data_8VH5 # _model_server_result.job_id chAPb4DbdLz86uOPkAQmqA _model_server_result.datetime_utc '2024-10-09 23:22:51' _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 8vh5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":2601}' # _entry.id 8VH5 # _exptl.entry_id 8VH5 _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 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 90 _cell.entry_id 8VH5 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VH5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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 _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 ? _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 I 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 B OG1 THR 21 B THR 56 1_555 G MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc2 G MG MG . B MG 301 1_555 H O1A GNP . B GNP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc3 G MG MG . B MG 301 1_555 H O2B GNP . B GNP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc4 G MG MG . B MG 301 1_555 H O3A GNP . B GNP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc5 G MG MG . B MG 301 1_555 H O2A GNP . B GNP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc6 G MG MG . B MG 301 1_555 H O2G GNP . B GNP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc7 D OG1 THR 21 D THR 56 1_555 K MG MG . D MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc8 K MG MG . D MG 301 1_555 L O1A GNP . D GNP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc9 K MG MG . D MG 301 1_555 L O2A GNP . D GNP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc10 K MG MG . D MG 301 1_555 L O2G GNP . D GNP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc11 K MG MG . D MG 301 1_555 L O2B GNP . D GNP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc12 K MG MG . D MG 301 1_555 L O3A GNP . D GNP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? # _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 8VH5 _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 E 3 GDP A 1 2601 2601 GDP GDP . F 4 ANP A 1 2602 2602 ANP ANP . G 5 MG B 1 301 1 MG MG . H 6 GNP B 1 302 210 GNP GNP . I 3 GDP C 1 2601 2601 GDP GDP . J 4 ANP C 1 2602 2602 ANP ANP . K 5 MG D 1 301 1 MG MG . L 6 GNP D 1 302 210 GNP GNP . # 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 . . . I 3 263.481 274.058 345.173 1 125.58 ? PB GDP 2601 C 1 HETATM 2 O O1B GDP . . . I 3 262.215 274.464 344.474 1 125.58 ? O1B GDP 2601 C 1 HETATM 3 O O2B GDP . . . I 3 263.802 272.623 344.856 1 125.58 ? O2B GDP 2601 C 1 HETATM 4 O O3B GDP . . . I 3 264.614 274.941 344.728 1 125.58 ? O3B GDP 2601 C 1 HETATM 5 O O3A GDP . . . I 3 263.293 274.212 346.751 1 125.58 ? O3A GDP 2601 C 1 HETATM 6 P PA GDP . . . I 3 264.609 274.158 347.652 1 125.58 ? PA GDP 2601 C 1 HETATM 7 O O1A GDP . . . I 3 265.682 273.41 346.913 1 125.58 ? O1A GDP 2601 C 1 HETATM 8 O O2A GDP . . . I 3 265.095 275.528 348.034 1 125.58 ? O2A GDP 2601 C 1 HETATM 9 O O5' GDP . . . I 3 264.121 273.388 348.965 1 125.58 ? O5' GDP 2601 C 1 HETATM 10 C C5' GDP . . . I 3 264.184 274.084 350.201 1 125.58 ? C5' GDP 2601 C 1 HETATM 11 C C4' GDP . . . I 3 264.022 273.105 351.352 1 125.58 ? C4' GDP 2601 C 1 HETATM 12 O O4' GDP . . . I 3 265.281 272.507 351.659 1 125.58 ? O4' GDP 2601 C 1 HETATM 13 C C3' GDP . . . I 3 263.551 273.793 352.623 1 125.58 ? C3' GDP 2601 C 1 HETATM 14 O O3' GDP . . . I 3 262.286 273.266 353.026 1 125.58 ? O3' GDP 2601 C 1 HETATM 15 C C2' GDP . . . I 3 264.579 273.461 353.681 1 125.58 ? C2' GDP 2601 C 1 HETATM 16 O O2' GDP . . . I 3 263.933 273.009 354.867 1 125.58 ? O2' GDP 2601 C 1 HETATM 17 C C1' GDP . . . I 3 265.374 272.33 353.072 1 125.58 ? C1' GDP 2601 C 1 HETATM 18 N N9 GDP . . . I 3 266.777 272.333 353.541 1 125.58 ? N9 GDP 2601 C 1 HETATM 19 C C8 GDP . . . I 3 267.865 272.521 352.782 1 125.58 ? C8 GDP 2601 C 1 HETATM 20 N N7 GDP . . . I 3 268.997 272.45 353.525 1 125.58 ? N7 GDP 2601 C 1 HETATM 21 C C5 GDP . . . I 3 268.634 272.213 354.791 1 125.58 ? C5 GDP 2601 C 1 HETATM 22 C C6 GDP . . . I 3 269.328 272.027 356.08 1 125.58 ? C6 GDP 2601 C 1 HETATM 23 O O6 GDP . . . I 3 270.567 272.071 356.163 1 125.58 ? O6 GDP 2601 C 1 HETATM 24 N N1 GDP . . . I 3 268.589 271.797 357.16 1 125.58 ? N1 GDP 2601 C 1 HETATM 25 C C2 GDP . . . I 3 267.25 271.735 357.107 1 125.58 ? C2 GDP 2601 C 1 HETATM 26 N N2 GDP . . . I 3 266.57 271.498 358.254 1 125.58 ? N2 GDP 2601 C 1 HETATM 27 N N3 GDP . . . I 3 266.545 271.897 355.96 1 125.58 ? N3 GDP 2601 C 1 HETATM 28 C C4 GDP . . . I 3 267.173 272.134 354.793 1 125.58 ? C4 GDP 2601 C 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #