data_4PFK # _model_server_result.job_id H23XvCU4NXoXU8AFLbJxiA _model_server_result.datetime_utc '2025-07-03 02:26:55' _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 4pfk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":326}' # _entry.id 4PFK # _exptl.entry_id 4PFK _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 2 _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 4PFK _cell.length_a 122.5 _cell.length_b 84.1 _cell.length_c 61.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PFK _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E N N ? 4 F 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 metalc ? metalc1 A O GLY 185 A GLY 185 1_555 D MG MG . A MG 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc2 A OE1 GLU 187 A GLU 187 1_555 D MG MG . A MG 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc3 E O2A ADP . A ADP 324 1_555 C MG MG . A MG 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.017 ? metalc ? metalc4 E O2B ADP . A ADP 324 1_555 C MG MG . A MG 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc5 E O1A ADP . A ADP 324 1_555 C MG MG . A MG 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc6 E O1B ADP . A ADP 324 1_555 C MG MG . A MG 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc7 F O2B ADP . A ADP 326 1_555 D MG MG . A MG 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc8 F O2A ADP . A ADP 326 1_555 D MG MG . A MG 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc9 D MG MG . A MG 327 1_555 G O HOH . A HOH 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc10 D MG MG . A MG 327 1_555 G O HOH . A HOH 387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? # _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 4PFK _atom_sites.fract_transf_matrix[1][1] 0.008163 _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] 0.011891 _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] 0.01626 _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 F6P A 1 323 323 F6P F6P . C 3 MG A 1 325 325 MG MG . D 3 MG A 1 327 327 MG MG . E 4 ADP A 1 324 324 ADP ADP . F 4 ADP A 1 326 326 ADP ADP . G 5 HOH A 1 328 1 HOH HOH . G 5 HOH A 2 329 2 HOH HOH . G 5 HOH A 3 330 3 HOH HOH . G 5 HOH A 4 331 4 HOH HOH . G 5 HOH A 5 332 5 HOH HOH . G 5 HOH A 6 333 6 HOH HOH . G 5 HOH A 7 334 7 HOH HOH . G 5 HOH A 8 335 8 HOH HOH . G 5 HOH A 9 336 9 HOH HOH . G 5 HOH A 10 337 10 HOH HOH . G 5 HOH A 11 338 15 HOH HOH . G 5 HOH A 12 339 16 HOH HOH . G 5 HOH A 13 340 17 HOH HOH . G 5 HOH A 14 341 18 HOH HOH . G 5 HOH A 15 342 19 HOH HOH . G 5 HOH A 16 343 20 HOH HOH . G 5 HOH A 17 344 21 HOH HOH . G 5 HOH A 18 345 22 HOH HOH . G 5 HOH A 19 346 23 HOH HOH . G 5 HOH A 20 347 24 HOH HOH . G 5 HOH A 21 348 25 HOH HOH . G 5 HOH A 22 349 26 HOH HOH . G 5 HOH A 23 350 27 HOH HOH . G 5 HOH A 24 351 28 HOH HOH . G 5 HOH A 25 352 29 HOH HOH . G 5 HOH A 26 353 30 HOH HOH . G 5 HOH A 27 354 31 HOH HOH . G 5 HOH A 28 355 32 HOH HOH . G 5 HOH A 29 356 33 HOH HOH . G 5 HOH A 30 357 34 HOH HOH . G 5 HOH A 31 358 37 HOH HOH . G 5 HOH A 32 359 39 HOH HOH . G 5 HOH A 33 360 43 HOH HOH . G 5 HOH A 34 361 45 HOH HOH . G 5 HOH A 35 362 46 HOH HOH . G 5 HOH A 36 363 47 HOH HOH . G 5 HOH A 37 364 48 HOH HOH . G 5 HOH A 38 365 49 HOH HOH . G 5 HOH A 39 366 50 HOH HOH . G 5 HOH A 40 367 51 HOH HOH . G 5 HOH A 41 368 53 HOH HOH . G 5 HOH A 42 369 54 HOH HOH . G 5 HOH A 43 370 55 HOH HOH . G 5 HOH A 44 371 56 HOH HOH . G 5 HOH A 45 372 58 HOH HOH . G 5 HOH A 46 373 59 HOH HOH . G 5 HOH A 47 374 63 HOH HOH . G 5 HOH A 48 375 66 HOH HOH . G 5 HOH A 49 376 67 HOH HOH . G 5 HOH A 50 377 68 HOH HOH . G 5 HOH A 51 378 69 HOH HOH . G 5 HOH A 52 379 70 HOH HOH . G 5 HOH A 53 380 72 HOH HOH . G 5 HOH A 54 381 73 HOH HOH . G 5 HOH A 55 382 74 HOH HOH . G 5 HOH A 56 383 75 HOH HOH . G 5 HOH A 57 384 76 HOH HOH . G 5 HOH A 58 385 77 HOH HOH . G 5 HOH A 59 386 79 HOH HOH . G 5 HOH A 60 387 80 HOH HOH . G 5 HOH A 61 388 81 HOH HOH . G 5 HOH A 62 389 83 HOH HOH . G 5 HOH A 63 390 84 HOH HOH . G 5 HOH A 64 391 85 HOH HOH . G 5 HOH A 65 392 86 HOH HOH . G 5 HOH A 66 393 87 HOH HOH . G 5 HOH A 67 394 88 HOH HOH . G 5 HOH A 68 395 89 HOH HOH . G 5 HOH A 69 396 90 HOH HOH . G 5 HOH A 70 397 91 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 . . . F 4 8.236 18.256 8.053 1 50.66 ? PB ADP 326 A 1 HETATM 2 O O1B ADP . . . F 4 7.491 17.886 6.833 1 46.15 ? O1B ADP 326 A 1 HETATM 3 O O2B ADP . . . F 4 8.299 17.23 9.11 1 45.14 ? O2B ADP 326 A 1 HETATM 4 O O3B ADP . . . F 4 9.553 18.831 7.688 1 52.52 ? O3B ADP 326 A 1 HETATM 5 P PA ADP . . . F 4 7.758 20.451 10.009 1 57.25 ? PA ADP 326 A 1 HETATM 6 O O1A ADP . . . F 4 8.626 21.615 9.722 1 57.86 ? O1A ADP 326 A 1 HETATM 7 O O2A ADP . . . F 4 8.437 19.676 11.093 1 62.69 ? O2A ADP 326 A 1 HETATM 8 O O3A ADP . . . F 4 7.52 19.557 8.695 1 56.07 ? O3A ADP 326 A 1 HETATM 9 O O5' ADP . . . F 4 6.284 20.747 10.477 1 57.54 ? O5' ADP 326 A 1 HETATM 10 C C5' ADP . . . F 4 5.266 19.862 11.015 1 53.16 ? C5' ADP 326 A 1 HETATM 11 C C4' ADP . . . F 4 3.943 20.275 10.394 1 54.55 ? C4' ADP 326 A 1 HETATM 12 O O4' ADP . . . F 4 3.781 21.723 10.572 1 58.53 ? O4' ADP 326 A 1 HETATM 13 C C3' ADP . . . F 4 3.777 20.025 8.889 1 52.36 ? C3' ADP 326 A 1 HETATM 14 O O3' ADP . . . F 4 2.446 19.902 8.459 1 43.17 ? O3' ADP 326 A 1 HETATM 15 C C2' ADP . . . F 4 4.317 21.354 8.315 1 56.06 ? C2' ADP 326 A 1 HETATM 16 O O2' ADP . . . F 4 3.992 21.521 6.952 1 53.58 ? O2' ADP 326 A 1 HETATM 17 C C1' ADP . . . F 4 3.659 22.346 9.29 1 61.78 ? C1' ADP 326 A 1 HETATM 18 N N9 ADP . . . F 4 4.314 23.659 9.352 1 69.55 ? N9 ADP 326 A 1 HETATM 19 C C8 ADP . . . F 4 5.627 23.876 9.684 1 72.22 ? C8 ADP 326 A 1 HETATM 20 N N7 ADP . . . F 4 5.993 25.142 9.674 1 73.57 ? N7 ADP 326 A 1 HETATM 21 C C5 ADP . . . F 4 4.845 25.795 9.301 1 74.85 ? C5 ADP 326 A 1 HETATM 22 C C6 ADP . . . F 4 4.614 27.18 9.109 1 75.23 ? C6 ADP 326 A 1 HETATM 23 N N6 ADP . . . F 4 5.563 28.1 9.278 1 71.4 ? N6 ADP 326 A 1 HETATM 24 N N1 ADP . . . F 4 3.359 27.517 8.732 1 77.16 ? N1 ADP 326 A 1 HETATM 25 C C2 ADP . . . F 4 2.415 26.525 8.574 1 77.84 ? C2 ADP 326 A 1 HETATM 26 N N3 ADP . . . F 4 2.533 25.237 8.724 1 75.67 ? N3 ADP 326 A 1 HETATM 27 C C4 ADP . . . F 4 3.8 24.913 9.096 1 73.87 ? C4 ADP 326 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #