data_2VP2 # _model_server_result.job_id RVM-HJFjHg0vTBCAD8rUZA _model_server_result.datetime_utc '2024-11-24 11:35:02' _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 2vp2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1209}' # _entry.id 2VP2 # _exptl.entry_id 2VP2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" _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 2VP2 _cell.length_a 119.742 _cell.length_b 65.055 _cell.length_c 69.188 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VP2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 D N N # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id DGT _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PG O1G DGT sing 83 n n PG O2G DGT sing 84 n n O1G HO1G DGT sing 85 n n O2G HO2G DGT sing 86 n n O3G PG DGT doub 87 n n O3B PG DGT sing 88 n n PB O3B DGT sing 89 n n PB O1B DGT sing 90 n n PB O3A DGT sing 91 n n O1B HO1B DGT sing 92 n n O2B PB DGT doub 93 n n PA O3A DGT sing 94 n n PA O1A DGT sing 95 n n O1A HO1A DGT sing 96 n n O2A PA DGT doub 97 n n O5' PA DGT sing 98 n n O5' C5' DGT sing 99 n n C5' H5' DGT sing 100 n n C5' "H5'A" DGT sing 101 n n C4' C5' DGT sing 102 n n C4' H4' DGT sing 103 n n O4' C4' DGT sing 104 n n C3' C4' DGT sing 105 n n C3' O3' DGT sing 106 n n C3' H3' DGT sing 107 n n O3' HO3' DGT sing 108 n n C2' C3' DGT sing 109 n n C2' C1' DGT sing 110 n n C2' H2' DGT sing 111 n n C2' "H2'A" DGT sing 112 n n C1' O4' DGT sing 113 n n C1' H1' DGT sing 114 n n N9 C1' DGT sing 115 n n N9 C4 DGT sing 116 n y C8 N9 DGT sing 117 n y C8 H8 DGT sing 118 n n N7 C8 DGT doub 119 n y N7 C5 DGT sing 120 n y C5 C6 DGT sing 121 n n C5 C4 DGT doub 122 n y C6 N1 DGT sing 123 n n O6 C6 DGT doub 124 n n N1 C2 DGT sing 125 n n C2 N3 DGT doub 126 n n C2 N2 DGT sing 127 n n N2 HN2 DGT sing 128 n n N2 HN2A DGT sing 129 n n C4 N3 DGT sing 130 n n N1 H16 DGT sing 131 n n # _atom_sites.entry_id 2VP2 _atom_sites.fract_transf_matrix[1][1] 0.008351 _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] 0.015372 _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] 0.014453 _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 DGT A 1 1210 1210 DGT DGT . D 2 DGT B 1 1209 1209 DGT DGT . E 3 HOH A 1 2001 2001 HOH HOH . E 3 HOH A 2 2002 2002 HOH HOH . E 3 HOH A 3 2003 2003 HOH HOH . E 3 HOH A 4 2004 2004 HOH HOH . E 3 HOH A 5 2005 2005 HOH HOH . E 3 HOH A 6 2006 2006 HOH HOH . E 3 HOH A 7 2007 2007 HOH HOH . E 3 HOH A 8 2008 2008 HOH HOH . E 3 HOH A 9 2009 2009 HOH HOH . E 3 HOH A 10 2010 2010 HOH HOH . E 3 HOH A 11 2011 2011 HOH HOH . E 3 HOH A 12 2012 2012 HOH HOH . E 3 HOH A 13 2013 2013 HOH HOH . E 3 HOH A 14 2014 2014 HOH HOH . E 3 HOH A 15 2015 2015 HOH HOH . E 3 HOH A 16 2016 2016 HOH HOH . E 3 HOH A 17 2017 2017 HOH HOH . E 3 HOH A 18 2018 2018 HOH HOH . E 3 HOH A 19 2019 2019 HOH HOH . E 3 HOH A 20 2020 2020 HOH HOH . E 3 HOH A 21 2021 2021 HOH HOH . E 3 HOH A 22 2022 2022 HOH HOH . E 3 HOH A 23 2023 2023 HOH HOH . E 3 HOH A 24 2024 2024 HOH HOH . E 3 HOH A 25 2025 2025 HOH HOH . E 3 HOH A 26 2026 2026 HOH HOH . E 3 HOH A 27 2027 2027 HOH HOH . E 3 HOH A 28 2028 2028 HOH HOH . E 3 HOH A 29 2029 2029 HOH HOH . E 3 HOH A 30 2030 2030 HOH HOH . E 3 HOH A 31 2031 2031 HOH HOH . E 3 HOH A 32 2032 2032 HOH HOH . E 3 HOH A 33 2033 2033 HOH HOH . E 3 HOH A 34 2034 2034 HOH HOH . E 3 HOH A 35 2035 2035 HOH HOH . E 3 HOH A 36 2036 2036 HOH HOH . E 3 HOH A 37 2037 2037 HOH HOH . E 3 HOH A 38 2038 2038 HOH HOH . E 3 HOH A 39 2039 2039 HOH HOH . E 3 HOH A 40 2040 2040 HOH HOH . E 3 HOH A 41 2041 2041 HOH HOH . E 3 HOH A 42 2042 2042 HOH HOH . E 3 HOH A 43 2043 2043 HOH HOH . E 3 HOH A 44 2044 2044 HOH HOH . E 3 HOH A 45 2045 2045 HOH HOH . E 3 HOH A 46 2046 2046 HOH HOH . E 3 HOH A 47 2047 2047 HOH HOH . E 3 HOH A 48 2048 2048 HOH HOH . E 3 HOH A 49 2049 2049 HOH HOH . E 3 HOH A 50 2050 2050 HOH HOH . E 3 HOH A 51 2051 2051 HOH HOH . E 3 HOH A 52 2052 2052 HOH HOH . E 3 HOH A 53 2053 2053 HOH HOH . E 3 HOH A 54 2054 2054 HOH HOH . E 3 HOH A 55 2055 2055 HOH HOH . E 3 HOH A 56 2056 2056 HOH HOH . E 3 HOH A 57 2057 2057 HOH HOH . E 3 HOH A 58 2058 2058 HOH HOH . E 3 HOH A 59 2059 2059 HOH HOH . E 3 HOH A 60 2060 2060 HOH HOH . E 3 HOH A 61 2061 2061 HOH HOH . E 3 HOH A 62 2062 2062 HOH HOH . E 3 HOH A 63 2063 2063 HOH HOH . E 3 HOH A 64 2064 2064 HOH HOH . E 3 HOH A 65 2065 2065 HOH HOH . E 3 HOH A 66 2066 2066 HOH HOH . F 3 HOH B 1 2001 2001 HOH HOH . F 3 HOH B 2 2002 2002 HOH HOH . F 3 HOH B 3 2003 2003 HOH HOH . F 3 HOH B 4 2004 2004 HOH HOH . F 3 HOH B 5 2005 2005 HOH HOH . F 3 HOH B 6 2006 2006 HOH HOH . F 3 HOH B 7 2007 2007 HOH HOH . F 3 HOH B 8 2008 2008 HOH HOH . F 3 HOH B 9 2009 2009 HOH HOH . F 3 HOH B 10 2010 2010 HOH HOH . F 3 HOH B 11 2011 2011 HOH HOH . F 3 HOH B 12 2012 2012 HOH HOH . F 3 HOH B 13 2013 2013 HOH HOH . F 3 HOH B 14 2014 2014 HOH HOH . F 3 HOH B 15 2015 2015 HOH HOH . F 3 HOH B 16 2016 2016 HOH HOH . F 3 HOH B 17 2017 2017 HOH HOH . F 3 HOH B 18 2018 2018 HOH HOH . F 3 HOH B 19 2019 2019 HOH HOH . F 3 HOH B 20 2020 2020 HOH HOH . F 3 HOH B 21 2021 2021 HOH HOH . F 3 HOH B 22 2022 2022 HOH HOH . F 3 HOH B 23 2023 2023 HOH HOH . F 3 HOH B 24 2024 2024 HOH HOH . F 3 HOH B 25 2025 2025 HOH HOH . F 3 HOH B 26 2026 2026 HOH HOH . F 3 HOH B 27 2027 2027 HOH HOH . F 3 HOH B 28 2028 2028 HOH HOH . F 3 HOH B 29 2029 2029 HOH HOH . F 3 HOH B 30 2030 2030 HOH HOH . F 3 HOH B 31 2031 2031 HOH HOH . F 3 HOH B 32 2032 2032 HOH HOH . F 3 HOH B 33 2033 2033 HOH HOH . F 3 HOH B 34 2034 2034 HOH HOH . F 3 HOH B 35 2035 2035 HOH HOH . F 3 HOH B 36 2036 2036 HOH HOH . F 3 HOH B 37 2037 2037 HOH HOH . F 3 HOH B 38 2038 2038 HOH HOH . F 3 HOH B 39 2039 2039 HOH HOH . F 3 HOH B 40 2040 2040 HOH HOH . F 3 HOH B 41 2041 2041 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 PG DGT . . . D 2 38.851 9.681 15.698 1 35.69 ? PG DGT 1209 B 1 HETATM 2 O O1G DGT . . . D 2 38.756 8.494 16.624 1 34.81 ? O1G DGT 1209 B 1 HETATM 3 O O2G DGT . . . D 2 39.349 9.329 14.312 1 34.31 ? O2G DGT 1209 B 1 HETATM 4 O O3G DGT . . . D 2 39.463 10.929 16.292 1 34.4 ? O3G DGT 1209 B 1 HETATM 5 O O3B DGT . . . D 2 37.299 10.123 15.435 1 35.14 ? O3B DGT 1209 B 1 HETATM 6 P PB DGT . . . D 2 36.232 9.229 14.597 1 31.79 ? PB DGT 1209 B 1 HETATM 7 O O1B DGT . . . D 2 36.213 7.846 15.196 1 32.74 ? O1B DGT 1209 B 1 HETATM 8 O O2B DGT . . . D 2 36.474 9.355 13.117 1 30.75 ? O2B DGT 1209 B 1 HETATM 9 O O3A DGT . . . D 2 34.837 9.96 15.008 1 33.68 ? O3A DGT 1209 B 1 HETATM 10 P PA DGT . . . D 2 34.341 11.432 14.542 1 32.83 ? PA DGT 1209 B 1 HETATM 11 O O1A DGT . . . D 2 35.534 12.33 14.338 1 32.32 ? O1A DGT 1209 B 1 HETATM 12 O O2A DGT . . . D 2 33.247 11.891 15.479 1 32.62 ? O2A DGT 1209 B 1 HETATM 13 O O5' DGT . . . D 2 33.723 11.137 13.087 1 32.79 ? O5' DGT 1209 B 1 HETATM 14 C C5' DGT . . . D 2 33.048 9.924 12.746 1 31.79 ? C5' DGT 1209 B 1 HETATM 15 C C4' DGT . . . D 2 32.262 10.129 11.451 1 31.85 ? C4' DGT 1209 B 1 HETATM 16 O O4' DGT . . . D 2 31.07 10.859 11.75 1 33.36 ? O4' DGT 1209 B 1 HETATM 17 C C3' DGT . . . D 2 33.013 10.971 10.413 1 32.23 ? C3' DGT 1209 B 1 HETATM 18 O O3' DGT . . . D 2 32.899 10.35 9.13 1 32.81 ? O3' DGT 1209 B 1 HETATM 19 C C2' DGT . . . D 2 32.302 12.303 10.337 1 32.6 ? C2' DGT 1209 B 1 HETATM 20 C C1' DGT . . . D 2 30.912 11.855 10.731 1 34.33 ? C1' DGT 1209 B 1 HETATM 21 N N9 DGT . . . D 2 30.007 12.937 11.15 1 34.14 ? N9 DGT 1209 B 1 HETATM 22 C C8 DGT . . . D 2 29.157 13.586 10.321 1 34.67 ? C8 DGT 1209 B 1 HETATM 23 N N7 DGT . . . D 2 28.431 14.517 10.996 1 34.86 ? N7 DGT 1209 B 1 HETATM 24 C C5 DGT . . . D 2 28.834 14.455 12.279 1 34.06 ? C5 DGT 1209 B 1 HETATM 25 C C6 DGT . . . D 2 28.469 15.158 13.519 1 34.37 ? C6 DGT 1209 B 1 HETATM 26 O O6 DGT . . . D 2 27.6 16.049 13.501 1 34.86 ? O6 DGT 1209 B 1 HETATM 27 N N1 DGT . . . D 2 29.093 14.821 14.655 1 34.59 ? N1 DGT 1209 B 1 HETATM 28 C C2 DGT . . . D 2 30.044 13.86 14.686 1 35.28 ? C2 DGT 1209 B 1 HETATM 29 N N2 DGT . . . D 2 30.621 13.612 15.885 1 35.06 ? N2 DGT 1209 B 1 HETATM 30 N N3 DGT . . . D 2 30.443 13.152 13.579 1 34.8 ? N3 DGT 1209 B 1 HETATM 31 C C4 DGT . . . D 2 29.873 13.413 12.377 1 33.82 ? C4 DGT 1209 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #