data_1V1A # _model_server_result.job_id wGm3UJ2XCosVSw0tPqxPiw _model_server_result.datetime_utc '2024-11-28 09:28:33' _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 1v1a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1303}' # _entry.id 1V1A # _exptl.entry_id 1V1A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-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 120 _cell.entry_id 1V1A _cell.length_a 84.321 _cell.length_b 84.321 _cell.length_c 168.701 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1V1A _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 42.1605 73.024128 0 3 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 84.321 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 1V1A _atom_sites.fract_transf_matrix[1][1] 0.011859 _atom_sites.fract_transf_matrix[1][2] 0.006847 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013694 _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] 0.005928 _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 KDG A 1 1302 1302 KDG KDG . D 3 ADP A 1 1303 1303 ADP ADP . E 2 KDG B 1 1302 1302 KDG KDG . F 3 ADP B 1 1303 1303 ADP ADP . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . G 4 HOH A 7 2007 2007 HOH HOH . G 4 HOH A 8 2008 2008 HOH HOH . G 4 HOH A 9 2009 2009 HOH HOH . G 4 HOH A 10 2010 2010 HOH HOH . G 4 HOH A 11 2011 2011 HOH HOH . G 4 HOH A 12 2012 2012 HOH HOH . G 4 HOH A 13 2013 2013 HOH HOH . G 4 HOH A 14 2014 2014 HOH HOH . G 4 HOH A 15 2015 2015 HOH HOH . G 4 HOH A 16 2016 2016 HOH HOH . G 4 HOH A 17 2017 2017 HOH HOH . G 4 HOH A 18 2018 2018 HOH HOH . G 4 HOH A 19 2019 2019 HOH HOH . G 4 HOH A 20 2020 2020 HOH HOH . G 4 HOH A 21 2021 2021 HOH HOH . G 4 HOH A 22 2022 2022 HOH HOH . G 4 HOH A 23 2023 2023 HOH HOH . G 4 HOH A 24 2024 2024 HOH HOH . G 4 HOH A 25 2025 2025 HOH HOH . G 4 HOH A 26 2026 2026 HOH HOH . G 4 HOH A 27 2027 2027 HOH HOH . G 4 HOH A 28 2028 2028 HOH HOH . G 4 HOH A 29 2029 2029 HOH HOH . G 4 HOH A 30 2030 2030 HOH HOH . G 4 HOH A 31 2031 2031 HOH HOH . G 4 HOH A 32 2032 2032 HOH HOH . G 4 HOH A 33 2033 2033 HOH HOH . G 4 HOH A 34 2034 2034 HOH HOH . G 4 HOH A 35 2035 2035 HOH HOH . G 4 HOH A 36 2036 2036 HOH HOH . G 4 HOH A 37 2037 2037 HOH HOH . G 4 HOH A 38 2038 2038 HOH HOH . G 4 HOH A 39 2039 2039 HOH HOH . G 4 HOH A 40 2040 2040 HOH HOH . G 4 HOH A 41 2041 2041 HOH HOH . G 4 HOH A 42 2042 2042 HOH HOH . G 4 HOH A 43 2043 2043 HOH HOH . G 4 HOH A 44 2044 2044 HOH HOH . G 4 HOH A 45 2045 2045 HOH HOH . G 4 HOH A 46 2046 2046 HOH HOH . G 4 HOH A 47 2047 2047 HOH HOH . G 4 HOH A 48 2048 2048 HOH HOH . G 4 HOH A 49 2049 2049 HOH HOH . G 4 HOH A 50 2050 2050 HOH HOH . G 4 HOH A 51 2051 2051 HOH HOH . G 4 HOH A 52 2052 2052 HOH HOH . G 4 HOH A 53 2053 2053 HOH HOH . G 4 HOH A 54 2054 2054 HOH HOH . G 4 HOH A 55 2055 2055 HOH HOH . G 4 HOH A 56 2056 2056 HOH HOH . G 4 HOH A 57 2057 2057 HOH HOH . G 4 HOH A 58 2058 2058 HOH HOH . G 4 HOH A 59 2059 2059 HOH HOH . G 4 HOH A 60 2060 2060 HOH HOH . G 4 HOH A 61 2061 2061 HOH HOH . G 4 HOH A 62 2062 2062 HOH HOH . G 4 HOH A 63 2063 2063 HOH HOH . G 4 HOH A 64 2064 2064 HOH HOH . G 4 HOH A 65 2065 2065 HOH HOH . G 4 HOH A 66 2066 2066 HOH HOH . G 4 HOH A 67 2067 2067 HOH HOH . G 4 HOH A 68 2068 2068 HOH HOH . G 4 HOH A 69 2069 2069 HOH HOH . G 4 HOH A 70 2070 2070 HOH HOH . G 4 HOH A 71 2071 2071 HOH HOH . G 4 HOH A 72 2072 2072 HOH HOH . G 4 HOH A 73 2073 2073 HOH HOH . G 4 HOH A 74 2074 2074 HOH HOH . G 4 HOH A 75 2075 2075 HOH HOH . G 4 HOH A 76 2076 2076 HOH HOH . G 4 HOH A 77 2077 2077 HOH HOH . G 4 HOH A 78 2078 2078 HOH HOH . G 4 HOH A 79 2079 2079 HOH HOH . G 4 HOH A 80 2080 2080 HOH HOH . G 4 HOH A 81 2081 2081 HOH HOH . G 4 HOH A 82 2082 2082 HOH HOH . G 4 HOH A 83 2083 2083 HOH HOH . G 4 HOH A 84 2084 2084 HOH HOH . G 4 HOH A 85 2085 2085 HOH HOH . G 4 HOH A 86 2086 2086 HOH HOH . G 4 HOH A 87 2087 2087 HOH HOH . G 4 HOH A 88 2088 2088 HOH HOH . G 4 HOH A 89 2089 2089 HOH HOH . G 4 HOH A 90 2090 2090 HOH HOH . G 4 HOH A 91 2091 2091 HOH HOH . G 4 HOH A 92 2092 2092 HOH HOH . G 4 HOH A 93 2093 2093 HOH HOH . G 4 HOH A 94 2094 2094 HOH HOH . G 4 HOH A 95 2095 2095 HOH HOH . G 4 HOH A 96 2096 2096 HOH HOH . G 4 HOH A 97 2097 2097 HOH HOH . G 4 HOH A 98 2098 2098 HOH HOH . G 4 HOH A 99 2099 2099 HOH HOH . G 4 HOH A 100 2100 2100 HOH HOH . G 4 HOH A 101 2101 2101 HOH HOH . G 4 HOH A 102 2102 2102 HOH HOH . G 4 HOH A 103 2103 2103 HOH HOH . G 4 HOH A 104 2104 2104 HOH HOH . G 4 HOH A 105 2105 2105 HOH HOH . G 4 HOH A 106 2106 2106 HOH HOH . G 4 HOH A 107 2107 2107 HOH HOH . G 4 HOH A 108 2108 2108 HOH HOH . G 4 HOH A 109 2109 2109 HOH HOH . G 4 HOH A 110 2110 2110 HOH HOH . G 4 HOH A 111 2111 2111 HOH HOH . G 4 HOH A 112 2112 2112 HOH HOH . G 4 HOH A 113 2113 2113 HOH HOH . G 4 HOH A 114 2114 2114 HOH HOH . G 4 HOH A 115 2115 2115 HOH HOH . G 4 HOH A 116 2116 2116 HOH HOH . G 4 HOH A 117 2117 2117 HOH HOH . G 4 HOH A 118 2118 2118 HOH HOH . G 4 HOH A 119 2119 2119 HOH HOH . G 4 HOH A 120 2120 2120 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 HOH HOH . H 4 HOH B 7 2007 2007 HOH HOH . H 4 HOH B 8 2008 2008 HOH HOH . H 4 HOH B 9 2009 2009 HOH HOH . H 4 HOH B 10 2010 2010 HOH HOH . H 4 HOH B 11 2011 2011 HOH HOH . H 4 HOH B 12 2012 2012 HOH HOH . H 4 HOH B 13 2013 2013 HOH HOH . H 4 HOH B 14 2014 2014 HOH HOH . H 4 HOH B 15 2015 2015 HOH HOH . H 4 HOH B 16 2016 2016 HOH HOH . H 4 HOH B 17 2017 2017 HOH HOH . H 4 HOH B 18 2018 2018 HOH HOH . H 4 HOH B 19 2019 2019 HOH HOH . H 4 HOH B 20 2020 2020 HOH HOH . H 4 HOH B 21 2021 2021 HOH HOH . H 4 HOH B 22 2022 2022 HOH HOH . H 4 HOH B 23 2023 2023 HOH HOH . H 4 HOH B 24 2024 2024 HOH HOH . H 4 HOH B 25 2025 2025 HOH HOH . H 4 HOH B 26 2026 2026 HOH HOH . H 4 HOH B 27 2027 2027 HOH HOH . H 4 HOH B 28 2028 2028 HOH HOH . H 4 HOH B 29 2029 2029 HOH HOH . H 4 HOH B 30 2030 2030 HOH HOH . H 4 HOH B 31 2031 2031 HOH HOH . H 4 HOH B 32 2032 2032 HOH HOH . H 4 HOH B 33 2033 2033 HOH HOH . H 4 HOH B 34 2034 2034 HOH HOH . H 4 HOH B 35 2035 2035 HOH HOH . H 4 HOH B 36 2036 2036 HOH HOH . H 4 HOH B 37 2037 2037 HOH HOH . H 4 HOH B 38 2038 2038 HOH HOH . H 4 HOH B 39 2039 2039 HOH HOH . H 4 HOH B 40 2040 2040 HOH HOH . H 4 HOH B 41 2041 2041 HOH HOH . H 4 HOH B 42 2042 2042 HOH HOH . H 4 HOH B 43 2043 2043 HOH HOH . H 4 HOH B 44 2044 2044 HOH HOH . H 4 HOH B 45 2045 2045 HOH HOH . H 4 HOH B 46 2046 2046 HOH HOH . H 4 HOH B 47 2047 2047 HOH HOH . H 4 HOH B 48 2048 2048 HOH HOH . H 4 HOH B 49 2049 2049 HOH HOH . H 4 HOH B 50 2050 2050 HOH HOH . H 4 HOH B 51 2051 2051 HOH HOH . H 4 HOH B 52 2052 2052 HOH HOH . H 4 HOH B 53 2053 2053 HOH HOH . H 4 HOH B 54 2054 2054 HOH HOH . H 4 HOH B 55 2055 2055 HOH HOH . H 4 HOH B 56 2056 2056 HOH HOH . H 4 HOH B 57 2057 2057 HOH HOH . H 4 HOH B 58 2058 2058 HOH HOH . H 4 HOH B 59 2059 2059 HOH HOH . H 4 HOH B 60 2060 2060 HOH HOH . H 4 HOH B 61 2061 2061 HOH HOH . H 4 HOH B 62 2062 2062 HOH HOH . H 4 HOH B 63 2063 2063 HOH HOH . H 4 HOH B 64 2064 2064 HOH HOH . H 4 HOH B 65 2065 2065 HOH HOH . H 4 HOH B 66 2066 2066 HOH HOH . H 4 HOH B 67 2067 2067 HOH HOH . H 4 HOH B 68 2068 2068 HOH HOH . H 4 HOH B 69 2069 2069 HOH HOH . H 4 HOH B 70 2070 2070 HOH HOH . H 4 HOH B 71 2071 2071 HOH HOH . H 4 HOH B 72 2072 2072 HOH HOH . H 4 HOH B 73 2073 2073 HOH HOH . H 4 HOH B 74 2074 2074 HOH HOH . H 4 HOH B 75 2075 2075 HOH HOH . H 4 HOH B 76 2076 2076 HOH HOH . H 4 HOH B 77 2077 2077 HOH HOH . H 4 HOH B 78 2078 2078 HOH HOH . H 4 HOH B 79 2079 2079 HOH HOH . H 4 HOH B 80 2080 2080 HOH HOH . H 4 HOH B 81 2081 2081 HOH HOH . H 4 HOH B 82 2082 2082 HOH HOH . H 4 HOH B 83 2083 2083 HOH HOH . H 4 HOH B 84 2084 2084 HOH HOH . H 4 HOH B 85 2085 2085 HOH HOH . H 4 HOH B 86 2086 2086 HOH HOH . H 4 HOH B 87 2087 2087 HOH HOH . H 4 HOH B 88 2088 2088 HOH HOH . H 4 HOH B 89 2089 2089 HOH HOH . H 4 HOH B 90 2090 2090 HOH HOH . H 4 HOH B 91 2091 2091 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 ADP . . . D 3 28.983 40.149 20.441 1 182.16 ? PB ADP 1303 A 1 HETATM 2 O O1B ADP . . . D 3 28.387 38.902 20.081 1 188.05 ? O1B ADP 1303 A 1 HETATM 3 O O2B ADP . . . D 3 27.906 41.122 20.539 1 181.56 ? O2B ADP 1303 A 1 HETATM 4 O O3B ADP . . . D 3 29.718 40.018 21.857 1 178.41 ? O3B ADP 1303 A 1 HETATM 5 P PA ADP . . . D 3 30.392 39.549 18.193 1 174.7 ? PA ADP 1303 A 1 HETATM 6 O O1A ADP . . . D 3 29.388 39.567 17.159 1 173.47 ? O1A ADP 1303 A 1 HETATM 7 O O2A ADP . . . D 3 30.468 38.2 18.738 1 173.67 ? O2A ADP 1303 A 1 HETATM 8 O O3A ADP . . . D 3 30.017 40.626 19.339 1 179.11 ? O3A ADP 1303 A 1 HETATM 9 O O5' ADP . . . D 3 31.726 39.866 17.581 1 169.69 ? O5' ADP 1303 A 1 HETATM 10 C C5' ADP . . . D 3 31.977 41.108 17.649 1 158.49 ? C5' ADP 1303 A 1 HETATM 11 C C4' ADP . . . D 3 33.418 41.49 17.48 1 150.36 ? C4' ADP 1303 A 1 HETATM 12 O O4' ADP . . . D 3 34.123 40.687 18.467 1 146.99 ? O4' ADP 1303 A 1 HETATM 13 C C3' ADP . . . D 3 33.658 40.987 16.118 1 148.35 ? C3' ADP 1303 A 1 HETATM 14 O O3' ADP . . . D 3 33.402 41.893 15.052 1 149.91 ? O3' ADP 1303 A 1 HETATM 15 C C2' ADP . . . D 3 35.111 40.471 16.271 1 144.05 ? C2' ADP 1303 A 1 HETATM 16 O O2' ADP . . . D 3 36.028 41.5 15.954 1 136.45 ? O2' ADP 1303 A 1 HETATM 17 C C1' ADP . . . D 3 35.242 40.021 17.777 1 142.91 ? C1' ADP 1303 A 1 HETATM 18 N N9 ADP . . . D 3 35.14 38.535 17.983 1 144.68 ? N9 ADP 1303 A 1 HETATM 19 C C8 ADP . . . D 3 34.121 37.75 18.564 1 143.56 ? C8 ADP 1303 A 1 HETATM 20 N N7 ADP . . . D 3 34.371 36.467 18.578 1 140.35 ? N7 ADP 1303 A 1 HETATM 21 C C5 ADP . . . D 3 35.625 36.402 17.971 1 145.05 ? C5 ADP 1303 A 1 HETATM 22 C C6 ADP . . . D 3 36.513 35.298 17.655 1 144.89 ? C6 ADP 1303 A 1 HETATM 23 N N6 ADP . . . D 3 36.201 34.05 17.934 1 145.87 ? N6 ADP 1303 A 1 HETATM 24 N N1 ADP . . . D 3 37.73 35.58 17.028 1 141.31 ? N1 ADP 1303 A 1 HETATM 25 C C2 ADP . . . D 3 38.07 36.846 16.727 1 141.61 ? C2 ADP 1303 A 1 HETATM 26 N N3 ADP . . . D 3 37.329 37.957 16.97 1 142.49 ? N3 ADP 1303 A 1 HETATM 27 C C4 ADP . . . D 3 36.096 37.651 17.612 1 144.47 ? C4 ADP 1303 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #