data_3V70 # _model_server_result.job_id -BBoGzXLNjI8G5ahZ1xmng _model_server_result.datetime_utc '2025-07-02 14:12:04' _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 3v70 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 3V70 # _exptl.entry_id 3V70 _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 3V70 _cell.length_a 81.348 _cell.length_b 81.348 _cell.length_c 178.934 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3V70 _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 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,G 1 1 B,E,F,H 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 G O HOH . A HOH 1 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc2 G O HOH . A HOH 2 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc3 G O HOH . A HOH 3 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc4 A OG SER 35 A SER 41 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc5 C O3B GDP . A GDP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc6 H O HOH . B HOH 4 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc7 H O HOH . B HOH 5 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc8 H O HOH . B HOH 6 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc9 B OG SER 35 B SER 41 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc10 E O3B GDP . B GDP 401 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? # _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 3V70 _atom_sites.fract_transf_matrix[1][1] 0.012293 _atom_sites.fract_transf_matrix[1][2] 0.007097 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014195 _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] 0.005589 _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 1 401 401 GDP GDP . D 3 MG A 1 402 402 MG MG . E 2 GDP B 1 401 401 GDP GDP . F 3 MG B 1 402 402 MG MG . G 4 HOH A 1 1 1 HOH HOH . G 4 HOH A 2 2 2 HOH HOH . G 4 HOH A 3 3 3 HOH HOH . G 4 HOH A 4 254 10 HOH HOH . G 4 HOH A 5 255 11 HOH HOH . G 4 HOH A 6 256 12 HOH HOH . G 4 HOH A 7 257 17 HOH HOH . G 4 HOH A 8 258 18 HOH HOH . G 4 HOH A 9 259 19 HOH HOH . G 4 HOH A 10 260 20 HOH HOH . G 4 HOH A 11 261 21 HOH HOH . G 4 HOH A 12 262 22 HOH HOH . G 4 HOH A 13 263 23 HOH HOH . G 4 HOH A 14 264 25 HOH HOH . G 4 HOH A 15 265 27 HOH HOH . G 4 HOH A 16 266 31 HOH HOH . G 4 HOH A 17 267 32 HOH HOH . G 4 HOH A 18 268 35 HOH HOH . G 4 HOH A 19 269 36 HOH HOH . G 4 HOH A 20 270 37 HOH HOH . G 4 HOH A 21 271 38 HOH HOH . G 4 HOH A 22 272 39 HOH HOH . G 4 HOH A 23 273 40 HOH HOH . H 4 HOH B 1 4 4 HOH HOH . H 4 HOH B 2 5 5 HOH HOH . H 4 HOH B 3 6 6 HOH HOH . H 4 HOH B 4 254 7 HOH HOH . H 4 HOH B 5 255 8 HOH HOH . H 4 HOH B 6 256 9 HOH HOH . H 4 HOH B 7 257 13 HOH HOH . H 4 HOH B 8 258 14 HOH HOH . H 4 HOH B 9 259 15 HOH HOH . H 4 HOH B 10 260 16 HOH HOH . H 4 HOH B 11 261 24 HOH HOH . H 4 HOH B 12 262 26 HOH HOH . H 4 HOH B 13 263 28 HOH HOH . H 4 HOH B 14 264 29 HOH HOH . H 4 HOH B 15 265 30 HOH HOH . H 4 HOH B 16 266 33 HOH HOH . H 4 HOH B 17 267 34 HOH HOH . H 4 HOH B 18 268 41 HOH HOH . H 4 HOH B 19 269 42 HOH HOH . H 4 HOH B 20 270 43 HOH HOH . H 4 HOH B 21 271 44 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 . . . C 2 22.776 25.581 115.678 1 25.83 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . C 2 22.611 27.094 115.781 1 26.87 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . C 2 22.725 24.875 117.038 1 24.57 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . C 2 21.857 24.958 114.618 1 24.13 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . C 2 24.309 25.303 115.273 1 27.3 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . C 2 24.836 24.883 113.797 1 29.91 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . C 2 24.553 25.952 112.845 1 29.9 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . C 2 24.394 23.51 113.432 1 28.41 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . C 2 26.422 24.825 114.101 1 31.62 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . C 2 27.172 26.004 114.459 1 33.49 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . C 2 28.593 25.872 113.918 1 35.37 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . C 2 29.233 24.704 114.532 1 34.84 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . C 2 28.621 25.657 112.407 1 35.83 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . C 2 29.618 26.463 111.756 1 39.49 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . C 2 28.961 24.179 112.281 1 35.26 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . C 2 29.653 23.908 111.103 1 35.99 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . C 2 29.797 23.885 113.511 1 35.37 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . C 2 29.735 22.454 113.951 1 35.67 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . C 2 28.648 21.767 114.367 1 33.64 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . C 2 28.993 20.511 114.691 1 33.28 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . C 2 30.298 20.381 114.475 1 34.85 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . C 2 31.269 19.297 114.634 1 35.65 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . C 2 30.907 18.175 115.062 1 34.8 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . C 2 32.544 19.556 114.318 1 38.57 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . C 2 32.957 20.776 113.862 1 39.47 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . C 2 34.248 20.97 113.559 1 41.23 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . C 2 32.105 21.824 113.707 1 38.22 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . C 2 30.785 21.655 114.004 1 36.22 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #