data_5AQK # _model_server_result.job_id RzCh0PgAV1zUniTs2RbH_A _model_server_result.datetime_utc '2024-11-22 06:26:53' _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 5aqk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1260}' # _entry.id 5AQK # _exptl.entry_id 5AQK _exptl.method 'X-RAY DIFFRACTION' # _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 115.05 _cell.angle_gamma 90 _cell.entry_id 5AQK _cell.length_a 115.003 _cell.length_b 39.894 _cell.length_c 127.514 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5AQK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _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,I,J,K _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 ? 3 C N N ? 3 I N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 56 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 201 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 114 _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 259 _struct_conn.ptnr2_symmetry 1_555 _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 2.027 _struct_conn.pdbx_value_order ? # _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 92 n n PB O2B GDP sing 93 n n PB O3B GDP sing 94 n n PB O3A GDP sing 95 n n O2B HOB2 GDP sing 96 n n O3B HOB3 GDP sing 97 n n O3A PA GDP sing 98 n n PA O1A GDP doub 99 n n PA O2A GDP sing 100 n n PA O5' GDP sing 101 n n O2A HOA2 GDP sing 102 n n O5' C5' GDP sing 103 n n C5' C4' GDP sing 104 n n C5' H5' GDP sing 105 n n C5' "H5''" GDP sing 106 n n C4' O4' GDP sing 107 n n C4' C3' GDP sing 108 n n C4' H4' GDP sing 109 n n O4' C1' GDP sing 110 n n C3' O3' GDP sing 111 n n C3' C2' GDP sing 112 n n C3' H3' GDP sing 113 n n O3' HO3' GDP sing 114 n n C2' O2' GDP sing 115 n n C2' C1' GDP sing 116 n n C2' H2' GDP sing 117 n n O2' HO2' GDP sing 118 n n C1' N9 GDP sing 119 n n C1' H1' GDP sing 120 n n N9 C8 GDP sing 121 n y N9 C4 GDP sing 122 n y C8 N7 GDP doub 123 n y C8 H8 GDP sing 124 n n N7 C5 GDP sing 125 n y C5 C6 GDP sing 126 n n C5 C4 GDP doub 127 n y C6 O6 GDP doub 128 n n C6 N1 GDP sing 129 n n N1 C2 GDP sing 130 n n N1 HN1 GDP sing 131 n n C2 N2 GDP sing 132 n n C2 N3 GDP doub 133 n n N2 HN21 GDP sing 134 n n N2 HN22 GDP sing 135 n n N3 C4 GDP sing 136 n n # _atom_sites.entry_id 5AQK _atom_sites.fract_transf_matrix[1][1] 0.008695 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004064 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025066 _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] 0.008657 _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 3 GDP A 1 1382 1382 GDP GDP . D 4 GOL A 1 1383 1383 GOL GOL . E 4 GOL A 1 1384 1384 GOL GOL . F 4 GOL A 1 1385 1385 GOL GOL . G 5 TRS A 1 1386 1386 TRS TRS . H 6 DMS A 1 1387 1387 DMS DMS . I 3 GDP B 1 1260 1260 GDP GDP . J 7 HOH A 1 2001 2001 HOH HOH . J 7 HOH A 2 2002 2002 HOH HOH . J 7 HOH A 3 2003 2003 HOH HOH . J 7 HOH A 4 2004 2004 HOH HOH . J 7 HOH A 5 2005 2005 HOH HOH . J 7 HOH A 6 2006 2006 HOH HOH . J 7 HOH A 7 2007 2007 HOH HOH . J 7 HOH A 8 2008 2008 HOH HOH . J 7 HOH A 9 2009 2009 HOH HOH . J 7 HOH A 10 2010 2010 HOH HOH . J 7 HOH A 11 2011 2011 HOH HOH . J 7 HOH A 12 2012 2012 HOH HOH . J 7 HOH A 13 2013 2013 HOH HOH . J 7 HOH A 14 2014 2014 HOH HOH . J 7 HOH A 15 2015 2015 HOH HOH . J 7 HOH A 16 2016 2016 HOH HOH . J 7 HOH A 17 2017 2017 HOH HOH . J 7 HOH A 18 2018 2018 HOH HOH . J 7 HOH A 19 2019 2019 HOH HOH . J 7 HOH A 20 2020 2020 HOH HOH . J 7 HOH A 21 2021 2021 HOH HOH . J 7 HOH A 22 2022 2022 HOH HOH . J 7 HOH A 23 2023 2023 HOH HOH . J 7 HOH A 24 2024 2024 HOH HOH . J 7 HOH A 25 2025 2025 HOH HOH . J 7 HOH A 26 2026 2026 HOH HOH . J 7 HOH A 27 2027 2027 HOH HOH . J 7 HOH A 28 2028 2028 HOH HOH . J 7 HOH A 29 2029 2029 HOH HOH . J 7 HOH A 30 2030 2030 HOH HOH . J 7 HOH A 31 2031 2031 HOH HOH . J 7 HOH A 32 2032 2032 HOH HOH . J 7 HOH A 33 2033 2033 HOH HOH . J 7 HOH A 34 2034 2034 HOH HOH . J 7 HOH A 35 2035 2035 HOH HOH . J 7 HOH A 36 2036 2036 HOH HOH . J 7 HOH A 37 2037 2037 HOH HOH . J 7 HOH A 38 2038 2038 HOH HOH . J 7 HOH A 39 2039 2039 HOH HOH . J 7 HOH A 40 2040 2040 HOH HOH . J 7 HOH A 41 2041 2041 HOH HOH . J 7 HOH A 42 2042 2042 HOH HOH . J 7 HOH A 43 2043 2043 HOH HOH . J 7 HOH A 44 2044 2044 HOH HOH . J 7 HOH A 45 2045 2045 HOH HOH . J 7 HOH A 46 2046 2046 HOH HOH . J 7 HOH A 47 2047 2047 HOH HOH . J 7 HOH A 48 2048 2048 HOH HOH . J 7 HOH A 49 2049 2049 HOH HOH . J 7 HOH A 50 2050 2050 HOH HOH . J 7 HOH A 51 2051 2051 HOH HOH . J 7 HOH A 52 2052 2052 HOH HOH . J 7 HOH A 53 2053 2053 HOH HOH . J 7 HOH A 54 2054 2054 HOH HOH . J 7 HOH A 55 2055 2055 HOH HOH . J 7 HOH A 56 2056 2056 HOH HOH . J 7 HOH A 57 2057 2057 HOH HOH . J 7 HOH A 58 2058 2058 HOH HOH . J 7 HOH A 59 2059 2059 HOH HOH . J 7 HOH A 60 2060 2060 HOH HOH . J 7 HOH A 61 2061 2061 HOH HOH . J 7 HOH A 62 2062 2062 HOH HOH . J 7 HOH A 63 2063 2063 HOH HOH . J 7 HOH A 64 2064 2064 HOH HOH . J 7 HOH A 65 2065 2065 HOH HOH . J 7 HOH A 66 2066 2066 HOH HOH . J 7 HOH A 67 2067 2067 HOH HOH . J 7 HOH A 68 2068 2068 HOH HOH . J 7 HOH A 69 2069 2069 HOH HOH . J 7 HOH A 70 2070 2070 HOH HOH . J 7 HOH A 71 2071 2071 HOH HOH . J 7 HOH A 72 2072 2072 HOH HOH . J 7 HOH A 73 2073 2073 HOH HOH . J 7 HOH A 74 2074 2074 HOH HOH . J 7 HOH A 75 2075 2075 HOH HOH . J 7 HOH A 76 2076 2076 HOH HOH . J 7 HOH A 77 2077 2077 HOH HOH . J 7 HOH A 78 2078 2078 HOH HOH . J 7 HOH A 79 2079 2079 HOH HOH . J 7 HOH A 80 2080 2080 HOH HOH . J 7 HOH A 81 2081 2081 HOH HOH . J 7 HOH A 82 2082 2082 HOH HOH . J 7 HOH A 83 2083 2083 HOH HOH . J 7 HOH A 84 2084 2084 HOH HOH . J 7 HOH A 85 2085 2085 HOH HOH . J 7 HOH A 86 2086 2086 HOH HOH . J 7 HOH A 87 2087 2087 HOH HOH . J 7 HOH A 88 2088 2088 HOH HOH . J 7 HOH A 89 2089 2089 HOH HOH . J 7 HOH A 90 2090 2090 HOH HOH . J 7 HOH A 91 2091 2091 HOH HOH . J 7 HOH A 92 2092 2092 HOH HOH . J 7 HOH A 93 2093 2093 HOH HOH . J 7 HOH A 94 2094 2094 HOH HOH . J 7 HOH A 95 2095 2095 HOH HOH . J 7 HOH A 96 2096 2096 HOH HOH . K 7 HOH B 1 2001 2001 HOH HOH . K 7 HOH B 2 2002 2002 HOH HOH . K 7 HOH B 3 2003 2003 HOH HOH . K 7 HOH B 4 2004 2004 HOH HOH . K 7 HOH B 5 2005 2005 HOH HOH . K 7 HOH B 6 2006 2006 HOH HOH . K 7 HOH B 7 2007 2007 HOH HOH . K 7 HOH B 8 2008 2008 HOH HOH . K 7 HOH B 9 2009 2009 HOH HOH . K 7 HOH B 10 2010 2010 HOH HOH . K 7 HOH B 11 2011 2011 HOH HOH . K 7 HOH B 12 2012 2012 HOH HOH . K 7 HOH B 13 2013 2013 HOH HOH . K 7 HOH B 14 2014 2014 HOH HOH . K 7 HOH B 15 2015 2015 HOH HOH . K 7 HOH B 16 2016 2016 HOH HOH . K 7 HOH B 17 2017 2017 HOH HOH . K 7 HOH B 18 2018 2018 HOH HOH . K 7 HOH B 19 2019 2019 HOH HOH . K 7 HOH B 20 2020 2020 HOH HOH . K 7 HOH B 21 2021 2021 HOH HOH . K 7 HOH B 22 2022 2022 HOH HOH . K 7 HOH B 23 2023 2023 HOH HOH . K 7 HOH B 24 2024 2024 HOH HOH . K 7 HOH B 25 2025 2025 HOH HOH . K 7 HOH B 26 2026 2026 HOH HOH . K 7 HOH B 27 2027 2027 HOH HOH . K 7 HOH B 28 2028 2028 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 . . . I 3 43.277 35.115 155.708 1 78.68 ? PB GDP 1260 B 1 HETATM 2 O O1B GDP . . . I 3 43.052 33.981 154.752 1 80.09 ? O1B GDP 1260 B 1 HETATM 3 O O2B GDP . . . I 3 42.453 34.99 157.009 1 78.62 ? O2B GDP 1260 B 1 HETATM 4 O O3B GDP . . . I 3 42.982 36.485 155.079 1 80.83 ? O3B GDP 1260 B 1 HETATM 5 O O3A GDP . . . I 3 44.816 35.15 156.126 1 74.27 ? O3A GDP 1260 B 1 HETATM 6 P PA GDP . . . I 3 45.822 34.016 156.624 1 67.93 ? PA GDP 1260 B 1 HETATM 7 O O1A GDP . . . I 3 46.149 33.096 155.504 1 67.33 ? O1A GDP 1260 B 1 HETATM 8 O O2A GDP . . . I 3 47.096 34.698 157.105 1 67.48 ? O2A GDP 1260 B 1 HETATM 9 O O5' GDP . . . I 3 45.029 33.356 157.855 1 61.56 ? O5' GDP 1260 B 1 HETATM 10 C C5' GDP . . . I 3 45.538 32.576 158.959 1 53.6 ? C5' GDP 1260 B 1 HETATM 11 C C4' GDP . . . I 3 44.882 32.965 160.267 1 46.46 ? C4' GDP 1260 B 1 HETATM 12 O O4' GDP . . . I 3 45.893 33.096 161.292 1 41.57 ? O4' GDP 1260 B 1 HETATM 13 C C3' GDP . . . I 3 44.117 34.287 160.306 1 44.7 ? C3' GDP 1260 B 1 HETATM 14 O O3' GDP . . . I 3 43.145 34.296 161.345 1 42.52 ? O3' GDP 1260 B 1 HETATM 15 C C2' GDP . . . I 3 45.228 35.282 160.634 1 44.37 ? C2' GDP 1260 B 1 HETATM 16 O O2' GDP . . . I 3 44.758 36.494 161.21 1 47.44 ? O2' GDP 1260 B 1 HETATM 17 C C1' GDP . . . I 3 46.077 34.464 161.616 1 39.94 ? C1' GDP 1260 B 1 HETATM 18 N N9 GDP . . . I 3 47.508 34.761 161.533 1 34.92 ? N9 GDP 1260 B 1 HETATM 19 C C8 GDP . . . I 3 48.18 35.434 160.54 1 32.81 ? C8 GDP 1260 B 1 HETATM 20 N N7 GDP . . . I 3 49.453 35.605 160.803 1 29.88 ? N7 GDP 1260 B 1 HETATM 21 C C5 GDP . . . I 3 49.629 34.998 162.036 1 25.41 ? C5 GDP 1260 B 1 HETATM 22 C C6 GDP . . . I 3 50.778 34.83 162.813 1 25.82 ? C6 GDP 1260 B 1 HETATM 23 O O6 GDP . . . I 3 51.865 35.368 162.616 1 25.22 ? O6 GDP 1260 B 1 HETATM 24 N N1 GDP . . . I 3 50.56 34.051 163.94 1 28.49 ? N1 GDP 1260 B 1 HETATM 25 C C2 GDP . . . I 3 49.348 33.523 164.302 1 27.06 ? C2 GDP 1260 B 1 HETATM 26 N N2 GDP . . . I 3 49.295 32.846 165.45 1 25.46 ? N2 GDP 1260 B 1 HETATM 27 N N3 GDP . . . I 3 48.239 33.701 163.588 1 25.03 ? N3 GDP 1260 B 1 HETATM 28 C C4 GDP . . . I 3 48.446 34.451 162.484 1 27.67 ? C4 GDP 1260 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #