data_1O6B # _model_server_result.job_id BdJlDpJqXawaw4-ClJe0LQ _model_server_result.datetime_utc '2024-11-02 13:24:36' _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 1o6b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":173}' # _entry.id 1O6B # _exptl.entry_id 1O6B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 1O6B _cell.length_a 115.42 _cell.length_b 115.42 _cell.length_c 115.42 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1O6B _symmetry.cell_setting ? _symmetry.Int_Tables_number 213 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA,PQS hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 1 A,B,C,D,E,F 2 1,2,3,4,5,6 # 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' 8_746 -z+2,x-1/2,-y+3/2 0 0 -1 1 0 0 0 -1 0 230.84 -57.71 173.13 3 'crystal symmetry operation' 11_567 y+1/2,-z+3/2,-x+2 0 1 0 0 0 -1 -1 0 0 57.71 173.13 230.84 4 'crystal symmetry operation' 14_666 -y+7/4,-x+7/4,-z+7/4 0 -1 0 -1 0 0 0 0 -1 201.985 201.985 201.985 5 'crystal symmetry operation' 18_745 -x+9/4,z-1/4,y+1/4 -1 0 0 0 0 1 0 1 0 259.695 -28.855 28.855 6 'crystal symmetry operation' 22_564 z+1/4,-y+5/4,x-1/4 0 0 1 0 -1 0 1 0 0 28.855 144.275 -28.855 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A C GLU 99 A GLU 99 1_555 A N MSE 100 A MSE 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 A C MSE 100 A MSE 100 1_555 A N GLN 101 A GLN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C PHE 117 A PHE 117 1_555 A N MSE 118 A MSE 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C MSE 118 A MSE 118 1_555 A N MSE 119 A MSE 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? covale ? covale5 A C MSE 119 A MSE 119 1_555 A N ALA 120 A ALA 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.315 ? metalc ? metalc1 A OD1 ASP 139 A ASP 139 13_547 C MG MG . A MG 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.809 ? metalc ? metalc2 C MG MG . A MG 171 1_555 F O HOH . A HOH 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc3 C MG MG . A MG 171 1_555 F O HOH . A HOH 174 13_547 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc4 C MG MG . A MG 171 1_555 F O HOH . A HOH 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? # _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 1O6B _atom_sites.fract_transf_matrix[1][1] 0.008664 _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] 0.008664 _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] 0.008664 _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 PO4 A 1 170 2 PO4 PO4 . C 3 MG A 1 171 3 MG MG . D 4 CL A 1 172 4 CL CL . E 5 ADP A 1 173 1 ADP ADP . F 6 HOH A 1 174 5 HOH HOH . F 6 HOH A 2 175 6 HOH HOH . F 6 HOH A 3 176 7 HOH HOH . F 6 HOH A 4 177 8 HOH HOH . F 6 HOH A 5 178 9 HOH HOH . F 6 HOH A 6 179 10 HOH HOH . F 6 HOH A 7 180 11 HOH HOH . F 6 HOH A 8 181 12 HOH HOH . F 6 HOH A 9 182 13 HOH HOH . F 6 HOH A 10 183 14 HOH HOH . F 6 HOH A 11 184 15 HOH HOH . F 6 HOH A 12 185 16 HOH HOH . F 6 HOH A 13 186 17 HOH HOH . F 6 HOH A 14 187 18 HOH HOH . F 6 HOH A 15 188 19 HOH HOH . F 6 HOH A 16 189 20 HOH HOH . F 6 HOH A 17 190 21 HOH HOH . F 6 HOH A 18 191 22 HOH HOH . F 6 HOH A 19 192 23 HOH HOH . F 6 HOH A 20 193 24 HOH HOH . F 6 HOH A 21 194 25 HOH HOH . F 6 HOH A 22 195 26 HOH HOH . F 6 HOH A 23 196 27 HOH HOH . F 6 HOH A 24 197 28 HOH HOH . F 6 HOH A 25 198 29 HOH HOH . F 6 HOH A 26 199 30 HOH HOH . F 6 HOH A 27 200 31 HOH HOH . F 6 HOH A 28 201 32 HOH HOH . F 6 HOH A 29 202 33 HOH HOH . F 6 HOH A 30 203 34 HOH HOH . F 6 HOH A 31 204 35 HOH HOH . F 6 HOH A 32 205 36 HOH HOH . F 6 HOH A 33 206 37 HOH HOH . F 6 HOH A 34 207 38 HOH HOH . F 6 HOH A 35 208 39 HOH HOH . F 6 HOH A 36 209 40 HOH HOH . F 6 HOH A 37 210 41 HOH HOH . F 6 HOH A 38 211 42 HOH HOH . F 6 HOH A 39 212 43 HOH HOH . F 6 HOH A 40 213 44 HOH HOH . F 6 HOH A 41 214 45 HOH HOH . F 6 HOH A 42 215 46 HOH HOH . F 6 HOH A 43 216 47 HOH HOH . F 6 HOH A 44 217 48 HOH HOH . F 6 HOH A 45 218 49 HOH HOH . F 6 HOH A 46 219 50 HOH HOH . F 6 HOH A 47 220 51 HOH HOH . F 6 HOH A 48 221 52 HOH HOH . F 6 HOH A 49 222 53 HOH HOH . F 6 HOH A 50 223 54 HOH HOH . F 6 HOH A 51 224 55 HOH HOH . F 6 HOH A 52 225 56 HOH HOH . F 6 HOH A 53 226 57 HOH HOH . F 6 HOH A 54 227 58 HOH HOH . F 6 HOH A 55 228 59 HOH HOH . F 6 HOH A 56 229 60 HOH HOH . F 6 HOH A 57 230 61 HOH HOH . F 6 HOH A 58 231 62 HOH HOH . F 6 HOH A 59 232 63 HOH HOH . F 6 HOH A 60 233 64 HOH HOH . F 6 HOH A 61 234 65 HOH HOH . F 6 HOH A 62 235 66 HOH HOH . F 6 HOH A 63 236 67 HOH HOH . F 6 HOH A 64 237 68 HOH HOH . F 6 HOH A 65 238 69 HOH HOH . F 6 HOH A 66 239 70 HOH HOH . F 6 HOH A 67 240 71 HOH HOH . F 6 HOH A 68 241 72 HOH HOH . F 6 HOH A 69 242 73 HOH HOH . F 6 HOH A 70 243 74 HOH HOH . F 6 HOH A 71 244 75 HOH HOH . F 6 HOH A 72 245 76 HOH HOH . F 6 HOH A 73 246 77 HOH HOH . F 6 HOH A 74 247 78 HOH HOH . F 6 HOH A 75 248 79 HOH HOH . F 6 HOH A 76 249 80 HOH HOH . F 6 HOH A 77 250 81 HOH HOH . F 6 HOH A 78 251 82 HOH HOH . F 6 HOH A 79 252 83 HOH HOH . F 6 HOH A 80 253 84 HOH HOH . F 6 HOH A 81 254 85 HOH HOH . F 6 HOH A 82 255 86 HOH HOH . F 6 HOH A 83 256 87 HOH HOH . F 6 HOH A 84 257 88 HOH HOH . F 6 HOH A 85 258 89 HOH HOH . F 6 HOH A 86 259 90 HOH HOH . F 6 HOH A 87 260 91 HOH HOH . F 6 HOH A 88 261 92 HOH HOH . F 6 HOH A 89 262 93 HOH HOH . F 6 HOH A 90 263 94 HOH HOH . F 6 HOH A 91 264 95 HOH HOH . F 6 HOH A 92 265 96 HOH HOH . F 6 HOH A 93 266 97 HOH HOH . F 6 HOH A 94 267 98 HOH HOH . F 6 HOH A 95 268 99 HOH HOH . F 6 HOH A 96 269 100 HOH HOH . F 6 HOH A 97 270 101 HOH HOH . F 6 HOH A 98 271 102 HOH HOH . F 6 HOH A 99 272 103 HOH HOH . F 6 HOH A 100 273 104 HOH HOH . F 6 HOH A 101 274 105 HOH HOH . F 6 HOH A 102 275 106 HOH HOH . F 6 HOH A 103 276 107 HOH HOH . F 6 HOH A 104 277 108 HOH HOH . F 6 HOH A 105 278 109 HOH HOH . F 6 HOH A 106 279 110 HOH HOH . F 6 HOH A 107 280 111 HOH HOH . F 6 HOH A 108 281 112 HOH HOH . F 6 HOH A 109 282 113 HOH HOH . F 6 HOH A 110 283 114 HOH HOH . F 6 HOH A 111 284 115 HOH HOH . F 6 HOH A 112 285 116 HOH HOH . F 6 HOH A 113 286 117 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 . . . E 5 125.034 72.34 120.959 0.5 46.69 ? PB ADP 173 A 1 HETATM 2 O O1B ADP . . . E 5 124.234 73.565 121.254 0.5 48.77 ? O1B ADP 173 A 1 HETATM 3 O O2B ADP . . . E 5 125.679 72.439 119.502 0.5 48.8 ? O2B ADP 173 A 1 HETATM 4 O O3B ADP . . . E 5 124.029 71.062 121.03 0.5 48.06 ? O3B ADP 173 A 1 HETATM 5 P PA ADP . . . E 5 127.691 72.395 122.197 0.5 48.55 ? PA ADP 173 A 1 HETATM 6 O O1A ADP . . . E 5 128.147 72.357 123.632 0.5 46.61 ? O1A ADP 173 A 1 HETATM 7 O O2A ADP . . . E 5 128.495 71.331 121.319 0.5 47.94 ? O2A ADP 173 A 1 HETATM 8 O O3A ADP . . . E 5 126.142 72.165 122.066 0.5 48.42 ? O3A ADP 173 A 1 HETATM 9 O O5' ADP . . . E 5 128.08 73.896 121.618 0.5 49.59 ? O5' ADP 173 A 1 HETATM 10 C C5' ADP . . . E 5 129.111 74.639 122.262 0.5 49.31 ? C5' ADP 173 A 1 HETATM 11 C C4' ADP . . . E 5 129.423 76.028 121.837 0.5 49.6 ? C4' ADP 173 A 1 HETATM 12 O O4' ADP . . . E 5 130.828 76.233 121.598 0.5 49.44 ? O4' ADP 173 A 1 HETATM 13 C C3' ADP . . . E 5 128.76 76.479 120.504 0.5 49.39 ? C3' ADP 173 A 1 HETATM 14 O O3' ADP . . . E 5 128.932 77.864 120.427 0.5 49.56 ? O3' ADP 173 A 1 HETATM 15 C C2' ADP . . . E 5 129.742 75.783 119.552 0.5 49.76 ? C2' ADP 173 A 1 HETATM 16 O O2' ADP . . . E 5 129.519 76.097 118.222 0.5 50.81 ? O2' ADP 173 A 1 HETATM 17 C C1' ADP . . . E 5 131.069 76.258 120.172 0.5 48.98 ? C1' ADP 173 A 1 HETATM 18 N N9 ADP . . . E 5 132.114 75.258 119.856 0.5 48.54 ? N9 ADP 173 A 1 HETATM 19 C C8 ADP . . . E 5 131.949 73.892 120.025 0.5 49.11 ? C8 ADP 173 A 1 HETATM 20 N N7 ADP . . . E 5 132.993 73.181 119.744 0.5 48.4 ? N7 ADP 173 A 1 HETATM 21 C C5 ADP . . . E 5 133.923 74.111 119.307 0.5 47.87 ? C5 ADP 173 A 1 HETATM 22 C C6 ADP . . . E 5 135.242 73.99 118.824 0.5 48.15 ? C6 ADP 173 A 1 HETATM 23 N N6 ADP . . . E 5 135.922 72.839 118.706 0.5 46.84 ? N6 ADP 173 A 1 HETATM 24 N N1 ADP . . . E 5 135.918 75.12 118.488 0.5 48.26 ? N1 ADP 173 A 1 HETATM 25 C C2 ADP . . . E 5 135.266 76.27 118.591 0.5 49.05 ? C2 ADP 173 A 1 HETATM 26 N N3 ADP . . . E 5 134.029 76.508 118.995 0.5 48.77 ? N3 ADP 173 A 1 HETATM 27 C C4 ADP . . . E 5 133.378 75.382 119.371 0.5 48.49 ? C4 ADP 173 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #