data_2FME # _model_server_result.job_id 3brKdBEQe6nIhzTFKfqGVw _model_server_result.datetime_utc '2024-10-22 03:42:56' _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 2fme # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":371}' # _entry.id 2FME # _exptl.entry_id 2FME _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 96.5 _cell.angle_gamma 90 _cell.entry_id 2FME _cell.length_a 159.8 _cell.length_b 80 _cell.length_c 69.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2FME _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 ? monomeric 1 author_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,D,E,I 1 1 B,F,G,H,J 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 ? 4 E N N ? 4 H 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 OG1 THR 112 A THR 112 1_555 C MG MG . A MG 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc2 C MG MG . A MG 369 1_555 E O3B ADP . A ADP 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc3 C MG MG . A MG 369 1_555 I O HOH . A HOH 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc4 C MG MG . A MG 369 1_555 I O HOH . A HOH 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc5 C MG MG . A MG 369 1_555 I O HOH . A HOH 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc6 C MG MG . A MG 369 1_555 I O HOH . A HOH 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc7 B OG1 THR 112 B THR 112 1_555 F MG MG . B MG 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc8 F MG MG . B MG 369 1_555 H O3B ADP . B ADP 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc9 F MG MG . B MG 369 1_555 J O HOH . B HOH 372 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc10 F MG MG . B MG 369 1_555 J O HOH . B HOH 376 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc11 F MG MG . B MG 369 1_555 J O HOH . B HOH 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc12 F MG MG . B MG 369 1_555 J O HOH . B HOH 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? # _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 51 n n PB O2B ADP sing 52 n n PB O3B ADP sing 53 n n PB O3A ADP sing 54 n n O2B HOB2 ADP sing 55 n n O3B HOB3 ADP sing 56 n n PA O1A ADP doub 57 n n PA O2A ADP sing 58 n n PA O3A ADP sing 59 n n PA O5' ADP sing 60 n n O2A HOA2 ADP sing 61 n n O5' C5' ADP sing 62 n n C5' C4' ADP sing 63 n n C5' "H5'1" ADP sing 64 n n C5' "H5'2" ADP sing 65 n n C4' O4' ADP sing 66 n n C4' C3' ADP sing 67 n n C4' H4' ADP sing 68 n n O4' C1' ADP sing 69 n n C3' O3' ADP sing 70 n n C3' C2' ADP sing 71 n n C3' H3' ADP sing 72 n n O3' HO3' ADP sing 73 n n C2' O2' ADP sing 74 n n C2' C1' ADP sing 75 n n C2' H2' ADP sing 76 n n O2' HO2' ADP sing 77 n n C1' N9 ADP sing 78 n n C1' H1' ADP sing 79 n n N9 C8 ADP sing 80 n y N9 C4 ADP sing 81 n y C8 N7 ADP doub 82 n y C8 H8 ADP sing 83 n n N7 C5 ADP sing 84 n y C5 C6 ADP sing 85 n y C5 C4 ADP doub 86 n y C6 N6 ADP sing 87 n n C6 N1 ADP doub 88 n y N6 HN61 ADP sing 89 n n N6 HN62 ADP sing 90 n n N1 C2 ADP sing 91 n y C2 N3 ADP doub 92 n y C2 H2 ADP sing 93 n n N3 C4 ADP sing 94 n y # _atom_sites.entry_id 2FME _atom_sites.fract_transf_matrix[1][1] 0.006258 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000713 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0125 _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] 0.014544 _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 MG A 1 369 1 MG MG . D 3 3QC A 1 370 1 3QC 3QC . E 4 ADP A 1 371 1 ADP ADP . F 2 MG B 1 369 2 MG MG . G 3 3QC B 1 370 2 3QC 3QC . H 4 ADP B 1 371 2 ADP ADP . I 5 HOH A 1 372 5 HOH HOH . I 5 HOH A 2 373 7 HOH HOH . I 5 HOH A 3 374 8 HOH HOH . I 5 HOH A 4 375 9 HOH HOH . I 5 HOH A 5 376 11 HOH HOH . I 5 HOH A 6 377 12 HOH HOH . I 5 HOH A 7 378 13 HOH HOH . I 5 HOH A 8 379 14 HOH HOH . I 5 HOH A 9 380 16 HOH HOH . I 5 HOH A 10 381 17 HOH HOH . I 5 HOH A 11 382 19 HOH HOH . I 5 HOH A 12 383 21 HOH HOH . I 5 HOH A 13 384 23 HOH HOH . I 5 HOH A 14 385 25 HOH HOH . I 5 HOH A 15 386 26 HOH HOH . I 5 HOH A 16 387 28 HOH HOH . I 5 HOH A 17 388 30 HOH HOH . I 5 HOH A 18 389 31 HOH HOH . I 5 HOH A 19 390 32 HOH HOH . I 5 HOH A 20 391 34 HOH HOH . I 5 HOH A 21 392 35 HOH HOH . I 5 HOH A 22 393 41 HOH HOH . I 5 HOH A 23 394 42 HOH HOH . I 5 HOH A 24 395 44 HOH HOH . I 5 HOH A 25 396 46 HOH HOH . I 5 HOH A 26 397 49 HOH HOH . I 5 HOH A 27 398 51 HOH HOH . I 5 HOH A 28 399 52 HOH HOH . I 5 HOH A 29 400 53 HOH HOH . I 5 HOH A 30 401 55 HOH HOH . I 5 HOH A 31 402 57 HOH HOH . I 5 HOH A 32 403 62 HOH HOH . I 5 HOH A 33 404 63 HOH HOH . I 5 HOH A 34 405 64 HOH HOH . I 5 HOH A 35 406 67 HOH HOH . I 5 HOH A 36 407 70 HOH HOH . I 5 HOH A 37 408 71 HOH HOH . I 5 HOH A 38 409 72 HOH HOH . I 5 HOH A 39 410 73 HOH HOH . I 5 HOH A 40 411 74 HOH HOH . I 5 HOH A 41 412 75 HOH HOH . I 5 HOH A 42 413 76 HOH HOH . I 5 HOH A 43 414 80 HOH HOH . I 5 HOH A 44 415 83 HOH HOH . I 5 HOH A 45 416 84 HOH HOH . I 5 HOH A 46 417 86 HOH HOH . I 5 HOH A 47 418 89 HOH HOH . I 5 HOH A 48 419 90 HOH HOH . I 5 HOH A 49 420 91 HOH HOH . I 5 HOH A 50 421 93 HOH HOH . I 5 HOH A 51 422 95 HOH HOH . I 5 HOH A 52 423 96 HOH HOH . I 5 HOH A 53 424 97 HOH HOH . I 5 HOH A 54 425 101 HOH HOH . I 5 HOH A 55 426 102 HOH HOH . I 5 HOH A 56 427 104 HOH HOH . I 5 HOH A 57 428 105 HOH HOH . I 5 HOH A 58 429 107 HOH HOH . I 5 HOH A 59 430 108 HOH HOH . I 5 HOH A 60 431 109 HOH HOH . I 5 HOH A 61 432 110 HOH HOH . I 5 HOH A 62 433 113 HOH HOH . I 5 HOH A 63 434 114 HOH HOH . I 5 HOH A 64 435 116 HOH HOH . I 5 HOH A 65 436 118 HOH HOH . I 5 HOH A 66 437 121 HOH HOH . I 5 HOH A 67 438 124 HOH HOH . I 5 HOH A 68 439 126 HOH HOH . I 5 HOH A 69 440 129 HOH HOH . I 5 HOH A 70 441 132 HOH HOH . I 5 HOH A 71 442 137 HOH HOH . I 5 HOH A 72 443 140 HOH HOH . I 5 HOH A 73 444 143 HOH HOH . I 5 HOH A 74 445 144 HOH HOH . I 5 HOH A 75 446 146 HOH HOH . I 5 HOH A 76 447 147 HOH HOH . I 5 HOH A 77 448 149 HOH HOH . I 5 HOH A 78 449 150 HOH HOH . I 5 HOH A 79 450 153 HOH HOH . I 5 HOH A 80 451 158 HOH HOH . I 5 HOH A 81 452 159 HOH HOH . I 5 HOH A 82 453 160 HOH HOH . I 5 HOH A 83 454 161 HOH HOH . I 5 HOH A 84 455 162 HOH HOH . I 5 HOH A 85 456 163 HOH HOH . I 5 HOH A 86 457 164 HOH HOH . I 5 HOH A 87 458 165 HOH HOH . I 5 HOH A 88 459 166 HOH HOH . I 5 HOH A 89 460 167 HOH HOH . I 5 HOH A 90 461 168 HOH HOH . I 5 HOH A 91 462 169 HOH HOH . I 5 HOH A 92 463 172 HOH HOH . I 5 HOH A 93 464 175 HOH HOH . I 5 HOH A 94 465 177 HOH HOH . I 5 HOH A 95 466 178 HOH HOH . I 5 HOH A 96 467 179 HOH HOH . I 5 HOH A 97 468 180 HOH HOH . J 5 HOH B 1 372 3 HOH HOH . J 5 HOH B 2 373 4 HOH HOH . J 5 HOH B 3 374 6 HOH HOH . J 5 HOH B 4 375 10 HOH HOH . J 5 HOH B 5 376 15 HOH HOH . J 5 HOH B 6 377 18 HOH HOH . J 5 HOH B 7 378 20 HOH HOH . J 5 HOH B 8 379 22 HOH HOH . J 5 HOH B 9 380 24 HOH HOH . J 5 HOH B 10 381 27 HOH HOH . J 5 HOH B 11 382 29 HOH HOH . J 5 HOH B 12 383 33 HOH HOH . J 5 HOH B 13 384 36 HOH HOH . J 5 HOH B 14 385 37 HOH HOH . J 5 HOH B 15 386 38 HOH HOH . J 5 HOH B 16 387 39 HOH HOH . J 5 HOH B 17 388 40 HOH HOH . J 5 HOH B 18 389 43 HOH HOH . J 5 HOH B 19 390 45 HOH HOH . J 5 HOH B 20 391 47 HOH HOH . J 5 HOH B 21 392 48 HOH HOH . J 5 HOH B 22 393 50 HOH HOH . J 5 HOH B 23 394 54 HOH HOH . J 5 HOH B 24 395 56 HOH HOH . J 5 HOH B 25 396 58 HOH HOH . J 5 HOH B 26 397 59 HOH HOH . J 5 HOH B 27 398 60 HOH HOH . J 5 HOH B 28 399 61 HOH HOH . J 5 HOH B 29 400 65 HOH HOH . J 5 HOH B 30 401 66 HOH HOH . J 5 HOH B 31 402 68 HOH HOH . J 5 HOH B 32 403 69 HOH HOH . J 5 HOH B 33 404 77 HOH HOH . J 5 HOH B 34 405 78 HOH HOH . J 5 HOH B 35 406 79 HOH HOH . J 5 HOH B 36 407 81 HOH HOH . J 5 HOH B 37 408 82 HOH HOH . J 5 HOH B 38 409 85 HOH HOH . J 5 HOH B 39 410 87 HOH HOH . J 5 HOH B 40 411 88 HOH HOH . J 5 HOH B 41 412 92 HOH HOH . J 5 HOH B 42 413 94 HOH HOH . J 5 HOH B 43 414 98 HOH HOH . J 5 HOH B 44 415 99 HOH HOH . J 5 HOH B 45 416 100 HOH HOH . J 5 HOH B 46 417 103 HOH HOH . J 5 HOH B 47 418 106 HOH HOH . J 5 HOH B 48 419 111 HOH HOH . J 5 HOH B 49 420 112 HOH HOH . J 5 HOH B 50 421 115 HOH HOH . J 5 HOH B 51 422 117 HOH HOH . J 5 HOH B 52 423 119 HOH HOH . J 5 HOH B 53 424 120 HOH HOH . J 5 HOH B 54 425 122 HOH HOH . J 5 HOH B 55 426 123 HOH HOH . J 5 HOH B 56 427 125 HOH HOH . J 5 HOH B 57 428 127 HOH HOH . J 5 HOH B 58 429 128 HOH HOH . J 5 HOH B 59 430 130 HOH HOH . J 5 HOH B 60 431 131 HOH HOH . J 5 HOH B 61 432 133 HOH HOH . J 5 HOH B 62 433 134 HOH HOH . J 5 HOH B 63 434 135 HOH HOH . J 5 HOH B 64 435 136 HOH HOH . J 5 HOH B 65 436 138 HOH HOH . J 5 HOH B 66 437 139 HOH HOH . J 5 HOH B 67 438 141 HOH HOH . J 5 HOH B 68 439 142 HOH HOH . J 5 HOH B 69 440 145 HOH HOH . J 5 HOH B 70 441 148 HOH HOH . J 5 HOH B 71 442 151 HOH HOH . J 5 HOH B 72 443 152 HOH HOH . J 5 HOH B 73 444 154 HOH HOH . J 5 HOH B 74 445 155 HOH HOH . J 5 HOH B 75 446 156 HOH HOH . J 5 HOH B 76 447 157 HOH HOH . J 5 HOH B 77 448 170 HOH HOH . J 5 HOH B 78 449 171 HOH HOH . J 5 HOH B 79 450 173 HOH HOH . J 5 HOH B 80 451 174 HOH HOH . J 5 HOH B 81 452 176 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 . . . H 4 13.101 19.616 56.453 1 23.74 ? PB ADP 371 B 1 HETATM 2 O O1B ADP . . . H 4 12.03 18.909 55.709 1 16.97 ? O1B ADP 371 B 1 HETATM 3 O O2B ADP . . . H 4 12.593 20.902 57.038 1 13.32 ? O2B ADP 371 B 1 HETATM 4 O O3B ADP . . . H 4 13.632 18.773 57.521 1 15.64 ? O3B ADP 371 B 1 HETATM 5 P PA ADP . . . H 4 15.514 19.04 55.231 1 19.33 ? PA ADP 371 B 1 HETATM 6 O O1A ADP . . . H 4 16.419 19.022 56.417 1 18.26 ? O1A ADP 371 B 1 HETATM 7 O O2A ADP . . . H 4 15.059 17.7 54.852 1 17.43 ? O2A ADP 371 B 1 HETATM 8 O O3A ADP . . . H 4 14.296 19.894 55.503 1 16.63 ? O3A ADP 371 B 1 HETATM 9 O O5' ADP . . . H 4 16.274 19.706 54.047 1 18.24 ? O5' ADP 371 B 1 HETATM 10 C C5' ADP . . . H 4 15.726 19.542 52.719 1 20.9 ? C5' ADP 371 B 1 HETATM 11 C C4' ADP . . . H 4 16.673 19.757 51.528 1 23.28 ? C4' ADP 371 B 1 HETATM 12 O O4' ADP . . . H 4 17.251 21.07 51.637 1 22.53 ? O4' ADP 371 B 1 HETATM 13 C C3' ADP . . . H 4 17.821 18.716 51.513 1 23.07 ? C3' ADP 371 B 1 HETATM 14 O O3' ADP . . . H 4 18.424 18.757 50.262 1 29.37 ? O3' ADP 371 B 1 HETATM 15 C C2' ADP . . . H 4 18.705 19.447 52.527 1 24.65 ? C2' ADP 371 B 1 HETATM 16 O O2' ADP . . . H 4 20.108 19.034 52.441 1 23.53 ? O2' ADP 371 B 1 HETATM 17 C C1' ADP . . . H 4 18.607 20.889 52.018 1 24.05 ? C1' ADP 371 B 1 HETATM 18 N N9 ADP . . . H 4 19.062 21.805 53.047 1 23.85 ? N9 ADP 371 B 1 HETATM 19 C C8 ADP . . . H 4 18.277 22.286 54.05 1 24.58 ? C8 ADP 371 B 1 HETATM 20 N N7 ADP . . . H 4 18.92 23.217 54.797 1 24.78 ? N7 ADP 371 B 1 HETATM 21 C C5 ADP . . . H 4 20.159 23.36 54.255 1 24.26 ? C5 ADP 371 B 1 HETATM 22 C C6 ADP . . . H 4 21.329 24.121 54.434 1 24.5 ? C6 ADP 371 B 1 HETATM 23 N N6 ADP . . . H 4 21.382 25.069 55.368 1 24.55 ? N6 ADP 371 B 1 HETATM 24 N N1 ADP . . . H 4 22.445 23.965 53.651 1 23.7 ? N1 ADP 371 B 1 HETATM 25 C C2 ADP . . . H 4 22.514 23.058 52.609 1 24.49 ? C2 ADP 371 B 1 HETATM 26 N N3 ADP . . . H 4 21.39 22.292 52.359 1 25.19 ? N3 ADP 371 B 1 HETATM 27 C C4 ADP . . . H 4 20.259 22.441 53.149 1 25.29 ? C4 ADP 371 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 27 #