data_9G0Q # _model_server_result.job_id 7YYo-3oe8tzey3VIh8mDdQ _model_server_result.datetime_utc '2025-01-18 05:07:27' _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 9g0q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":501}' # _entry.id 9G0Q # _exptl.entry_id 9G0Q _exptl.method 'ELECTRON MICROSCOPY' # _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 12-meric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q N N ? 3 R 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 G OE1 GLU 70 a GLU 70 1_555 T MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc2 S O1G GTP . a GTP 501 1_555 T MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc3 S O1B GTP . a GTP 501 1_555 T MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc4 H OE1 GLU 70 b GLU 70 1_555 V MG MG . b MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc5 U O1G GTP . b GTP 501 1_555 V MG MG . b MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc6 U O1B GTP . b GTP 501 1_555 V MG MG . b MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc7 I OE1 GLU 70 c GLU 70 1_555 X MG MG . c MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc8 W O1G GTP . c GTP 501 1_555 X MG MG . c MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc9 W O1B GTP . c GTP 501 1_555 X MG MG . c MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc10 J OE1 GLU 70 d GLU 70 1_555 Z MG MG . d MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc11 Y O1G GTP . d GTP 501 1_555 Z MG MG . d MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc12 Y O1B GTP . d GTP 501 1_555 Z MG MG . d MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc13 K OE1 GLU 70 e GLU 70 1_555 BA MG MG . e MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc14 AA O1G GTP . e GTP 501 1_555 BA MG MG . e MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc15 AA O1B GTP . e GTP 501 1_555 BA MG MG . e MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc16 L OE1 GLU 70 f GLU 70 1_555 DA MG MG . f MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc17 CA O1G GTP . f GTP 501 1_555 DA MG MG . f MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc18 CA O1B GTP . f GTP 501 1_555 DA MG MG . f MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? # _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 9G0Q _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 M 3 GDP A 1 501 501 GDP GDP . N 3 GDP B 1 501 501 GDP GDP . O 3 GDP C 1 501 501 GDP GDP . P 3 GDP D 1 501 501 GDP GDP . Q 3 GDP E 1 501 501 GDP GDP . R 3 GDP F 1 501 501 GDP GDP . S 4 GTP a 1 501 501 GTP GTP . T 5 MG a 1 502 502 MG MG . U 4 GTP b 1 501 501 GTP GTP . V 5 MG b 1 502 502 MG MG . W 4 GTP c 1 501 501 GTP GTP . X 5 MG c 1 502 502 MG MG . Y 4 GTP d 1 501 501 GTP GTP . Z 5 MG d 1 502 502 MG MG . AA 4 GTP e 1 501 501 GTP GTP . BA 5 MG e 1 502 502 MG MG . CA 4 GTP f 1 501 501 GTP GTP . DA 5 MG f 1 502 502 MG MG . # 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 . . . N 3 197.65 344.211 82.63 1 57.25 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . N 3 196.869 345.119 83.545 1 67.64 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . N 3 197.066 344.286 81.24 1 48.22 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . N 3 197.618 342.799 83.156 1 58.98 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . N 3 199.172 344.709 82.596 1 55.73 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . N 3 200.321 343.799 83.243 1 61.18 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . N 3 200.7 342.688 82.297 1 60.48 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . N 3 199.863 343.234 84.565 1 55.12 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . N 3 201.525 344.843 83.455 1 59.52 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . N 3 202.855 344.51 83.075 1 47.05 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . N 3 203.813 344.719 84.236 1 38.35 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . N 3 203.622 343.661 85.166 1 50.07 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . N 3 205.236 344.616 83.74 1 40.94 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . N 3 205.911 345.856 83.941 1 57.15 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . N 3 205.907 343.523 84.541 1 45.35 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . N 3 207.02 344.056 85.26 1 55.27 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . N 3 204.855 343.034 85.512 1 44.82 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . N 3 204.67 341.573 85.39 1 46.99 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . N 3 204.003 340.961 84.4 1 48.26 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . N 3 203.999 339.619 84.578 1 51.62 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . N 3 204.668 339.363 85.713 1 46.48 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . N 3 205.033 338.154 86.477 1 47.7 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . N 3 204.695 337.021 86.083 1 55.83 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . N 3 205.727 338.315 87.605 1 40.81 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . N 3 206.113 339.523 88.044 1 38.85 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . N 3 206.819 339.597 89.192 1 43.05 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . N 3 205.817 340.675 87.397 1 40.3 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . N 3 205.108 340.654 86.248 1 44.38 ? C4 GDP 501 B 1 HETATM 29 H H3 GDP . . . N 3 206.129 341.557 87.777 1 40.3 ? H3 GDP 501 B 1 HETATM 30 H H5' GDP . . . N 3 202.888 343.465 82.767 1 47.05 ? H5' GDP 501 B 1 HETATM 31 H "H5''" GDP . . . N 3 203.159 345.141 82.24 1 47.05 ? "H5''" GDP 501 B 1 HETATM 32 H H4' GDP . . . N 3 203.639 345.685 84.71 1 38.35 ? H4' GDP 501 B 1 HETATM 33 H H3' GDP . . . N 3 205.242 344.357 82.681 1 40.94 ? H3' GDP 501 B 1 HETATM 34 H HO3' GDP . . . N 3 206.86 345.714 83.902 1 57.15 ? HO3' GDP 501 B 1 HETATM 35 H H2' GDP . . . N 3 206.228 342.713 83.887 1 45.35 ? H2' GDP 501 B 1 HETATM 36 H HO2' GDP . . . N 3 206.867 343.962 86.203 1 55.27 ? HO2' GDP 501 B 1 HETATM 37 H H1' GDP . . . N 3 205.136 343.294 86.533 1 44.82 ? H1' GDP 501 B 1 HETATM 38 H H8 GDP . . . N 3 203.532 341.47 83.572 1 48.26 ? H8 GDP 501 B 1 HETATM 39 H HN21 GDP . . . N 3 207.05 338.754 89.698 1 43.05 ? HN21 GDP 501 B 1 HETATM 40 H HN22 GDP . . . N 3 207.116 340.495 89.545 1 43.05 ? HN22 GDP 501 B 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 92 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #