data_2YVO # _model_server_result.job_id KLAAD7uO4I6RO_J3Ssamjg _model_server_result.datetime_utc '2024-10-18 23:29:40' _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 2yvo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2001}' # _entry.id 2YVO # _exptl.entry_id 2YVO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _entity.pdbx_number_of_molecules 1 _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 2YVO _cell.length_a 40.699 _cell.length_b 100.899 _cell.length_c 97.172 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YVO _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA,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 1,2 # 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_656 -x+1,y,-z+3/2 -1 0 0 0 1 0 0 0 -1 40.699 0 145.758 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 2YVO _atom_sites.fract_transf_matrix[1][1] 0.024571 _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] 0.009911 _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] 0.010291 _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 B 2 MG A 1 1001 1001 MG MG . C 2 MG A 1 1002 1002 MG MG . D 2 MG A 1 1003 1003 MG MG . E 3 AMP A 1 2001 2001 AMP AMP . F 4 HOH A 1 2002 1 HOH HOH . F 4 HOH A 2 2003 2 HOH HOH . F 4 HOH A 3 2004 3 HOH HOH . F 4 HOH A 4 2005 4 HOH HOH . F 4 HOH A 5 2006 5 HOH HOH . F 4 HOH A 6 2007 6 HOH HOH . F 4 HOH A 7 2008 7 HOH HOH . F 4 HOH A 8 2009 8 HOH HOH . F 4 HOH A 9 2010 9 HOH HOH . F 4 HOH A 10 2011 10 HOH HOH . F 4 HOH A 11 2012 11 HOH HOH . F 4 HOH A 12 2013 12 HOH HOH . F 4 HOH A 13 2014 13 HOH HOH . F 4 HOH A 14 2015 14 HOH HOH . F 4 HOH A 15 2016 15 HOH HOH . F 4 HOH A 16 2017 16 HOH HOH . F 4 HOH A 17 2018 17 HOH HOH . F 4 HOH A 18 2019 18 HOH HOH . F 4 HOH A 19 2020 19 HOH HOH . F 4 HOH A 20 2021 20 HOH HOH . F 4 HOH A 21 2022 21 HOH HOH . F 4 HOH A 22 2023 22 HOH HOH . F 4 HOH A 23 2024 23 HOH HOH . F 4 HOH A 24 2025 24 HOH HOH . F 4 HOH A 25 2026 25 HOH HOH . F 4 HOH A 26 2027 26 HOH HOH . F 4 HOH A 27 2028 27 HOH HOH . F 4 HOH A 28 2029 28 HOH HOH . F 4 HOH A 29 2030 29 HOH HOH . F 4 HOH A 30 2031 30 HOH HOH . F 4 HOH A 31 2032 31 HOH HOH . F 4 HOH A 32 2033 32 HOH HOH . F 4 HOH A 33 2034 33 HOH HOH . F 4 HOH A 34 2035 34 HOH HOH . F 4 HOH A 35 2036 35 HOH HOH . F 4 HOH A 36 2037 36 HOH HOH . F 4 HOH A 37 2038 37 HOH HOH . F 4 HOH A 38 2039 38 HOH HOH . F 4 HOH A 39 2040 39 HOH HOH . F 4 HOH A 40 2041 40 HOH HOH . F 4 HOH A 41 2042 41 HOH HOH . F 4 HOH A 42 2043 42 HOH HOH . F 4 HOH A 43 2044 43 HOH HOH . F 4 HOH A 44 2045 44 HOH HOH . F 4 HOH A 45 2046 45 HOH HOH . F 4 HOH A 46 2047 46 HOH HOH . F 4 HOH A 47 2048 47 HOH HOH . F 4 HOH A 48 2049 48 HOH HOH . F 4 HOH A 49 2050 49 HOH HOH . F 4 HOH A 50 2051 50 HOH HOH . F 4 HOH A 51 2052 51 HOH HOH . F 4 HOH A 52 2053 52 HOH HOH . F 4 HOH A 53 2054 53 HOH HOH . F 4 HOH A 54 2055 54 HOH HOH . F 4 HOH A 55 2056 55 HOH HOH . F 4 HOH A 56 2057 56 HOH HOH . F 4 HOH A 57 2058 57 HOH HOH . F 4 HOH A 58 2059 58 HOH HOH . F 4 HOH A 59 2060 59 HOH HOH . F 4 HOH A 60 2061 60 HOH HOH . F 4 HOH A 61 2062 61 HOH HOH . F 4 HOH A 62 2063 62 HOH HOH . F 4 HOH A 63 2064 63 HOH HOH . F 4 HOH A 64 2065 64 HOH HOH . F 4 HOH A 65 2066 65 HOH HOH . F 4 HOH A 66 2067 66 HOH HOH . F 4 HOH A 67 2068 67 HOH HOH . F 4 HOH A 68 2069 68 HOH HOH . F 4 HOH A 69 2070 69 HOH HOH . F 4 HOH A 70 2071 70 HOH HOH . F 4 HOH A 71 2072 71 HOH HOH . F 4 HOH A 72 2073 72 HOH HOH . F 4 HOH A 73 2074 73 HOH HOH . F 4 HOH A 74 2075 74 HOH HOH . F 4 HOH A 75 2076 75 HOH HOH . F 4 HOH A 76 2077 76 HOH HOH . F 4 HOH A 77 2078 77 HOH HOH . F 4 HOH A 78 2079 78 HOH HOH . F 4 HOH A 79 2080 79 HOH HOH . F 4 HOH A 80 2081 80 HOH HOH . F 4 HOH A 81 2082 81 HOH HOH . F 4 HOH A 82 2083 82 HOH HOH . F 4 HOH A 83 2084 83 HOH HOH . F 4 HOH A 84 2085 84 HOH HOH . F 4 HOH A 85 2086 85 HOH HOH . F 4 HOH A 86 2087 86 HOH HOH . F 4 HOH A 87 2088 87 HOH HOH . F 4 HOH A 88 2089 88 HOH HOH . F 4 HOH A 89 2090 89 HOH HOH . F 4 HOH A 90 2091 90 HOH HOH . F 4 HOH A 91 2092 91 HOH HOH . F 4 HOH A 92 2093 92 HOH HOH . F 4 HOH A 93 2094 93 HOH HOH . F 4 HOH A 94 2095 94 HOH HOH . F 4 HOH A 95 2096 95 HOH HOH . F 4 HOH A 96 2097 96 HOH HOH . F 4 HOH A 97 2098 97 HOH HOH . F 4 HOH A 98 2099 98 HOH HOH . F 4 HOH A 99 2100 99 HOH HOH . F 4 HOH A 100 2101 100 HOH HOH . F 4 HOH A 101 2102 101 HOH HOH . F 4 HOH A 102 2103 102 HOH HOH . F 4 HOH A 103 2104 103 HOH HOH . F 4 HOH A 104 2105 104 HOH HOH . F 4 HOH A 105 2106 105 HOH HOH . F 4 HOH A 106 2107 106 HOH HOH . F 4 HOH A 107 2108 107 HOH HOH . F 4 HOH A 108 2109 108 HOH HOH . F 4 HOH A 109 2110 109 HOH HOH . F 4 HOH A 110 2111 110 HOH HOH . F 4 HOH A 111 2112 111 HOH HOH . F 4 HOH A 112 2113 112 HOH HOH . F 4 HOH A 113 2114 113 HOH HOH . F 4 HOH A 114 2115 114 HOH HOH . F 4 HOH A 115 2116 115 HOH HOH . F 4 HOH A 116 2117 116 HOH HOH . F 4 HOH A 117 2118 117 HOH HOH . F 4 HOH A 118 2119 118 HOH HOH . F 4 HOH A 119 2120 119 HOH HOH . F 4 HOH A 120 2121 120 HOH HOH . F 4 HOH A 121 2122 121 HOH HOH . F 4 HOH A 122 2123 122 HOH HOH . F 4 HOH A 123 2124 123 HOH HOH . F 4 HOH A 124 2125 124 HOH HOH . F 4 HOH A 125 2126 125 HOH HOH . F 4 HOH A 126 2127 126 HOH HOH . F 4 HOH A 127 2128 127 HOH HOH . F 4 HOH A 128 2129 128 HOH HOH . F 4 HOH A 129 2130 129 HOH HOH . F 4 HOH A 130 2131 130 HOH HOH . F 4 HOH A 131 2132 131 HOH HOH . F 4 HOH A 132 2133 132 HOH HOH . F 4 HOH A 133 2134 133 HOH HOH . F 4 HOH A 134 2135 134 HOH HOH . F 4 HOH A 135 2136 135 HOH HOH . F 4 HOH A 136 2137 136 HOH HOH . F 4 HOH A 137 2138 137 HOH HOH . F 4 HOH A 138 2139 138 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 P AMP . . . E 3 11.432 31.405 61.963 1 7.68 ? P AMP 2001 A 1 HETATM 2 O O1P AMP . . . E 3 11.458 30.238 60.964 1 7.89 ? O1P AMP 2001 A 1 HETATM 3 O O2P AMP . . . E 3 12.364 31.119 63.087 1 9.45 ? O2P AMP 2001 A 1 HETATM 4 O O3P AMP . . . E 3 10.012 31.658 62.517 1 8.01 ? O3P AMP 2001 A 1 HETATM 5 O O5' AMP . . . E 3 12.043 32.768 61.365 1 12.73 ? O5' AMP 2001 A 1 HETATM 6 C C5' AMP . . . E 3 11.59 33.513 60.342 1 18.03 ? C5' AMP 2001 A 1 HETATM 7 C C4' AMP . . . E 3 12.347 34.868 60.256 1 17.83 ? C4' AMP 2001 A 1 HETATM 8 O O4' AMP . . . E 3 12.678 35.632 61.478 1 17.47 ? O4' AMP 2001 A 1 HETATM 9 C C3' AMP . . . E 3 13.618 34.798 59.415 1 20.26 ? C3' AMP 2001 A 1 HETATM 10 O O3' AMP . . . E 3 13.441 35.404 58.167 1 21.24 ? O3' AMP 2001 A 1 HETATM 11 C C2' AMP . . . E 3 14.693 35.467 60.235 1 19.22 ? C2' AMP 2001 A 1 HETATM 12 O O2' AMP . . . E 3 15.554 36.304 59.485 1 23.42 ? O2' AMP 2001 A 1 HETATM 13 C C1' AMP . . . E 3 13.977 36.221 61.339 1 16.58 ? C1' AMP 2001 A 1 HETATM 14 N N9 AMP . . . E 3 14.85 36.278 62.558 1 13.04 ? N9 AMP 2001 A 1 HETATM 15 C C8 AMP . . . E 3 15.113 35.295 63.483 1 11.88 ? C8 AMP 2001 A 1 HETATM 16 N N7 AMP . . . E 3 16.018 35.772 64.401 1 11.24 ? N7 AMP 2001 A 1 HETATM 17 C C5 AMP . . . E 3 16.323 37.046 64.053 1 10.8 ? C5 AMP 2001 A 1 HETATM 18 C C6 AMP . . . E 3 17.205 37.969 64.633 1 10.54 ? C6 AMP 2001 A 1 HETATM 19 N N6 AMP . . . E 3 17.917 37.632 65.702 1 9.71 ? N6 AMP 2001 A 1 HETATM 20 N N1 AMP . . . E 3 17.309 39.24 64.028 1 9.33 ? N1 AMP 2001 A 1 HETATM 21 C C2 AMP . . . E 3 16.571 39.588 62.898 1 9.04 ? C2 AMP 2001 A 1 HETATM 22 N N3 AMP . . . E 3 15.703 38.656 62.321 1 10.29 ? N3 AMP 2001 A 1 HETATM 23 C C4 AMP . . . E 3 15.593 37.396 62.908 1 11.57 ? C4 AMP 2001 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 383 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 23 #