data_1MK1 # _model_server_result.job_id -gelaZ7LtCF9C7uglLoxQw _model_server_result.datetime_utc '2025-03-06 07:51:20' _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 1mk1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":208}' # _entry.id 1MK1 # _exptl.entry_id 1MK1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE-5-DIPHOSPHORIBOSE _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 120 _cell.entry_id 1MK1 _cell.length_a 64.088 _cell.length_b 64.088 _cell.length_c 182.393 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MK1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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' 12_555 x,x-y,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 30.398833 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id APR _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _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 N1 C2 APR sing 13 n y N1 C6 APR doub 14 n y C2 N3 APR doub 15 n y C2 H2 APR sing 16 n n N3 C4 APR sing 17 n y C4 C5 APR doub 18 n y C4 N9 APR sing 19 n y C5 C6 APR sing 20 n y C5 N7 APR sing 21 n y C6 N6 APR sing 22 n n N6 H61 APR sing 23 n n N6 H62 APR sing 24 n n N7 C8 APR doub 25 n y C8 N9 APR sing 26 n y C8 H8 APR sing 27 n n N9 C1' APR sing 28 n n C1' C2' APR sing 29 n n C1' O4' APR sing 30 n n C1' "H'1" APR sing 31 n n C2' O2' APR sing 32 n n C2' C3' APR sing 33 n n C2' "H'2" APR sing 34 n n O2' "HO'2" APR sing 35 n n C3' O3' APR sing 36 n n C3' C4' APR sing 37 n n C3' "H'3" APR sing 38 n n O3' "HO'3" APR sing 39 n n O4' C4' APR sing 40 n n C4' C5' APR sing 41 n n C4' "H'4" APR sing 42 n n C5' O5' APR sing 43 n n C5' "H5'1" APR sing 44 n n C5' "H5'2" APR sing 45 n n O5' PA APR sing 46 n n PA O1A APR doub 47 n n PA O2A APR sing 48 n n PA O3A APR sing 49 n n O2A HOA2 APR sing 50 n n O3A PB APR sing 51 n n PB O1B APR doub 52 n n PB O2B APR sing 53 n n PB O5D APR sing 54 n n O2B HOB2 APR sing 55 n n O5D C5D APR sing 56 n n C5D C4D APR sing 57 n n C5D H5R1 APR sing 58 n n C5D H5R2 APR sing 59 n n O4D C1D APR sing 60 n n O4D C4D APR sing 61 n n O1D C1D APR sing 62 n n O1D HOR1 APR sing 63 n n C1D C2D APR sing 64 n n C1D "HR'1" APR sing 65 n n O2D C2D APR sing 66 n n O2D HOR2 APR sing 67 n n C2D C3D APR sing 68 n n C2D "HR'2" APR sing 69 n n O3D C3D APR sing 70 n n O3D HOR3 APR sing 71 n n C3D C4D APR sing 72 n n C3D "HR'3" APR sing 73 n n C4D "HR'4" APR sing 74 n n # _atom_sites.entry_id 1MK1 _atom_sites.fract_transf_matrix[1][1] 0.015604 _atom_sites.fract_transf_matrix[1][2] 0.009009 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018017 _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] 0.005483 _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 APR A 1 208 201 APR APR . C 3 HOH A 1 209 1 HOH HOH . C 3 HOH A 2 210 2 HOH HOH . C 3 HOH A 3 211 3 HOH HOH . C 3 HOH A 4 212 4 HOH HOH . C 3 HOH A 5 213 5 HOH HOH . C 3 HOH A 6 214 6 HOH HOH . C 3 HOH A 7 215 7 HOH HOH . C 3 HOH A 8 216 8 HOH HOH . C 3 HOH A 9 217 9 HOH HOH . C 3 HOH A 10 218 10 HOH HOH . C 3 HOH A 11 219 11 HOH HOH . C 3 HOH A 12 220 12 HOH HOH . C 3 HOH A 13 221 13 HOH HOH . C 3 HOH A 14 222 14 HOH HOH . C 3 HOH A 15 223 15 HOH HOH . C 3 HOH A 16 224 16 HOH HOH . C 3 HOH A 17 225 17 HOH HOH . C 3 HOH A 18 226 18 HOH HOH . C 3 HOH A 19 227 19 HOH HOH . C 3 HOH A 20 228 20 HOH HOH . C 3 HOH A 21 229 21 HOH HOH . C 3 HOH A 22 230 22 HOH HOH . C 3 HOH A 23 231 23 HOH HOH . C 3 HOH A 24 232 24 HOH HOH . C 3 HOH A 25 233 25 HOH HOH . C 3 HOH A 26 234 26 HOH HOH . C 3 HOH A 27 235 29 HOH HOH . C 3 HOH A 28 236 30 HOH HOH . C 3 HOH A 29 237 31 HOH HOH . C 3 HOH A 30 238 32 HOH HOH . C 3 HOH A 31 239 33 HOH HOH . C 3 HOH A 32 240 34 HOH HOH . C 3 HOH A 33 241 35 HOH HOH . C 3 HOH A 34 242 36 HOH HOH . C 3 HOH A 35 243 38 HOH HOH . C 3 HOH A 36 244 39 HOH HOH . C 3 HOH A 37 245 41 HOH HOH . C 3 HOH A 38 246 43 HOH HOH . C 3 HOH A 39 247 44 HOH HOH . C 3 HOH A 40 248 45 HOH HOH . C 3 HOH A 41 249 46 HOH HOH . C 3 HOH A 42 250 47 HOH HOH . C 3 HOH A 43 251 48 HOH HOH . C 3 HOH A 44 252 50 HOH HOH . C 3 HOH A 45 253 51 HOH HOH . C 3 HOH A 46 254 53 HOH HOH . C 3 HOH A 47 255 54 HOH HOH . C 3 HOH A 48 256 55 HOH HOH . C 3 HOH A 49 257 56 HOH HOH . C 3 HOH A 50 258 57 HOH HOH . C 3 HOH A 51 259 58 HOH HOH . C 3 HOH A 52 260 59 HOH HOH . C 3 HOH A 53 261 60 HOH HOH . C 3 HOH A 54 262 61 HOH HOH . C 3 HOH A 55 263 62 HOH HOH . C 3 HOH A 56 264 63 HOH HOH . C 3 HOH A 57 265 64 HOH HOH . C 3 HOH A 58 266 65 HOH HOH . C 3 HOH A 59 267 66 HOH HOH . C 3 HOH A 60 268 67 HOH HOH . C 3 HOH A 61 269 68 HOH HOH . C 3 HOH A 62 270 70 HOH HOH . C 3 HOH A 63 271 71 HOH HOH . C 3 HOH A 64 272 72 HOH HOH . C 3 HOH A 65 273 75 HOH HOH . C 3 HOH A 66 274 77 HOH HOH . C 3 HOH A 67 275 78 HOH HOH . C 3 HOH A 68 276 79 HOH HOH . C 3 HOH A 69 277 80 HOH HOH . C 3 HOH A 70 278 82 HOH HOH . C 3 HOH A 71 279 83 HOH HOH . C 3 HOH A 72 280 86 HOH HOH . C 3 HOH A 73 281 87 HOH HOH . C 3 HOH A 74 282 88 HOH HOH . C 3 HOH A 75 283 89 HOH HOH . C 3 HOH A 76 284 91 HOH HOH . C 3 HOH A 77 285 95 HOH HOH . C 3 HOH A 78 286 96 HOH HOH . C 3 HOH A 79 287 97 HOH HOH . C 3 HOH A 80 288 99 HOH HOH . C 3 HOH A 81 289 100 HOH HOH . C 3 HOH A 82 290 101 HOH HOH . C 3 HOH A 83 291 102 HOH HOH . C 3 HOH A 84 292 106 HOH HOH . C 3 HOH A 85 293 107 HOH HOH . C 3 HOH A 86 294 108 HOH HOH . C 3 HOH A 87 295 109 HOH HOH . C 3 HOH A 88 296 113 HOH HOH . C 3 HOH A 89 297 114 HOH HOH . C 3 HOH A 90 298 115 HOH HOH . C 3 HOH A 91 299 117 HOH HOH . C 3 HOH A 92 300 118 HOH HOH . C 3 HOH A 93 301 122 HOH HOH . C 3 HOH A 94 302 123 HOH HOH . C 3 HOH A 95 303 127 HOH HOH . C 3 HOH A 96 304 130 HOH HOH . C 3 HOH A 97 305 131 HOH HOH . C 3 HOH A 98 306 132 HOH HOH . C 3 HOH A 99 307 134 HOH HOH . C 3 HOH A 100 308 135 HOH HOH . C 3 HOH A 101 309 136 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 N N1 APR . . . B 2 33.22 21.943 5.463 1 47.65 ? N1 APR 208 A 1 HETATM 2 C C2 APR . . . B 2 33.081 23.062 4.683 1 47.29 ? C2 APR 208 A 1 HETATM 3 N N3 APR . . . B 2 31.881 23.259 4.051 1 47.07 ? N3 APR 208 A 1 HETATM 4 C C4 APR . . . B 2 30.854 22.374 4.192 1 47.9 ? C4 APR 208 A 1 HETATM 5 C C5 APR . . . B 2 31.011 21.239 4.991 1 47.87 ? C5 APR 208 A 1 HETATM 6 C C6 APR . . . B 2 32.191 21.044 5.61 1 46.5 ? C6 APR 208 A 1 HETATM 7 N N6 APR . . . B 2 32.328 19.94 6.375 1 44.64 ? N6 APR 208 A 1 HETATM 8 N N7 APR . . . B 2 29.853 20.507 4.978 1 49.08 ? N7 APR 208 A 1 HETATM 9 C C8 APR . . . B 2 28.974 21.168 4.179 1 48.9 ? C8 APR 208 A 1 HETATM 10 N N9 APR . . . B 2 29.577 22.308 3.694 1 49.08 ? N9 APR 208 A 1 HETATM 11 C C1' APR . . . B 2 28.898 23.245 2.785 1 50.41 ? C1' APR 208 A 1 HETATM 12 C C2' APR . . . B 2 29.019 23.495 1.303 1 51.04 ? C2' APR 208 A 1 HETATM 13 O O2' APR . . . B 2 29.384 24.871 1.213 1 53.03 ? O2' APR 208 A 1 HETATM 14 C C3' APR . . . B 2 27.625 23.117 0.935 1 50.22 ? C3' APR 208 A 1 HETATM 15 O O3' APR . . . B 2 27.381 23.592 -0.367 1 52.94 ? O3' APR 208 A 1 HETATM 16 O O4' APR . . . B 2 27.73 23.997 3.161 1 48.28 ? O4' APR 208 A 1 HETATM 17 C C4' APR . . . B 2 26.829 23.885 2.023 1 48.75 ? C4' APR 208 A 1 HETATM 18 C C5' APR . . . B 2 25.698 22.856 2.093 1 46.64 ? C5' APR 208 A 1 HETATM 19 O O5' APR . . . B 2 24.58 23.526 2.621 1 42.88 ? O5' APR 208 A 1 HETATM 20 P PA APR . . . B 2 23.183 22.906 2.919 1 39.49 ? PA APR 208 A 1 HETATM 21 O O1A APR . . . B 2 22.724 22.322 1.549 1 39.88 ? O1A APR 208 A 1 HETATM 22 O O2A APR . . . B 2 22.409 24.146 3.441 1 38.42 ? O2A APR 208 A 1 HETATM 23 O O3A APR . . . B 2 23.182 21.823 4.055 1 39.56 ? O3A APR 208 A 1 HETATM 24 P PB APR . . . B 2 23.685 20.376 4.348 1 34.14 ? PB APR 208 A 1 HETATM 25 O O1B APR . . . B 2 25.208 20.208 4.188 1 34.69 ? O1B APR 208 A 1 HETATM 26 O O2B APR . . . B 2 22.992 19.338 3.414 1 33.17 ? O2B APR 208 A 1 HETATM 27 O O5D APR . . . B 2 23.309 19.949 5.775 1 34.58 ? O5D APR 208 A 1 HETATM 28 C C5D APR . . . B 2 21.984 19.972 6.295 1 33.34 ? C5D APR 208 A 1 HETATM 29 O O4D APR . . . B 2 22.288 17.717 7.009 1 34.59 ? O4D APR 208 A 1 HETATM 30 O O1D APR . . . B 2 22.945 15.972 8.053 1 33.9 ? O1D APR 208 A 1 HETATM 31 C C1D APR . . . B 2 23.499 17.121 7.446 1 34.29 ? C1D APR 208 A 1 HETATM 32 O O2D APR . . . B 2 24.741 17.456 9.388 1 34.2 ? O2D APR 208 A 1 HETATM 33 C C2D APR . . . B 2 24.285 18.139 8.254 1 32.94 ? C2D APR 208 A 1 HETATM 34 O O3D APR . . . B 2 22.556 19.296 9.682 1 33.63 ? O3D APR 208 A 1 HETATM 35 C C3D APR . . . B 2 23.288 19.228 8.481 1 33.65 ? C3D APR 208 A 1 HETATM 36 C C4D APR . . . B 2 22.083 19.035 7.512 1 34.11 ? C4D APR 208 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #