data_1OIV # _model_server_result.job_id 2c8sqhJPlhMEOxUtSTW_iQ _model_server_result.datetime_utc '2024-11-24 12:14:51' _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 1oiv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1175}' # _entry.id 1OIV # _exptl.entry_id 1OIV _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 90 _cell.entry_id 1OIV _cell.length_a 47.349 _cell.length_b 69.701 _cell.length_c 108.277 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1OIV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,G,H _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 F N 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 79 n n PB O2B GDP sing 80 n n PB O3B GDP sing 81 n n PB O3A GDP sing 82 n n O2B HOB2 GDP sing 83 n n O3B HOB3 GDP sing 84 n n O3A PA GDP sing 85 n n PA O1A GDP doub 86 n n PA O2A GDP sing 87 n n PA O5' GDP sing 88 n n O2A HOA2 GDP sing 89 n n O5' C5' GDP sing 90 n n C5' C4' GDP sing 91 n n C5' H5' GDP sing 92 n n C5' "H5''" GDP sing 93 n n C4' O4' GDP sing 94 n n C4' C3' GDP sing 95 n n C4' H4' GDP sing 96 n n O4' C1' GDP sing 97 n n C3' O3' GDP sing 98 n n C3' C2' GDP sing 99 n n C3' H3' GDP sing 100 n n O3' HO3' GDP sing 101 n n C2' O2' GDP sing 102 n n C2' C1' GDP sing 103 n n C2' H2' GDP sing 104 n n O2' HO2' GDP sing 105 n n C1' N9 GDP sing 106 n n C1' H1' GDP sing 107 n n N9 C8 GDP sing 108 n y N9 C4 GDP sing 109 n y C8 N7 GDP doub 110 n y C8 H8 GDP sing 111 n n N7 C5 GDP sing 112 n y C5 C6 GDP sing 113 n n C5 C4 GDP doub 114 n y C6 O6 GDP doub 115 n n C6 N1 GDP sing 116 n n N1 C2 GDP sing 117 n n N1 HN1 GDP sing 118 n n C2 N2 GDP sing 119 n n C2 N3 GDP doub 120 n n N2 HN21 GDP sing 121 n n N2 HN22 GDP sing 122 n n N3 C4 GDP sing 123 n n # _atom_sites.entry_id 1OIV _atom_sites.fract_transf_matrix[1][1] 0.02112 _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] 0.014347 _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] 0.009235 _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 1174 1174 GDP GDP . D 3 SO4 A 1 1175 1175 SO4 SO4 . E 4 EDO B 1 1174 1174 EDO EDO . F 2 GDP B 1 1175 1175 GDP GDP . G 5 HOH A 1 2001 2001 HOH HOH . G 5 HOH A 2 2002 2002 HOH HOH . G 5 HOH A 3 2003 2003 HOH HOH . G 5 HOH A 4 2004 2004 HOH HOH . G 5 HOH A 5 2005 2005 HOH HOH . G 5 HOH A 6 2006 2006 HOH HOH . G 5 HOH A 7 2007 2007 HOH HOH . G 5 HOH A 8 2008 2008 HOH HOH . G 5 HOH A 9 2009 2009 HOH HOH . G 5 HOH A 10 2010 2010 HOH HOH . G 5 HOH A 11 2011 2011 HOH HOH . G 5 HOH A 12 2012 2012 HOH HOH . G 5 HOH A 13 2013 2013 HOH HOH . G 5 HOH A 14 2014 2014 HOH HOH . G 5 HOH A 15 2015 2015 HOH HOH . G 5 HOH A 16 2016 2016 HOH HOH . G 5 HOH A 17 2017 2017 HOH HOH . G 5 HOH A 18 2018 2018 HOH HOH . G 5 HOH A 19 2019 2019 HOH HOH . G 5 HOH A 20 2020 2020 HOH HOH . G 5 HOH A 21 2021 2021 HOH HOH . G 5 HOH A 22 2022 2022 HOH HOH . G 5 HOH A 23 2023 2023 HOH HOH . G 5 HOH A 24 2024 2024 HOH HOH . G 5 HOH A 25 2025 2025 HOH HOH . G 5 HOH A 26 2026 2026 HOH HOH . G 5 HOH A 27 2027 2027 HOH HOH . G 5 HOH A 28 2028 2028 HOH HOH . G 5 HOH A 29 2029 2029 HOH HOH . G 5 HOH A 30 2030 2030 HOH HOH . G 5 HOH A 31 2031 2031 HOH HOH . G 5 HOH A 32 2032 2032 HOH HOH . G 5 HOH A 33 2033 2033 HOH HOH . G 5 HOH A 34 2034 2034 HOH HOH . G 5 HOH A 35 2035 2035 HOH HOH . G 5 HOH A 36 2036 2036 HOH HOH . G 5 HOH A 37 2037 2037 HOH HOH . G 5 HOH A 38 2038 2038 HOH HOH . G 5 HOH A 39 2039 2039 HOH HOH . G 5 HOH A 40 2040 2040 HOH HOH . G 5 HOH A 41 2041 2041 HOH HOH . G 5 HOH A 42 2042 2042 HOH HOH . G 5 HOH A 43 2043 2043 HOH HOH . G 5 HOH A 44 2044 2044 HOH HOH . G 5 HOH A 45 2045 2045 HOH HOH . G 5 HOH A 46 2046 2046 HOH HOH . G 5 HOH A 47 2047 2047 HOH HOH . G 5 HOH A 48 2048 2048 HOH HOH . G 5 HOH A 49 2049 2049 HOH HOH . G 5 HOH A 50 2050 2050 HOH HOH . G 5 HOH A 51 2051 2051 HOH HOH . G 5 HOH A 52 2052 2052 HOH HOH . G 5 HOH A 53 2053 2053 HOH HOH . G 5 HOH A 54 2054 2054 HOH HOH . G 5 HOH A 55 2055 2055 HOH HOH . G 5 HOH A 56 2056 2056 HOH HOH . G 5 HOH A 57 2057 2057 HOH HOH . G 5 HOH A 58 2058 2058 HOH HOH . G 5 HOH A 59 2059 2059 HOH HOH . G 5 HOH A 60 2060 2060 HOH HOH . G 5 HOH A 61 2061 2061 HOH HOH . G 5 HOH A 62 2062 2062 HOH HOH . G 5 HOH A 63 2063 2063 HOH HOH . G 5 HOH A 64 2064 2064 HOH HOH . G 5 HOH A 65 2065 2065 HOH HOH . G 5 HOH A 66 2066 2066 HOH HOH . G 5 HOH A 67 2067 2067 HOH HOH . G 5 HOH A 68 2068 2068 HOH HOH . G 5 HOH A 69 2069 2069 HOH HOH . G 5 HOH A 70 2070 2070 HOH HOH . G 5 HOH A 71 2071 2071 HOH HOH . G 5 HOH A 72 2072 2072 HOH HOH . G 5 HOH A 73 2073 2073 HOH HOH . G 5 HOH A 74 2074 2074 HOH HOH . G 5 HOH A 75 2075 2075 HOH HOH . G 5 HOH A 76 2076 2076 HOH HOH . G 5 HOH A 77 2077 2077 HOH HOH . G 5 HOH A 78 2078 2078 HOH HOH . G 5 HOH A 79 2079 2079 HOH HOH . G 5 HOH A 80 2080 2080 HOH HOH . G 5 HOH A 81 2081 2081 HOH HOH . G 5 HOH A 82 2082 2082 HOH HOH . G 5 HOH A 83 2083 2083 HOH HOH . G 5 HOH A 84 2084 2084 HOH HOH . H 5 HOH B 1 2001 2001 HOH HOH . H 5 HOH B 2 2002 2002 HOH HOH . H 5 HOH B 3 2003 2003 HOH HOH . H 5 HOH B 4 2004 2004 HOH HOH . H 5 HOH B 5 2005 2005 HOH HOH . H 5 HOH B 6 2006 2006 HOH HOH . H 5 HOH B 7 2007 2007 HOH HOH . H 5 HOH B 8 2008 2008 HOH HOH . H 5 HOH B 9 2009 2009 HOH HOH . H 5 HOH B 10 2010 2010 HOH HOH . H 5 HOH B 11 2011 2011 HOH HOH . H 5 HOH B 12 2012 2012 HOH HOH . H 5 HOH B 13 2013 2013 HOH HOH . H 5 HOH B 14 2014 2014 HOH HOH . H 5 HOH B 15 2015 2015 HOH HOH . H 5 HOH B 16 2016 2016 HOH HOH . H 5 HOH B 17 2017 2017 HOH HOH . H 5 HOH B 18 2018 2018 HOH HOH . H 5 HOH B 19 2019 2019 HOH HOH . H 5 HOH B 20 2020 2020 HOH HOH . H 5 HOH B 21 2021 2021 HOH HOH . H 5 HOH B 22 2022 2022 HOH HOH . H 5 HOH B 23 2023 2023 HOH HOH . H 5 HOH B 24 2024 2024 HOH HOH . H 5 HOH B 25 2025 2025 HOH HOH . H 5 HOH B 26 2026 2026 HOH HOH . H 5 HOH B 27 2027 2027 HOH HOH . H 5 HOH B 28 2028 2028 HOH HOH . H 5 HOH B 29 2029 2029 HOH HOH . H 5 HOH B 30 2030 2030 HOH HOH . H 5 HOH B 31 2031 2031 HOH HOH . H 5 HOH B 32 2032 2032 HOH HOH . H 5 HOH B 33 2033 2033 HOH HOH . H 5 HOH B 34 2034 2034 HOH HOH . H 5 HOH B 35 2035 2035 HOH HOH . H 5 HOH B 36 2036 2036 HOH HOH . H 5 HOH B 37 2037 2037 HOH HOH . H 5 HOH B 38 2038 2038 HOH HOH . H 5 HOH B 39 2039 2039 HOH HOH . H 5 HOH B 40 2040 2040 HOH HOH . H 5 HOH B 41 2041 2041 HOH HOH . H 5 HOH B 42 2042 2042 HOH HOH . H 5 HOH B 43 2043 2043 HOH HOH . H 5 HOH B 44 2044 2044 HOH HOH . H 5 HOH B 45 2045 2045 HOH HOH . H 5 HOH B 46 2046 2046 HOH HOH . H 5 HOH B 47 2047 2047 HOH HOH . H 5 HOH B 48 2048 2048 HOH HOH . H 5 HOH B 49 2049 2049 HOH HOH . H 5 HOH B 50 2050 2050 HOH HOH . H 5 HOH B 51 2051 2051 HOH HOH . H 5 HOH B 52 2052 2052 HOH HOH . H 5 HOH B 53 2053 2053 HOH HOH . H 5 HOH B 54 2054 2054 HOH HOH . H 5 HOH B 55 2055 2055 HOH HOH . H 5 HOH B 56 2056 2056 HOH HOH . H 5 HOH B 57 2057 2057 HOH HOH . H 5 HOH B 58 2058 2058 HOH HOH . H 5 HOH B 59 2059 2059 HOH HOH . H 5 HOH B 60 2060 2060 HOH HOH . H 5 HOH B 61 2061 2061 HOH HOH . H 5 HOH B 62 2062 2062 HOH HOH . H 5 HOH B 63 2063 2063 HOH HOH . H 5 HOH B 64 2064 2064 HOH HOH . H 5 HOH B 65 2065 2065 HOH HOH . H 5 HOH B 66 2066 2066 HOH HOH . H 5 HOH B 67 2067 2067 HOH HOH . H 5 HOH B 68 2068 2068 HOH HOH . H 5 HOH B 69 2069 2069 HOH HOH . H 5 HOH B 70 2070 2070 HOH HOH . H 5 HOH B 71 2071 2071 HOH HOH . H 5 HOH B 72 2072 2072 HOH HOH . H 5 HOH B 73 2073 2073 HOH HOH . H 5 HOH B 74 2074 2074 HOH HOH . H 5 HOH B 75 2075 2075 HOH HOH . H 5 HOH B 76 2076 2076 HOH HOH . H 5 HOH B 77 2077 2077 HOH HOH . H 5 HOH B 78 2078 2078 HOH HOH . H 5 HOH B 79 2079 2079 HOH HOH . H 5 HOH B 80 2080 2080 HOH HOH . H 5 HOH B 81 2081 2081 HOH HOH . H 5 HOH B 82 2082 2082 HOH HOH . H 5 HOH B 83 2083 2083 HOH HOH . H 5 HOH B 84 2084 2084 HOH HOH . H 5 HOH B 85 2085 2085 HOH HOH . H 5 HOH B 86 2086 2086 HOH HOH . H 5 HOH B 87 2087 2087 HOH HOH . H 5 HOH B 88 2088 2088 HOH HOH . H 5 HOH B 89 2089 2089 HOH HOH . H 5 HOH B 90 2090 2090 HOH HOH . H 5 HOH B 91 2091 2091 HOH HOH . H 5 HOH B 92 2092 2092 HOH HOH . H 5 HOH B 93 2093 2093 HOH HOH . H 5 HOH B 94 2094 2094 HOH HOH . H 5 HOH B 95 2095 2095 HOH HOH . H 5 HOH B 96 2096 2096 HOH HOH . H 5 HOH B 97 2097 2097 HOH HOH . H 5 HOH B 98 2098 2098 HOH HOH . H 5 HOH B 99 2099 2099 HOH HOH . H 5 HOH B 100 2100 2100 HOH HOH . H 5 HOH B 101 2101 2101 HOH HOH . H 5 HOH B 102 2102 2102 HOH HOH . H 5 HOH B 103 2103 2103 HOH HOH . H 5 HOH B 104 2104 2104 HOH HOH . H 5 HOH B 105 2105 2105 HOH HOH . H 5 HOH B 106 2106 2106 HOH HOH . H 5 HOH B 107 2107 2107 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 . . . F 2 -1.61 8.148 -7.553 1 17.01 ? PB GDP 1175 B 1 HETATM 2 O O1B GDP . . . F 2 -0.753 9.34 -7.546 1 17.74 ? O1B GDP 1175 B 1 HETATM 3 O O2B GDP . . . F 2 -1.319 7.097 -8.582 1 15.22 ? O2B GDP 1175 B 1 HETATM 4 O O3B GDP . . . F 2 -1.582 7.274 -6.295 1 19.53 ? O3B GDP 1175 B 1 HETATM 5 O O3A GDP . . . F 2 -3.219 8.505 -7.982 1 16.98 ? O3A GDP 1175 B 1 HETATM 6 P PA GDP . . . F 2 -4.151 9.577 -7.215 1 17.58 ? PA GDP 1175 B 1 HETATM 7 O O1A GDP . . . F 2 -5.071 8.532 -6.719 1 16.06 ? O1A GDP 1175 B 1 HETATM 8 O O2A GDP . . . F 2 -3.695 10.48 -6.14 1 16.93 ? O2A GDP 1175 B 1 HETATM 9 O O5' GDP . . . F 2 -4.931 10.185 -8.457 1 15.68 ? O5' GDP 1175 B 1 HETATM 10 C C5' GDP . . . F 2 -4.482 11.222 -9.293 1 15.56 ? C5' GDP 1175 B 1 HETATM 11 C C4' GDP . . . F 2 -5.719 11.97 -9.787 1 16.6 ? C4' GDP 1175 B 1 HETATM 12 O O4' GDP . . . F 2 -6.605 11.262 -10.749 1 16.05 ? O4' GDP 1175 B 1 HETATM 13 C C3' GDP . . . F 2 -6.749 12.403 -8.684 1 16.68 ? C3' GDP 1175 B 1 HETATM 14 O O3' GDP . . . F 2 -7.223 13.696 -9.126 1 16.18 ? O3' GDP 1175 B 1 HETATM 15 C C2' GDP . . . F 2 -7.888 11.372 -8.773 1 15.69 ? C2' GDP 1175 B 1 HETATM 16 O O2' GDP . . . F 2 -9.161 11.846 -8.37 1 15.04 ? O2' GDP 1175 B 1 HETATM 17 C C1' GDP . . . F 2 -7.873 10.992 -10.22 1 15.23 ? C1' GDP 1175 B 1 HETATM 18 N N9 GDP . . . F 2 -8.299 9.568 -10.466 1 17.1 ? N9 GDP 1175 B 1 HETATM 19 C C8 GDP . . . F 2 -7.978 8.379 -9.869 1 15.8 ? C8 GDP 1175 B 1 HETATM 20 N N7 GDP . . . F 2 -8.598 7.363 -10.391 1 15.11 ? N7 GDP 1175 B 1 HETATM 21 C C5 GDP . . . F 2 -9.386 7.902 -11.402 1 15.57 ? C5 GDP 1175 B 1 HETATM 22 C C6 GDP . . . F 2 -10.3 7.304 -12.334 1 14.03 ? C6 GDP 1175 B 1 HETATM 23 O O6 GDP . . . F 2 -10.593 6.103 -12.427 1 19 ? O6 GDP 1175 B 1 HETATM 24 N N1 GDP . . . F 2 -10.892 8.255 -13.212 1 15.42 ? N1 GDP 1175 B 1 HETATM 25 C C2 GDP . . . F 2 -10.636 9.617 -13.188 1 15.3 ? C2 GDP 1175 B 1 HETATM 26 N N2 GDP . . . F 2 -11.277 10.354 -14.089 1 16.36 ? N2 GDP 1175 B 1 HETATM 27 N N3 GDP . . . F 2 -9.779 10.195 -12.304 1 17.83 ? N3 GDP 1175 B 1 HETATM 28 C C4 GDP . . . F 2 -9.213 9.276 -11.47 1 15.99 ? C4 GDP 1175 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 798 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 28 #