data_6V5V # _model_server_result.job_id Y0wD4R8MjZ7oXhPf7hG3Kw _model_server_result.datetime_utc '2024-12-23 06:52:03' _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 6v5v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6V5V # _exptl.entry_id 6V5V _exptl.method 'ELECTRON MICROSCOPY' # _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 6V5V _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 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id GDP _pdbx_nonpoly_scheme.pdb_strand_id g _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 501 _pdbx_nonpoly_scheme.auth_seq_num 999 _pdbx_nonpoly_scheme.pdb_mon_id GDP _pdbx_nonpoly_scheme.auth_mon_id GDP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . B 2 122.863 218.359 264.314 1 120.15 ? PB GDP 501 g 1 HETATM 2 O O1B GDP . . . B 2 122.134 219.59 263.84 1 120.15 ? O1B GDP 501 g 1 HETATM 3 O O2B GDP . . . B 2 121.879 217.397 264.933 1 120.15 ? O2B GDP 501 g 1 HETATM 4 O O3B GDP . . . B 2 123.901 218.744 265.34 1 120.15 ? O3B GDP 501 g 1 HETATM 5 O O3A GDP . . . B 2 123.583 217.658 263.059 1 120.15 ? O3A GDP 501 g 1 HETATM 6 P PA GDP . . . B 2 124.619 216.456 263.313 1 120.15 ? PA GDP 501 g 1 HETATM 7 O O1A GDP . . . B 2 125.854 216.971 264.01 1 120.15 ? O1A GDP 501 g 1 HETATM 8 O O2A GDP . . . B 2 123.971 215.359 264.12 1 120.15 ? O2A GDP 501 g 1 HETATM 9 O O5' GDP . . . B 2 124.983 215.937 261.836 1 120.15 ? O5' GDP 501 g 1 HETATM 10 C C5' GDP . . . B 2 125.615 214.672 261.667 1 120.15 ? C5' GDP 501 g 1 HETATM 11 C C4' GDP . . . B 2 125.978 214.485 260.202 1 120.15 ? C4' GDP 501 g 1 HETATM 12 O O4' GDP . . . B 2 126.97 215.444 259.841 1 120.15 ? O4' GDP 501 g 1 HETATM 13 C C3' GDP . . . B 2 126.566 213.11 259.943 1 120.15 ? C3' GDP 501 g 1 HETATM 14 O O3' GDP . . . B 2 125.655 212.326 259.17 1 120.15 ? O3' GDP 501 g 1 HETATM 15 C C2' GDP . . . B 2 127.834 213.341 259.151 1 120.15 ? C2' GDP 501 g 1 HETATM 16 O O2' GDP . . . B 2 127.706 212.752 257.855 1 120.15 ? O2' GDP 501 g 1 HETATM 17 C C1' GDP . . . B 2 127.969 214.846 259.015 1 120.15 ? C1' GDP 501 g 1 HETATM 18 N N9 GDP . . . B 2 129.31 215.279 259.472 1 120.15 ? N9 GDP 501 g 1 HETATM 19 C C8 GDP . . . B 2 129.64 215.595 260.736 1 120.15 ? C8 GDP 501 g 1 HETATM 20 N N7 GDP . . . B 2 130.944 215.958 260.825 1 120.15 ? N7 GDP 501 g 1 HETATM 21 C C5 GDP . . . B 2 131.47 215.874 259.591 1 120.15 ? C5 GDP 501 g 1 HETATM 22 C C6 GDP . . . B 2 132.795 216.115 258.98 1 120.15 ? C6 GDP 501 g 1 HETATM 23 O O6 GDP . . . B 2 133.762 216.496 259.672 1 120.15 ? O6 GDP 501 g 1 HETATM 24 N N1 GDP . . . B 2 132.926 215.914 257.664 1 120.15 ? N1 GDP 501 g 1 HETATM 25 C C2 GDP . . . B 2 131.9 215.503 256.896 1 120.15 ? C2 GDP 501 g 1 HETATM 26 N N2 GDP . . . B 2 132.119 215.323 255.573 1 120.15 ? N2 GDP 501 g 1 HETATM 27 N N3 GDP . . . B 2 130.659 215.262 257.388 1 120.15 ? N3 GDP 501 g 1 HETATM 28 C C4 GDP . . . B 2 130.39 215.425 258.703 1 120.15 ? C4 GDP 501 g 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #