 HOH BBB 10 310 2 HOH HOH . R 7 HOH BBB 11 311 21 HOH HOH . R 7 HOH BBB 12 312 62 HOH HOH . R 7 HOH BBB 13 313 99 HOH HOH . R 7 HOH BBB 14 314 64 HOH HOH . R 7 HOH BBB 15 315 142 HOH HOH . R 7 HOH BBB 16 316 27 HOH HOH . R 7 HOH BBB 17 317 119 HOH HOH . R 7 HOH BBB 18 318 25 HOH HOH . R 7 HOH BBB 19 319 7 HOH HOH . R 7 HOH BBB 20 320 23 HOH HOH . R 7 HOH BBB 21 321 97 HOH HOH . R 7 HOH BBB 22 322 63 HOH HOH . R 7 HOH BBB 23 323 76 HOH HOH . R 7 HOH BBB 24 324 70 HOH HOH . R 7 HOH BBB 25 325 56 HOH HOH . R 7 HOH BBB 26 326 110 HOH HOH . R 7 HOH BBB 27 327 14 HOH HOH . R 7 HOH BBB 28 328 134 HOH HOH . R 7 HOH BBB 29 329 75 HOH HOH . R 7 HOH BBB 30 330 28 HOH HOH . R 7 HOH BBB 31 331 116 HOH HOH . R 7 HOH BBB 32 332 59 HOH HOH . R 7 HOH BBB 33 333 41 HOH HOH . R 7 HOH BBB 34 334 46 HOH HOH . R 7 HOH BBB 35 335 48 HOH HOH . R 7 HOH BBB 36 336 58 HOH HOH . R 7 HOH BBB 37 337 114 HOH HOH . R 7 HOH BBB 38 338 66 HOH HOH . R 7 HOH BBB 39 339 117 HOH HOH . R 7 HOH BBB 40 340 53 HOH HOH . R 7 HOH BBB 41 341 67 HOH HOH . R 7 HOH BBB 42 342 69 HOH HOH . R 7 HOH BBB 43 343 88 HOH HOH . R 7 HOH BBB 44 344 24 HOH HOH . R 7 HOH BBB 45 345 43 HOH HOH . S 7 HOH DDD 1 301 94 HOH HOH . S 7 HOH DDD 2 302 50 HOH HOH . S 7 HOH DDD 3 303 107 HOH HOH . S 7 HOH DDD 4 304 78 HOH HOH . S 7 HOH DDD 5 305 30 HOH HOH . S 7 HOH DDD 6 306 33 HOH HOH . S 7 HOH DDD 7 307 4 HOH HOH . S 7 HOH DDD 8 308 79 HOH HOH . S 7 HOH DDD 9 309 124 HOH HOH . S 7 HOH DDD 10 310 15 HOH HOH . S 7 HOH DDD 11 311 86 HOH HOH . S 7 HOH DDD 12 312 152 HOH HOH . S 7 HOH DDD 13 313 37 HOH HOH . S 7 HOH DDD 14 314 36 HOH HOH . S 7 HOH DDD 15 315 156 HOH HOH . S 7 HOH DDD 16 316 31 HOH HOH . S 7 HOH DDD 17 317 90 HOH HOH . S 7 HOH DDD 18 318 102 HOH HOH . S 7 HOH DDD 19 319 130 HOH HOH . S 7 HOH DDD 20 320 17 HOH HOH . S 7 HOH DDD 21 321 151 HOH HOH . S 7 HOH DDD 22 322 141 HOH HOH . S 7 HOH DDD 23 323 150 HOH HOH . S 7 HOH DDD 24 324 104 HOH HOH . S 7 HOH DDD 25 325 89 HOH HOH . S 7 HOH DDD 26 326 129 HOH HOH . S 7 HOH DDD 27 327 87 HOH HOH . S 7 HOH DDD 28 328 16 HOH HOH . S 7 HOH DDD 29 329 122 HOH HOH . T 7 HOH CCC 1 301 83 HOH HOH . T 7 HOH CCC 2 302 20 HOH HOH . T 7 HOH CCC 3 303 51 HOH HOH . T 7 HOH CCC 4 304 39 HOH HOH . T 7 HOH CCC 5 305 144 HOH HOH . T 7 HOH CCC 6 306 106 HOH HOH . T 7 HOH CCC 7 307 147 HOH HOH . T 7 HOH CCC 8 308 96 HOH HOH . T 7 HOH CCC 9 309 54 HOH HOH . T 7 HOH CCC 10 310 32 HOH HOH . T 7 HOH CCC 11 311 6 HOH HOH . T 7 HOH CCC 12 312 10 HOH HOH . T 7 HOH CCC 13 313 45 HOH HOH . T 7 HOH CCC 14 314 1 HOH HOH . T 7 HOH CCC 15 315 35 HOH HOH . T 7 HOH CCC 16 316 118 HOH HOH . T 7 HOH CCC 17 317 153 HOH HOH . T 7 HOH CCC 18 318 85 HOH HOH . T 7 HOH CCC 19 319 3 HOH HOH . T 7 HOH CCC 20 320 133 HOH HOH . T 7 HOH CCC 21 321 52 HOH HOH . T 7 HOH CCC 22 322 73 HOH HOH . T 7 HOH CCC 23 323 137 HOH HOH . T 7 HOH CCC 24 324 125 HOH HOH . T 7 HOH CCC 25 325 26 HOH HOH . T 7 HOH CCC 26 326 100 HOH HOH . T 7 HOH CCC 27 327 111 HOH HOH . T 7 HOH CCC 28 328 74 HOH HOH . T 7 HOH CCC 29 329 115 HOH HOH . T 7 HOH CCC 30 330 138 HOH HOH . T 7 HOH CCC 31 331 81 HOH HOH . T 7 HOH CCC 32 332 60 HOH HOH . T 7 HOH CCC 33 333 49 HOH HOH . T 7 HOH CCC 34 334 145 HOH HOH . T 7 HOH CCC 35 335 112 HOH HOH . T 7 HOH CCC 36 336 93 HOH HOH . T 7 HOH CCC 37 337 29 HOH HOH . T 7 HOH CCC 38 338 8 HOH HOH . T 7 HOH CCC 39 339 44 HOH HOH . T 7 HOH CCC 40 340 135 HOH HOH . T 7 HOH CCC 41 341 149 HOH HOH . T 7 HOH CCC 42 342 68 HOH HOH . T 7 HOH CCC 43 343 91 HOH HOH . T 7 HOH CCC 44 344 109 HOH HOH . T 7 HOH CCC 45 345 140 HOH HOH . T 7 HOH CCC 46 346 82 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 . . . H 3 23.328 65.442 68.548 1 44.66 ? PB GDP 202 BBB 1 HETATM 2 O O1B GDP . . . H 3 22.795 66.67 67.847 1 41.29 ? O1B GDP 202 BBB 1 HETATM 3 O O2B GDP . . . H 3 23.837 65.674 69.949 1 44.24 ? O2B GDP 202 BBB 1 HETATM 4 O O3B GDP . . . H 3 22.396 64.25 68.548 1 45.79 ? O3B GDP 202 BBB 1 HETATM 5 O O3A GDP . . . H 3 24.521 64.974 67.575 1 46.7 ? O3A GDP 202 BBB 1 HETATM 6 P PA GDP . . . H 3 25.138 65.781 66.323 1 43.79 ? PA GDP 202 BBB 1 HETATM 7 O O1A GDP . . . H 3 24.254 65.989 65.12 1 47.77 ? O1A GDP 202 BBB 1 HETATM 8 O O2A GDP . . . H 3 25.92 66.894 66.983 1 42.76 ? O2A GDP 202 BBB 1 HETATM 9 O O5' GDP . . . H 3 26.142 64.66 65.75 1 45.58 ? O5' GDP 202 BBB 1 HETATM 10 C C5' GDP . . . H 3 27.126 64.089 66.611 1 43.14 ? C5' GDP 202 BBB 1 HETATM 11 C C4' GDP . . . H 3 28.362 63.733 65.79 1 48.61 ? C4' GDP 202 BBB 1 HETATM 12 O O4' GDP . . . H 3 28.138 62.547 65.025 1 46.39 ? O4' GDP 202 BBB 1 HETATM 13 C C3' GDP . . . H 3 28.803 64.804 64.799 1 49.65 ? C3' GDP 202 BBB 1 HETATM 14 O O3' GDP . . . H 3 30.215 64.776 64.576 1 51.16 ? O3' GDP 202 BBB 1 HETATM 15 C C2' GDP . . . H 3 28.207 64.343 63.475 1 52.88 ? C2' GDP 202 BBB 1 HETATM 16 O O2' GDP . . . H 3 28.92 64.817 62.326 1 57.01 ? O2' GDP 202 BBB 1 HETATM 17 C C1' GDP . . . H 3 28.22 62.827 63.629 1 47.35 ? C1' GDP 202 BBB 1 HETATM 18 N N9 GDP . . . H 3 27.092 62.282 62.836 1 46.77 ? N9 GDP 202 BBB 1 HETATM 19 C C8 GDP . . . H 3 25.811 62.672 62.863 1 50.76 ? C8 GDP 202 BBB 1 HETATM 20 N N7 GDP . . . H 3 25.044 62.019 61.962 1 51.31 ? N7 GDP 202 BBB 1 HETATM 21 C C5 GDP . . . H 3 25.869 61.154 61.338 1 50.59 ? C5 GDP 202 BBB 1 HETATM 22 C C6 GDP . . . H 3 25.716 60.137 60.264 1 53.47 ? C6 GDP 202 BBB 1 HETATM 23 O O6 GDP . . . H 3 24.6 59.928 59.735 1 49.73 ? O6 GDP 202 BBB 1 HETATM 24 N N1 GDP . . . H 3 26.842 59.501 59.916 1 55.3 ? N1 GDP 202 BBB 1 HETATM 25 C C2 GDP . . . H 3 28.046 59.715 60.465 1 55.28 ? C2 GDP 202 BBB 1 HETATM 26 N N2 GDP . . . H 3 29.105 58.998 60.018 1 53.42 ? N2 GDP 202 BBB 1 HETATM 27 N N3 GDP . . . H 3 28.28 60.605 61.455 1 53.43 ? N3 GDP 202 BBB 1 HETATM 28 C C4 GDP . . . H 3 27.232 61.335 61.907 1 51.13 ? C4 GDP 202 BBB 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #