data_3LM9 # _model_server_result.job_id 3yZ_IdhO-dda6nYauw20EA _model_server_result.datetime_utc '2025-01-02 19:14:37' _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 3lm9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":3001}' # _entry.id 3LM9 # _exptl.entry_id 3LM9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 120 _cell.entry_id 3LM9 _cell.length_a 112.333 _cell.length_b 112.333 _cell.length_c 73.958 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LM9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,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' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -49.305333 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 ALA 3 A ALA 0 1_555 A N MSE 4 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C MSE 4 A MSE 1 1_555 A N LEU 5 A LEU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale3 A C LYS 35 A LYS 32 1_555 A N MSE 36 A MSE 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale4 A C MSE 36 A MSE 33 1_555 A N PRO 37 A PRO 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale5 A C GLU 96 A GLU 93 1_555 A N MSE 97 A MSE 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale6 A C MSE 97 A MSE 94 1_555 A N LYS 98 A LYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale7 A C GLU 153 A GLU 150 1_555 A N MSE 154 A MSE 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale8 A C MSE 154 A MSE 151 1_555 A N GLY 155 A GLY 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale9 A C PRO 225 A PRO 222 1_555 A N MLY 226 A MLY 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 A C MLY 226 A MLY 223 1_555 A N MLY 227 A MLY 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale11 A C MLY 227 A MLY 224 1_555 A N ILE 228 A ILE 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale12 A C VAL 234 A VAL 231 1_555 A N MSE 235 A MSE 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale13 A C MSE 235 A MSE 232 1_555 A N GLN 236 A GLN 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale14 A C ILE 251 A ILE 248 1_555 A N MSE 252 A MSE 249 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale15 A C MSE 252 A MSE 249 1_555 A N ASN 253 A ASN 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A ND1 HIS 156 A HIS 153 1_555 E ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc2 A SG CYS 171 A CYS 168 1_555 E ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc3 A ND1 HIS 174 A HIS 171 1_555 E ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc4 A SG CYS 177 A CYS 174 1_555 E ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _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 3LM9 _atom_sites.fract_transf_matrix[1][1] 0.008902 _atom_sites.fract_transf_matrix[1][2] 0.00514 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010279 _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] 0.013521 _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 FRU A 1 1001 1001 FRU FRU . C 3 SO4 A 1 2001 2001 SO4 SO4 . D 4 ADP A 1 3001 3001 ADP ADP . E 5 ZN A 1 302 302 ZN ZN . F 6 HOH A 1 300 1 HOH HOH . F 6 HOH A 2 301 3 HOH HOH . F 6 HOH A 3 303 4 HOH HOH . F 6 HOH A 4 304 5 HOH HOH . F 6 HOH A 5 305 7 HOH HOH . F 6 HOH A 6 306 8 HOH HOH . F 6 HOH A 7 307 11 HOH HOH . F 6 HOH A 8 308 12 HOH HOH . F 6 HOH A 9 309 13 HOH HOH . F 6 HOH A 10 310 14 HOH HOH . F 6 HOH A 11 311 15 HOH HOH . F 6 HOH A 12 312 16 HOH HOH . F 6 HOH A 13 313 17 HOH HOH . F 6 HOH A 14 314 20 HOH HOH . F 6 HOH A 15 315 21 HOH HOH . F 6 HOH A 16 316 22 HOH HOH . F 6 HOH A 17 317 26 HOH HOH . F 6 HOH A 18 318 30 HOH HOH . F 6 HOH A 19 319 34 HOH HOH . F 6 HOH A 20 320 37 HOH HOH . F 6 HOH A 21 321 38 HOH HOH . F 6 HOH A 22 322 42 HOH HOH . F 6 HOH A 23 323 48 HOH HOH . F 6 HOH A 24 324 58 HOH HOH . F 6 HOH A 25 325 61 HOH HOH . F 6 HOH A 26 326 66 HOH HOH . F 6 HOH A 27 327 70 HOH HOH . F 6 HOH A 28 328 74 HOH HOH . F 6 HOH A 29 329 77 HOH HOH . F 6 HOH A 30 330 87 HOH HOH . F 6 HOH A 31 331 89 HOH HOH . F 6 HOH A 32 332 101 HOH HOH . F 6 HOH A 33 333 132 HOH HOH . F 6 HOH A 34 334 133 HOH HOH . F 6 HOH A 35 335 135 HOH HOH . F 6 HOH A 36 336 136 HOH HOH . F 6 HOH A 37 337 137 HOH HOH . F 6 HOH A 38 338 138 HOH HOH . F 6 HOH A 39 339 140 HOH HOH . F 6 HOH A 40 340 141 HOH HOH . F 6 HOH A 41 341 142 HOH HOH . F 6 HOH A 42 342 143 HOH HOH . F 6 HOH A 43 343 144 HOH HOH . F 6 HOH A 44 344 145 HOH HOH . F 6 HOH A 45 345 146 HOH HOH . F 6 HOH A 46 346 147 HOH HOH . F 6 HOH A 47 347 148 HOH HOH . F 6 HOH A 48 348 149 HOH HOH . F 6 HOH A 49 349 150 HOH HOH . F 6 HOH A 50 350 151 HOH HOH . F 6 HOH A 51 351 152 HOH HOH . F 6 HOH A 52 352 153 HOH HOH . F 6 HOH A 53 353 155 HOH HOH . F 6 HOH A 54 354 156 HOH HOH . F 6 HOH A 55 355 157 HOH HOH . F 6 HOH A 56 356 158 HOH HOH . F 6 HOH A 57 357 159 HOH HOH . F 6 HOH A 58 358 160 HOH HOH . F 6 HOH A 59 359 161 HOH HOH . F 6 HOH A 60 360 162 HOH HOH . F 6 HOH A 61 361 163 HOH HOH . F 6 HOH A 62 362 164 HOH HOH . F 6 HOH A 63 363 165 HOH HOH . F 6 HOH A 64 364 166 HOH HOH . F 6 HOH A 65 365 167 HOH HOH . F 6 HOH A 66 366 168 HOH HOH . F 6 HOH A 67 367 1 HOH HOH . F 6 HOH A 68 368 2 HOH HOH . F 6 HOH A 69 369 3 HOH HOH . F 6 HOH A 70 370 4 HOH HOH . F 6 HOH A 71 371 7 HOH HOH . F 6 HOH A 72 372 10 HOH HOH . F 6 HOH A 73 373 12 HOH HOH . F 6 HOH A 74 374 13 HOH HOH . F 6 HOH A 75 375 15 HOH HOH . F 6 HOH A 76 376 20 HOH HOH . F 6 HOH A 77 377 28 HOH HOH . F 6 HOH A 78 378 34 HOH HOH . F 6 HOH A 79 379 38 HOH HOH . F 6 HOH A 80 380 48 HOH HOH . F 6 HOH A 81 381 61 HOH HOH . F 6 HOH A 82 382 71 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 . . . D 4 45.732 -33.94 -19.402 1 69.27 ? PB ADP 3001 A 1 HETATM 2 O O1B ADP . . . D 4 44.25 -34.218 -19.677 1 67.15 ? O1B ADP 3001 A 1 HETATM 3 O O2B ADP . . . D 4 46.262 -32.615 -20.016 1 68.5 ? O2B ADP 3001 A 1 HETATM 4 O O3B ADP . . . D 4 46.704 -35.094 -19.713 1 66.29 ? O3B ADP 3001 A 1 HETATM 5 P PA ADP . . . D 4 44.742 -33.819 -16.597 1 62.88 ? PA ADP 3001 A 1 HETATM 6 O O1A ADP . . . D 4 45.405 -33.233 -15.359 1 63.73 ? O1A ADP 3001 A 1 HETATM 7 O O2A ADP . . . D 4 44.217 -35.245 -16.482 1 59.11 ? O2A ADP 3001 A 1 HETATM 8 O O3A ADP . . . D 4 45.822 -33.724 -17.79 1 65.78 ? O3A ADP 3001 A 1 HETATM 9 O O5' ADP . . . D 4 43.674 -32.68 -17.021 1 65.11 ? O5' ADP 3001 A 1 HETATM 10 C C5' ADP . . . D 4 43.911 -31.267 -16.908 1 69.28 ? C5' ADP 3001 A 1 HETATM 11 C C4' ADP . . . D 4 42.629 -30.412 -16.73 1 71.93 ? C4' ADP 3001 A 1 HETATM 12 O O4' ADP . . . D 4 42.146 -30.597 -15.386 1 72.32 ? O4' ADP 3001 A 1 HETATM 13 C C3' ADP . . . D 4 42.857 -28.878 -16.956 1 74.58 ? C3' ADP 3001 A 1 HETATM 14 O O3' ADP . . . D 4 41.836 -28.192 -17.709 1 71.5 ? O3' ADP 3001 A 1 HETATM 15 C C2' ADP . . . D 4 42.967 -28.29 -15.541 1 76.11 ? C2' ADP 3001 A 1 HETATM 16 O O2' ADP . . . D 4 42.392 -26.987 -15.343 1 78.54 ? O2' ADP 3001 A 1 HETATM 17 C C1' ADP . . . D 4 42.249 -29.336 -14.661 1 76.1 ? C1' ADP 3001 A 1 HETATM 18 N N9 ADP . . . D 4 42.969 -29.583 -13.383 1 75.6 ? N9 ADP 3001 A 1 HETATM 19 C C8 ADP . . . D 4 44.279 -29.909 -13.18 1 76.03 ? C8 ADP 3001 A 1 HETATM 20 N N7 ADP . . . D 4 44.518 -30.096 -11.86 1 76.15 ? N7 ADP 3001 A 1 HETATM 21 C C5 ADP . . . D 4 43.343 -29.88 -11.232 1 76.9 ? C5 ADP 3001 A 1 HETATM 22 C C6 ADP . . . D 4 42.844 -29.903 -9.841 1 79.54 ? C6 ADP 3001 A 1 HETATM 23 N N6 ADP . . . D 4 43.708 -30.193 -8.841 1 81.58 ? N6 ADP 3001 A 1 HETATM 24 N N1 ADP . . . D 4 41.522 -29.629 -9.607 1 78.76 ? N1 ADP 3001 A 1 HETATM 25 C C2 ADP . . . D 4 40.651 -29.337 -10.614 1 76.16 ? C2 ADP 3001 A 1 HETATM 26 N N3 ADP . . . D 4 41.044 -29.291 -11.895 1 74.92 ? N3 ADP 3001 A 1 HETATM 27 C C4 ADP . . . D 4 42.333 -29.543 -12.237 1 75.51 ? C4 ADP 3001 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #