data_6B0C # _model_server_result.job_id 63EGNby_DjIiBVxsjLk-KQ _model_server_result.datetime_utc '2025-07-05 14:20:38' _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 6b0c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 6B0C # _exptl.entry_id 6B0C _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 ? # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 175-meric 175 'representative helical assembly' 1 ? pentameric 5 'helical asymmetric unit' 2 ? pentameric 5 'helical asymmetric unit, std helical frame' 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N 1 (1-35) A,B,C,D,E,F,G,H,I,J,K,L,M,N 2 27 A,B,C,D,E,F,G,H,I,J,K,L,M,N 3 H # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'helical symmetry operation' ? ? 0.923966 -0.382474 0 0.382474 0.923966 0 0 0 1 151.52938 -101.27356 -94.69 2 'helical symmetry operation' ? ? 0.999729 0.023298 0 -0.023298 0.999729 0 0 0 1 -7.60992 7.78933 -83.55 3 'helical symmetry operation' ? ? 0.905146 0.4251 0 -0.4251 0.905146 0 0 0 1 -109.14117 171.8364 -72.41 4 'helical symmetry operation' ? ? 0.656336 0.754469 0 -0.754469 0.656336 0 0 0 1 -135.76437 362.91554 -61.27 5 'helical symmetry operation' ? ? 0.295691 0.955284 0 -0.955284 0.295691 0 0 0 1 -82.94319 548.46865 -50.13 6 'helical symmetry operation' ? ? -0.115336 0.993327 0 -0.993327 -0.115336 0 0 0 1 40.32214 696.8792 -38.99 7 'helical symmetry operation' ? ? -0.506711 0.862116 0 -0.862116 -0.506711 0 0 0 1 213.02835 782.85942 -27.85 8 'helical symmetry operation' ? ? -0.811747 0.584009 0 -0.584009 -0.811747 0 0 0 1 405.74792 791.75907 -16.71 9 'helical symmetry operation' ? ? -0.978469 0.206392 0 -0.206392 -0.978469 0 0 0 1 585.64321 722.06174 -5.57 10 'helical symmetry operation' ? ? -0.978469 -0.206392 0 0.206392 -0.978469 0 0 0 1 722.06174 585.64321 5.57 11 'helical symmetry operation' ? ? -0.811747 -0.584009 0 0.584009 -0.811747 0 0 0 1 791.75907 405.74792 16.71 12 'helical symmetry operation' ? ? -0.506711 -0.862116 0 0.862116 -0.506711 0 0 0 1 782.85942 213.02835 27.85 13 'helical symmetry operation' ? ? -0.115336 -0.993327 0 0.993327 -0.115336 0 0 0 1 696.8792 40.32214 38.99 14 'helical symmetry operation' ? ? 0.295691 -0.955284 0 0.955284 0.295691 0 0 0 1 548.46865 -82.94319 50.13 15 'helical symmetry operation' ? ? 0.656336 -0.754469 0 0.754469 0.656336 0 0 0 1 362.91554 -135.76437 61.27 16 'helical symmetry operation' ? ? 0.905146 -0.4251 0 0.4251 0.905146 0 0 0 1 171.8364 -109.14117 72.41 17 'helical symmetry operation' ? ? 0.999729 -0.023298 0 0.023298 0.999729 0 0 0 1 7.78933 -7.60992 83.55 18 'helical symmetry operation' ? ? 0.923966 0.382474 0 -0.382474 0.923966 0 0 0 1 -101.27356 151.52938 94.69 19 'helical symmetry operation' ? ? -0.983012 0.18354 0 -0.18354 -0.983012 0 0 0 1 594.69694 716.01075 -89.12 20 'helical symmetry operation' ? ? -0.973395 -0.229132 0 0.229132 -0.973395 0 0 0 1 727.90016 576.45095 -77.98 21 'helical symmetry operation' ? ? -0.797921 -0.602762 0 0.602762 -0.797921 0 0 0 1 793.38737 394.98068 -66.84 22 'helical symmetry operation' ? ? -0.486488 -0.873687 0 0.873687 -0.486488 0 0 0 1 780.00014 202.52078 -55.7 23 'helical symmetry operation' ? ? -0.092162 -0.995744 0 0.995744 -0.092162 0 0 0 1 690.01955 31.86461 -44.56 24 'helical symmetry operation' ? ? 0.317867 -0.948135 0 0.948135 0.317867 0 0 0 1 538.77744 -87.90958 -33.42 25 'helical symmetry operation' ? ? 0.673735 -0.738973 0 0.738973 0.673735 0 0 0 1 352.04407 -136.39341 -22.28 26 'helical symmetry operation' ? ? 0.914805 -0.403897 0 0.403897 0.914805 0 0 0 1 161.63706 -105.32566 -11.14 27 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 28 'helical symmetry operation' ? ? 0.914805 0.403897 0 -0.403897 0.914805 0 0 0 1 -105.32566 161.63706 11.14 29 'helical symmetry operation' ? ? 0.673735 0.738973 0 -0.738973 0.673735 0 0 0 1 -136.39341 352.04407 22.28 30 'helical symmetry operation' ? ? 0.317867 0.948135 0 -0.948135 0.317867 0 0 0 1 -87.90958 538.77744 33.42 31 'helical symmetry operation' ? ? -0.092162 0.995744 0 -0.995744 -0.092162 0 0 0 1 31.86461 690.01955 44.56 32 'helical symmetry operation' ? ? -0.486488 0.873687 0 -0.873687 -0.486488 0 0 0 1 202.52078 780.00014 55.7 33 'helical symmetry operation' ? ? -0.797921 0.602762 0 -0.602762 -0.797921 0 0 0 1 394.98068 793.38737 66.84 34 'helical symmetry operation' ? ? -0.973395 0.229132 0 -0.229132 -0.973395 0 0 0 1 576.45095 727.90016 77.98 35 'helical symmetry operation' ? ? -0.983012 -0.18354 0 0.18354 -0.983012 0 0 0 1 716.01075 594.69694 89.12 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 H N N ? 6 K 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 OE2 GLU 71 A GLU 71 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.924 ? metalc ? metalc2 F O3G GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc3 F O3B GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc4 F O1B GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc5 C OE1 GLU 71 C GLU 71 1_555 J MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc6 I O1G GTP . C GTP 501 1_555 J MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc7 E OG SER 247 K SER 488 1_555 M MG MG . K MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc8 M MG MG . K MG 701 1_555 N O1G ANP . K ANP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc9 M MG MG . K MG 701 1_555 N O3G ANP . K ANP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc10 M MG MG . K MG 701 1_555 N O2B ANP . K ANP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? # _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 133 n n PB O2B GDP sing 134 n n PB O3B GDP sing 135 n n PB O3A GDP sing 136 n n O2B HOB2 GDP sing 137 n n O3B HOB3 GDP sing 138 n n O3A PA GDP sing 139 n n PA O1A GDP doub 140 n n PA O2A GDP sing 141 n n PA O5' GDP sing 142 n n O2A HOA2 GDP sing 143 n n O5' C5' GDP sing 144 n n C5' C4' GDP sing 145 n n C5' H5' GDP sing 146 n n C5' "H5''" GDP sing 147 n n C4' O4' GDP sing 148 n n C4' C3' GDP sing 149 n n C4' H4' GDP sing 150 n n O4' C1' GDP sing 151 n n C3' O3' GDP sing 152 n n C3' C2' GDP sing 153 n n C3' H3' GDP sing 154 n n O3' HO3' GDP sing 155 n n C2' O2' GDP sing 156 n n C2' C1' GDP sing 157 n n C2' H2' GDP sing 158 n n O2' HO2' GDP sing 159 n n C1' N9 GDP sing 160 n n C1' H1' GDP sing 161 n n N9 C8 GDP sing 162 n y N9 C4 GDP sing 163 n y C8 N7 GDP doub 164 n y C8 H8 GDP sing 165 n n N7 C5 GDP sing 166 n y C5 C6 GDP sing 167 n n C5 C4 GDP doub 168 n y C6 O6 GDP doub 169 n n C6 N1 GDP sing 170 n n N1 C2 GDP sing 171 n n N1 HN1 GDP sing 172 n n C2 N2 GDP sing 173 n n C2 N3 GDP doub 174 n n N2 HN21 GDP sing 175 n n N2 HN22 GDP sing 176 n n N3 C4 GDP sing 177 n n # _atom_sites.entry_id 6B0C _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 4 GTP A 1 501 501 GTP GTP . G 5 MG A 1 502 502 MG MG . H 6 GDP B 1 501 501 GDP GDP . I 4 GTP C 1 501 501 GTP GTP . J 5 MG C 1 502 502 MG MG . K 6 GDP D 1 501 501 GDP GDP . L 7 TA1 D 1 502 502 TA1 TA1 . M 5 MG K 1 701 806 MG MG . N 8 ANP K 1 702 807 ANP ANP . # 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 . . . K 6 281.729 214.724 343.312 1 48.38 ? PB GDP 501 D 1 HETATM 2 O O1B GDP . . . K 6 280.593 213.823 342.916 1 48.38 ? O1B GDP 501 D 1 HETATM 3 O O2B GDP . . . K 6 281.292 216.142 343.1 1 48.38 ? O2B GDP 501 D 1 HETATM 4 O O3B GDP . . . K 6 282.007 214.505 344.769 1 48.38 ? O3B GDP 501 D 1 HETATM 5 O O3A GDP . . . K 6 282.98 214.432 342.352 1 48.38 ? O3A GDP 501 D 1 HETATM 6 P PA GDP . . . K 6 284.518 214.479 342.8 1 48.38 ? PA GDP 501 D 1 HETATM 7 O O1A GDP . . . K 6 285.171 215.704 342.24 1 48.38 ? O1A GDP 501 D 1 HETATM 8 O O2A GDP . . . K 6 284.765 214.394 344.276 1 48.38 ? O2A GDP 501 D 1 HETATM 9 O O5' GDP . . . K 6 285.18 213.205 342.104 1 48.38 ? O5' GDP 501 D 1 HETATM 10 C C5' GDP . . . K 6 286.145 212.479 342.852 1 48.38 ? C5' GDP 501 D 1 HETATM 11 C C4' GDP . . . K 6 287.412 212.344 342.032 1 48.38 ? C4' GDP 501 D 1 HETATM 12 O O4' GDP . . . K 6 287.525 213.468 341.171 1 48.38 ? O4' GDP 501 D 1 HETATM 13 C C3' GDP . . . K 6 288.624 212.383 342.936 1 48.38 ? C3' GDP 501 D 1 HETATM 14 O O3' GDP . . . K 6 289.34 211.156 342.818 1 48.38 ? O3' GDP 501 D 1 HETATM 15 C C2' GDP . . . K 6 289.501 213.497 342.428 1 48.38 ? C2' GDP 501 D 1 HETATM 16 O O2' GDP . . . K 6 290.798 212.965 342.191 1 48.38 ? O2' GDP 501 D 1 HETATM 17 C C1' GDP . . . K 6 288.877 213.903 341.119 1 48.38 ? C1' GDP 501 D 1 HETATM 18 N N9 GDP . . . K 6 288.939 215.366 340.95 1 48.38 ? N9 GDP 501 D 1 HETATM 19 C C8 GDP . . . K 6 288.468 216.295 341.787 1 48.38 ? C8 GDP 501 D 1 HETATM 20 N N7 GDP . . . K 6 288.689 217.538 341.298 1 48.38 ? N7 GDP 501 D 1 HETATM 21 C C5 GDP . . . K 6 289.314 217.402 340.121 1 48.38 ? C5 GDP 501 D 1 HETATM 22 C C6 GDP . . . K 6 289.835 218.299 339.077 1 48.38 ? C6 GDP 501 D 1 HETATM 23 O O6 GDP . . . K 6 289.747 219.532 339.192 1 48.38 ? O6 GDP 501 D 1 HETATM 24 N N1 GDP . . . K 6 290.42 217.765 338.009 1 48.38 ? N1 GDP 501 D 1 HETATM 25 C C2 GDP . . . K 6 290.536 216.445 337.866 1 48.38 ? C2 GDP 501 D 1 HETATM 26 N N2 GDP . . . K 6 291.13 215.962 336.759 1 48.38 ? N2 GDP 501 D 1 HETATM 27 N N3 GDP . . . K 6 290.074 215.561 338.774 1 48.38 ? N3 GDP 501 D 1 HETATM 28 C C4 GDP . . . K 6 289.475 215.974 339.903 1 48.38 ? C4 GDP 501 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #