data_1AV5 # _model_server_result.job_id RVPrYTLrpEAlGU_PRtbkqQ _model_server_result.datetime_utc '2024-10-20 22:35:36' _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 1av5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":200}' # _entry.id 1AV5 # _exptl.entry_id 1AV5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 425.228 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 1AV5 _cell.length_a 46.2 _cell.length_b 77.8 _cell.length_c 80.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1AV5 _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 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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H17 N5 O9 P2' _chem_comp.formula_weight 425.228 _chem_comp.id AP2 _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 AP2 doub 19 n n PB O2B AP2 sing 20 n n PB O3B AP2 sing 21 n n PB C3A AP2 sing 22 n n O2B HOB2 AP2 sing 23 n n O3B HOB3 AP2 sing 24 n n C3A PA AP2 sing 25 n n C3A H3A1 AP2 sing 26 n n C3A H3A2 AP2 sing 27 n n PA O1A AP2 doub 28 n n PA O2A AP2 sing 29 n n PA O5' AP2 sing 30 n n O2A HOA2 AP2 sing 31 n n O5' C5' AP2 sing 32 n n C5' C4' AP2 sing 33 n n C5' "H5'1" AP2 sing 34 n n C5' "H5'2" AP2 sing 35 n n C4' O4' AP2 sing 36 n n C4' C3' AP2 sing 37 n n C4' H4' AP2 sing 38 n n O4' C1' AP2 sing 39 n n C3' O3' AP2 sing 40 n n C3' C2' AP2 sing 41 n n C3' H3' AP2 sing 42 n n O3' HO3' AP2 sing 43 n n C2' O2' AP2 sing 44 n n C2' C1' AP2 sing 45 n n C2' H2' AP2 sing 46 n n O2' HO2' AP2 sing 47 n n C1' N9 AP2 sing 48 n n C1' H1' AP2 sing 49 n n N9 C8 AP2 sing 50 n y N9 C4 AP2 sing 51 n y C8 N7 AP2 doub 52 n y C8 H8 AP2 sing 53 n n N7 C5 AP2 sing 54 n y C5 C6 AP2 sing 55 n y C5 C4 AP2 doub 56 n y C6 N6 AP2 sing 57 n n C6 N1 AP2 doub 58 n y N6 HN61 AP2 sing 59 n n N6 HN62 AP2 sing 60 n n N1 C2 AP2 sing 61 n y C2 N3 AP2 doub 62 n y C2 H2 AP2 sing 63 n n N3 C4 AP2 sing 64 n y # _atom_sites.entry_id 1AV5 _atom_sites.fract_transf_matrix[1][1] 0.021645 _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] 0.012853 _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] 0.012376 _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 AP2 B 1 200 200 AP2 AP2 . D 3 HOH A 1 127 1 HOH HOH . D 3 HOH A 2 128 2 HOH HOH . D 3 HOH A 3 129 6 HOH HOH . D 3 HOH A 4 130 8 HOH HOH . D 3 HOH A 5 131 9 HOH HOH . D 3 HOH A 6 132 11 HOH HOH . D 3 HOH A 7 133 12 HOH HOH . D 3 HOH A 8 134 13 HOH HOH . D 3 HOH A 9 135 14 HOH HOH . D 3 HOH A 10 136 16 HOH HOH . D 3 HOH A 11 137 17 HOH HOH . D 3 HOH A 12 138 18 HOH HOH . D 3 HOH A 13 139 19 HOH HOH . D 3 HOH A 14 140 21 HOH HOH . D 3 HOH A 15 141 23 HOH HOH . D 3 HOH A 16 142 24 HOH HOH . D 3 HOH A 17 143 25 HOH HOH . D 3 HOH A 18 144 26 HOH HOH . D 3 HOH A 19 145 27 HOH HOH . D 3 HOH A 20 146 28 HOH HOH . D 3 HOH A 21 147 29 HOH HOH . D 3 HOH A 22 148 30 HOH HOH . D 3 HOH A 23 149 31 HOH HOH . D 3 HOH A 24 150 32 HOH HOH . D 3 HOH A 25 151 33 HOH HOH . D 3 HOH A 26 152 34 HOH HOH . D 3 HOH A 27 153 36 HOH HOH . D 3 HOH A 28 154 37 HOH HOH . D 3 HOH A 29 155 38 HOH HOH . D 3 HOH A 30 156 39 HOH HOH . D 3 HOH A 31 157 40 HOH HOH . D 3 HOH A 32 158 41 HOH HOH . D 3 HOH A 33 159 42 HOH HOH . D 3 HOH A 34 160 43 HOH HOH . D 3 HOH A 35 161 44 HOH HOH . D 3 HOH A 36 162 45 HOH HOH . D 3 HOH A 37 163 46 HOH HOH . D 3 HOH A 38 164 47 HOH HOH . D 3 HOH A 39 165 48 HOH HOH . D 3 HOH A 40 166 49 HOH HOH . D 3 HOH A 41 167 52 HOH HOH . D 3 HOH A 42 168 55 HOH HOH . D 3 HOH A 43 169 56 HOH HOH . D 3 HOH A 44 170 58 HOH HOH . D 3 HOH A 45 171 59 HOH HOH . D 3 HOH A 46 172 60 HOH HOH . D 3 HOH A 47 173 61 HOH HOH . D 3 HOH A 48 174 67 HOH HOH . D 3 HOH A 49 175 70 HOH HOH . D 3 HOH A 50 176 71 HOH HOH . D 3 HOH A 51 177 76 HOH HOH . D 3 HOH A 52 178 77 HOH HOH . D 3 HOH A 53 179 79 HOH HOH . D 3 HOH A 54 180 80 HOH HOH . D 3 HOH A 55 181 81 HOH HOH . D 3 HOH A 56 182 82 HOH HOH . D 3 HOH A 57 183 83 HOH HOH . D 3 HOH A 58 184 85 HOH HOH . D 3 HOH A 59 185 86 HOH HOH . D 3 HOH A 60 186 88 HOH HOH . D 3 HOH A 61 187 90 HOH HOH . D 3 HOH A 62 188 95 HOH HOH . D 3 HOH A 63 189 97 HOH HOH . D 3 HOH A 64 190 100 HOH HOH . D 3 HOH A 65 191 101 HOH HOH . D 3 HOH A 66 192 112 HOH HOH . D 3 HOH A 67 193 113 HOH HOH . D 3 HOH A 68 194 114 HOH HOH . D 3 HOH A 69 195 115 HOH HOH . D 3 HOH A 70 196 116 HOH HOH . D 3 HOH A 71 197 118 HOH HOH . E 3 HOH B 1 201 3 HOH HOH . E 3 HOH B 2 202 4 HOH HOH . E 3 HOH B 3 203 5 HOH HOH . E 3 HOH B 4 204 7 HOH HOH . E 3 HOH B 5 205 10 HOH HOH . E 3 HOH B 6 206 15 HOH HOH . E 3 HOH B 7 207 20 HOH HOH . E 3 HOH B 8 208 22 HOH HOH . E 3 HOH B 9 209 35 HOH HOH . E 3 HOH B 10 210 50 HOH HOH . E 3 HOH B 11 211 51 HOH HOH . E 3 HOH B 12 212 53 HOH HOH . E 3 HOH B 13 213 54 HOH HOH . E 3 HOH B 14 214 57 HOH HOH . E 3 HOH B 15 215 62 HOH HOH . E 3 HOH B 16 216 63 HOH HOH . E 3 HOH B 17 217 64 HOH HOH . E 3 HOH B 18 218 65 HOH HOH . E 3 HOH B 19 219 66 HOH HOH . E 3 HOH B 20 220 68 HOH HOH . E 3 HOH B 21 221 69 HOH HOH . E 3 HOH B 22 222 73 HOH HOH . E 3 HOH B 23 223 74 HOH HOH . E 3 HOH B 24 224 78 HOH HOH . E 3 HOH B 25 225 84 HOH HOH . E 3 HOH B 26 226 87 HOH HOH . E 3 HOH B 27 227 89 HOH HOH . E 3 HOH B 28 228 91 HOH HOH . E 3 HOH B 29 229 92 HOH HOH . E 3 HOH B 30 230 93 HOH HOH . E 3 HOH B 31 231 94 HOH HOH . E 3 HOH B 32 232 96 HOH HOH . E 3 HOH B 33 233 98 HOH HOH . E 3 HOH B 34 234 99 HOH HOH . E 3 HOH B 35 235 102 HOH HOH . E 3 HOH B 36 236 103 HOH HOH . E 3 HOH B 37 237 104 HOH HOH . E 3 HOH B 38 238 105 HOH HOH . E 3 HOH B 39 239 106 HOH HOH . E 3 HOH B 40 240 107 HOH HOH . E 3 HOH B 41 241 108 HOH HOH . E 3 HOH B 42 242 109 HOH HOH . E 3 HOH B 43 243 110 HOH HOH . E 3 HOH B 44 244 111 HOH HOH . E 3 HOH B 45 245 117 HOH HOH . E 3 HOH B 46 246 119 HOH HOH . E 3 HOH B 47 247 120 HOH HOH . E 3 HOH B 48 248 121 HOH HOH . E 3 HOH B 49 249 122 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 AP2 . . . C 2 43.174 31.463 48.444 1 88.51 ? PB AP2 200 B 1 HETATM 2 O O1B AP2 . . . C 2 43.269 30.257 47.55 1 87.12 ? O1B AP2 200 B 1 HETATM 3 O O2B AP2 . . . C 2 43.689 32.654 47.774 1 89.9 ? O2B AP2 200 B 1 HETATM 4 O O3B AP2 . . . C 2 43.745 31.352 49.835 1 80.39 ? O3B AP2 200 B 1 HETATM 5 C C3A AP2 . . . C 2 41.443 31.652 48.624 1 79.35 ? C3A AP2 200 B 1 HETATM 6 P PA AP2 . . . C 2 40.545 32.747 49.426 1 68.02 ? PA AP2 200 B 1 HETATM 7 O O1A AP2 . . . C 2 40.998 34.147 49.336 1 70.52 ? O1A AP2 200 B 1 HETATM 8 O O2A AP2 . . . C 2 39.133 32.83 48.987 1 71.64 ? O2A AP2 200 B 1 HETATM 9 O O5' AP2 . . . C 2 40.596 32.35 50.978 1 73.31 ? O5' AP2 200 B 1 HETATM 10 C C5' AP2 . . . C 2 41.919 32.205 51.571 1 69.58 ? C5' AP2 200 B 1 HETATM 11 C C4' AP2 . . . C 2 41.977 32.45 53.114 1 60.88 ? C4' AP2 200 B 1 HETATM 12 O O4' AP2 . . . C 2 41.311 31.442 53.94 1 57.84 ? O4' AP2 200 B 1 HETATM 13 C C3' AP2 . . . C 2 43.473 32.249 53.389 1 54.12 ? C3' AP2 200 B 1 HETATM 14 O O3' AP2 . . . C 2 44.075 33.474 53.814 1 54.39 ? O3' AP2 200 B 1 HETATM 15 C C2' AP2 . . . C 2 43.55 31.113 54.538 1 51.03 ? C2' AP2 200 B 1 HETATM 16 O O2' AP2 . . . C 2 44.559 31.082 55.582 1 39.75 ? O2' AP2 200 B 1 HETATM 17 C C1' AP2 . . . C 2 42.185 31.346 55.14 1 56.65 ? C1' AP2 200 B 1 HETATM 18 N N9 AP2 . . . C 2 41.606 30.3 56.053 1 60.94 ? N9 AP2 200 B 1 HETATM 19 C C8 AP2 . . . C 2 41.488 28.948 55.787 1 59.96 ? C8 AP2 200 B 1 HETATM 20 N N7 AP2 . . . C 2 41.291 28.175 56.84 1 60.67 ? N7 AP2 200 B 1 HETATM 21 C C5 AP2 . . . C 2 41.28 29.113 57.901 1 59.12 ? C5 AP2 200 B 1 HETATM 22 C C6 AP2 . . . C 2 41.101 28.955 59.366 1 53.48 ? C6 AP2 200 B 1 HETATM 23 N N6 AP2 . . . C 2 40.909 27.733 59.917 1 44.19 ? N6 AP2 200 B 1 HETATM 24 N N1 AP2 . . . C 2 41.152 30.113 60.073 1 50.76 ? N1 AP2 200 B 1 HETATM 25 C C2 AP2 . . . C 2 41.344 31.339 59.532 1 55.31 ? C2 AP2 200 B 1 HETATM 26 N N3 AP2 . . . C 2 41.514 31.568 58.211 1 60.5 ? N3 AP2 200 B 1 HETATM 27 C C4 AP2 . . . C 2 41.47 30.404 57.447 1 58.88 ? C4 AP2 200 B 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #