data_1AFK # _model_server_result.job_id zRCUceXrJ09KQIo2B262AQ _model_server_result.datetime_utc '2024-10-26 10:23:15' _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 1afk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":125}' # _entry.id 1AFK # _exptl.entry_id 1AFK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-PHOSPHATE-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 90.09 _cell.angle_gamma 90 _cell.entry_id 1AFK _cell.length_a 101.54 _cell.length_b 33.36 _cell.length_c 73.25 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1AFK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 D N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 26 A CYS 26 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 40 A CYS 40 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 58 A CYS 58 1_555 A SG CYS 110 A CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf4 A SG CYS 65 A CYS 65 1_555 A SG CYS 72 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 B SG CYS 26 B CYS 26 1_555 B SG CYS 84 B CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 B SG CYS 40 B CYS 40 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf7 B SG CYS 58 B CYS 58 1_555 B SG CYS 110 B CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf8 B SG CYS 65 B CYS 65 1_555 B SG CYS 72 B CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id PAP _chem_comp.mon_nstd_flag . _chem_comp.name "3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1AFK _atom_sites.fract_transf_matrix[1][1] 0.009848 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000015 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.029976 _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] 0.013652 _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 PAP A 1 125 125 PAP PAP . D 2 PAP B 1 125 125 PAP PAP . E 3 HOH A 1 126 22 HOH HOH . E 3 HOH A 2 127 23 HOH HOH . E 3 HOH A 3 128 24 HOH HOH . E 3 HOH A 4 129 25 HOH HOH . E 3 HOH A 5 130 26 HOH HOH . E 3 HOH A 6 131 29 HOH HOH . E 3 HOH A 7 132 32 HOH HOH . E 3 HOH A 8 133 35 HOH HOH . E 3 HOH A 9 134 36 HOH HOH . E 3 HOH A 10 135 37 HOH HOH . E 3 HOH A 11 136 38 HOH HOH . E 3 HOH A 12 137 39 HOH HOH . E 3 HOH A 13 138 40 HOH HOH . E 3 HOH A 14 139 41 HOH HOH . E 3 HOH A 15 140 42 HOH HOH . E 3 HOH A 16 141 43 HOH HOH . E 3 HOH A 17 142 44 HOH HOH . E 3 HOH A 18 143 45 HOH HOH . E 3 HOH A 19 144 46 HOH HOH . E 3 HOH A 20 145 47 HOH HOH . E 3 HOH A 21 146 48 HOH HOH . E 3 HOH A 22 147 49 HOH HOH . E 3 HOH A 23 148 50 HOH HOH . E 3 HOH A 24 149 51 HOH HOH . E 3 HOH A 25 150 52 HOH HOH . E 3 HOH A 26 151 53 HOH HOH . E 3 HOH A 27 152 54 HOH HOH . E 3 HOH A 28 153 55 HOH HOH . E 3 HOH A 29 154 56 HOH HOH . E 3 HOH A 30 155 57 HOH HOH . E 3 HOH A 31 156 58 HOH HOH . E 3 HOH A 32 157 59 HOH HOH . E 3 HOH A 33 158 60 HOH HOH . E 3 HOH A 34 159 61 HOH HOH . E 3 HOH A 35 160 62 HOH HOH . E 3 HOH A 36 161 63 HOH HOH . E 3 HOH A 37 162 64 HOH HOH . E 3 HOH A 38 163 65 HOH HOH . E 3 HOH A 39 164 66 HOH HOH . E 3 HOH A 40 165 67 HOH HOH . E 3 HOH A 41 166 68 HOH HOH . E 3 HOH A 42 167 69 HOH HOH . E 3 HOH A 43 168 70 HOH HOH . E 3 HOH A 44 169 71 HOH HOH . E 3 HOH A 45 170 72 HOH HOH . E 3 HOH A 46 171 73 HOH HOH . E 3 HOH A 47 172 75 HOH HOH . E 3 HOH A 48 173 76 HOH HOH . E 3 HOH A 49 174 77 HOH HOH . E 3 HOH A 50 175 78 HOH HOH . E 3 HOH A 51 176 79 HOH HOH . E 3 HOH A 52 177 80 HOH HOH . E 3 HOH A 53 178 81 HOH HOH . E 3 HOH A 54 179 82 HOH HOH . E 3 HOH A 55 180 83 HOH HOH . E 3 HOH A 56 181 84 HOH HOH . E 3 HOH A 57 182 85 HOH HOH . E 3 HOH A 58 183 86 HOH HOH . E 3 HOH A 59 184 87 HOH HOH . E 3 HOH A 60 185 88 HOH HOH . E 3 HOH A 61 186 89 HOH HOH . E 3 HOH A 62 187 90 HOH HOH . E 3 HOH A 63 188 131 HOH HOH . E 3 HOH A 64 189 132 HOH HOH . E 3 HOH A 65 190 133 HOH HOH . E 3 HOH A 66 191 134 HOH HOH . E 3 HOH A 67 192 135 HOH HOH . E 3 HOH A 68 193 136 HOH HOH . E 3 HOH A 69 194 137 HOH HOH . E 3 HOH A 70 195 138 HOH HOH . E 3 HOH A 71 196 139 HOH HOH . E 3 HOH A 72 197 140 HOH HOH . E 3 HOH A 73 198 141 HOH HOH . E 3 HOH A 74 199 142 HOH HOH . E 3 HOH A 75 200 143 HOH HOH . E 3 HOH A 76 201 144 HOH HOH . E 3 HOH A 77 202 145 HOH HOH . E 3 HOH A 78 203 146 HOH HOH . E 3 HOH A 79 204 147 HOH HOH . E 3 HOH A 80 205 148 HOH HOH . E 3 HOH A 81 206 149 HOH HOH . E 3 HOH A 82 207 150 HOH HOH . E 3 HOH A 83 208 151 HOH HOH . E 3 HOH A 84 209 152 HOH HOH . E 3 HOH A 85 210 153 HOH HOH . E 3 HOH A 86 211 154 HOH HOH . E 3 HOH A 87 212 155 HOH HOH . E 3 HOH A 88 213 157 HOH HOH . E 3 HOH A 89 214 158 HOH HOH . E 3 HOH A 90 215 159 HOH HOH . E 3 HOH A 91 216 160 HOH HOH . E 3 HOH A 92 217 161 HOH HOH . E 3 HOH A 93 218 162 HOH HOH . F 3 HOH B 1 126 1 HOH HOH . F 3 HOH B 2 127 2 HOH HOH . F 3 HOH B 3 128 3 HOH HOH . F 3 HOH B 4 129 4 HOH HOH . F 3 HOH B 5 130 5 HOH HOH . F 3 HOH B 6 131 6 HOH HOH . F 3 HOH B 7 132 7 HOH HOH . F 3 HOH B 8 133 8 HOH HOH . F 3 HOH B 9 134 9 HOH HOH . F 3 HOH B 10 135 10 HOH HOH . F 3 HOH B 11 136 11 HOH HOH . F 3 HOH B 12 137 12 HOH HOH . F 3 HOH B 13 138 13 HOH HOH . F 3 HOH B 14 139 14 HOH HOH . F 3 HOH B 15 140 15 HOH HOH . F 3 HOH B 16 141 16 HOH HOH . F 3 HOH B 17 142 17 HOH HOH . F 3 HOH B 18 143 18 HOH HOH . F 3 HOH B 19 144 19 HOH HOH . F 3 HOH B 20 145 20 HOH HOH . F 3 HOH B 21 146 21 HOH HOH . F 3 HOH B 22 147 27 HOH HOH . F 3 HOH B 23 148 28 HOH HOH . F 3 HOH B 24 149 30 HOH HOH . F 3 HOH B 25 150 31 HOH HOH . F 3 HOH B 26 151 33 HOH HOH . F 3 HOH B 27 152 34 HOH HOH . F 3 HOH B 28 153 74 HOH HOH . F 3 HOH B 29 154 91 HOH HOH . F 3 HOH B 30 155 92 HOH HOH . F 3 HOH B 31 156 93 HOH HOH . F 3 HOH B 32 157 94 HOH HOH . F 3 HOH B 33 158 95 HOH HOH . F 3 HOH B 34 159 96 HOH HOH . F 3 HOH B 35 160 97 HOH HOH . F 3 HOH B 36 161 98 HOH HOH . F 3 HOH B 37 162 99 HOH HOH . F 3 HOH B 38 163 100 HOH HOH . F 3 HOH B 39 164 101 HOH HOH . F 3 HOH B 40 165 102 HOH HOH . F 3 HOH B 41 166 103 HOH HOH . F 3 HOH B 42 167 104 HOH HOH . F 3 HOH B 43 168 105 HOH HOH . F 3 HOH B 44 169 106 HOH HOH . F 3 HOH B 45 170 107 HOH HOH . F 3 HOH B 46 171 108 HOH HOH . F 3 HOH B 47 172 109 HOH HOH . F 3 HOH B 48 173 110 HOH HOH . F 3 HOH B 49 174 111 HOH HOH . F 3 HOH B 50 175 112 HOH HOH . F 3 HOH B 51 176 113 HOH HOH . F 3 HOH B 52 177 114 HOH HOH . F 3 HOH B 53 178 115 HOH HOH . F 3 HOH B 54 179 116 HOH HOH . F 3 HOH B 55 180 117 HOH HOH . F 3 HOH B 56 181 118 HOH HOH . F 3 HOH B 57 182 119 HOH HOH . F 3 HOH B 58 183 120 HOH HOH . F 3 HOH B 59 184 121 HOH HOH . F 3 HOH B 60 185 122 HOH HOH . F 3 HOH B 61 186 123 HOH HOH . F 3 HOH B 62 187 124 HOH HOH . F 3 HOH B 63 188 125 HOH HOH . F 3 HOH B 64 189 126 HOH HOH . F 3 HOH B 65 190 127 HOH HOH . F 3 HOH B 66 191 128 HOH HOH . F 3 HOH B 67 192 129 HOH HOH . F 3 HOH B 68 193 130 HOH HOH . F 3 HOH B 69 194 156 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 PAP . . . D 2 9.258 6.812 2.645 1 42.71 ? PB PAP 125 B 1 HETATM 2 O O1B PAP . . . D 2 10.422 6.162 1.996 1 41.46 ? O1B PAP 125 B 1 HETATM 3 O O2B PAP . . . D 2 8.945 6.26 4.012 1 44.05 ? O2B PAP 125 B 1 HETATM 4 O O3B PAP . . . D 2 8.067 7.007 1.764 1 42.42 ? O3B PAP 125 B 1 HETATM 5 P PA PAP . . . D 2 10.289 9.766 3.24 1 45.44 ? PA PAP 125 B 1 HETATM 6 O O1A PAP . . . D 2 10.561 9.64 4.712 1 44.56 ? O1A PAP 125 B 1 HETATM 7 O O2A PAP . . . D 2 9.823 11.13 2.79 1 45.17 ? O2A PAP 125 B 1 HETATM 8 O O3A PAP . . . D 2 9.292 8.504 2.626 1 43.62 ? O3A PAP 125 B 1 HETATM 9 O O5' PAP . . . D 2 11.481 9.226 2.221 1 41.38 ? O5' PAP 125 B 1 HETATM 10 C C5' PAP . . . D 2 11.05 8.984 0.867 1 37.59 ? C5' PAP 125 B 1 HETATM 11 C C4' PAP . . . D 2 11.886 9.754 -0.056 1 37.65 ? C4' PAP 125 B 1 HETATM 12 O O4' PAP . . . D 2 11.673 9.519 -1.454 1 36.22 ? O4' PAP 125 B 1 HETATM 13 C C3' PAP . . . D 2 11.59 11.105 0.204 1 38.78 ? C3' PAP 125 B 1 HETATM 14 O O3' PAP . . . D 2 12.911 11.729 -0.148 1 45.26 ? O3' PAP 125 B 1 HETATM 15 P P PAP . . . D 2 13.963 12.898 0.574 1 50.88 ? P PAP 125 B 1 HETATM 16 O O1 PAP . . . D 2 14.966 13.216 -0.521 1 47.76 ? O1 PAP 125 B 1 HETATM 17 O O2 PAP . . . D 2 13.1 14.071 1.018 1 48.87 ? O2 PAP 125 B 1 HETATM 18 O O3 PAP . . . D 2 14.472 12.027 1.692 1 48.79 ? O3 PAP 125 B 1 HETATM 19 C C2' PAP . . . D 2 10.395 11.134 -0.807 1 37.51 ? C2' PAP 125 B 1 HETATM 20 O O2' PAP . . . D 2 9.93 12.472 -0.479 1 37.82 ? O2' PAP 125 B 1 HETATM 21 C C1' PAP . . . D 2 11.404 10.789 -1.995 1 35.95 ? C1' PAP 125 B 1 HETATM 22 N N9 PAP . . . D 2 11.162 10.379 -3.457 1 35.15 ? N9 PAP 125 B 1 HETATM 23 C C8 PAP . . . D 2 12.127 10.402 -4.554 1 34.91 ? C8 PAP 125 B 1 HETATM 24 N N7 PAP . . . D 2 11.736 9.929 -5.752 1 31.85 ? N7 PAP 125 B 1 HETATM 25 C C5 PAP . . . D 2 10.38 9.561 -5.413 1 33.53 ? C5 PAP 125 B 1 HETATM 26 C C6 PAP . . . D 2 9.352 8.956 -6.172 1 30.77 ? C6 PAP 125 B 1 HETATM 27 N N6 PAP . . . D 2 9.548 8.784 -7.418 1 30.69 ? N6 PAP 125 B 1 HETATM 28 N N1 PAP . . . D 2 8.15 8.66 -5.608 1 29.69 ? N1 PAP 125 B 1 HETATM 29 C C2 PAP . . . D 2 7.987 8.988 -4.338 1 30.98 ? C2 PAP 125 B 1 HETATM 30 N N3 PAP . . . D 2 8.819 9.573 -3.446 1 33.34 ? N3 PAP 125 B 1 HETATM 31 C C4 PAP . . . D 2 10.034 9.831 -4.058 1 34.05 ? C4 PAP 125 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 226 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #