data_2ZS9 # _model_server_result.job_id ImeNEhgDBfTh9jdPyU153Q _model_server_result.datetime_utc '2024-10-11 13:27:58' _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 2zs9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":315}' # _entry.id 2ZS9 # _exptl.entry_id 2ZS9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 2ZS9 _cell.length_a 104.194 _cell.length_b 104.194 _cell.length_c 90.304 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZS9 _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,G,H,I,J,K,L,M,N,O _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' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 90.304 # _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 # 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 OE2 GLU 48 A GLU 48 1_555 K NA NA . A NA 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.191 ? metalc ? metalc2 A O THR 127 A THR 127 1_555 L NA NA . A NA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? metalc ? metalc3 A O SER 215 A SER 215 1_555 M NA NA . A NA 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? metalc ? metalc4 O O HOH . A HOH 401 1_555 L NA NA . A NA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc5 O O HOH . A HOH 404 1_555 L NA NA . A NA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc6 O O HOH . A HOH 478 1_555 M NA NA . A NA 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc7 D O3 GOL . A GOL 701 1_555 M NA NA . A NA 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? # _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 2ZS9 _atom_sites.fract_transf_matrix[1][1] 0.009597 _atom_sites.fract_transf_matrix[1][2] 0.005541 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011082 _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] 0.011074 _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 ADP A 1 315 315 ADP ADP . C 3 GOL A 1 700 700 GOL GOL . D 3 GOL A 1 701 701 GOL GOL . E 3 GOL A 1 702 702 GOL GOL . F 3 GOL A 1 703 703 GOL GOL . G 3 GOL A 1 704 704 GOL GOL . H 3 GOL A 1 705 705 GOL GOL . I 3 GOL A 1 706 706 GOL GOL . J 3 GOL A 1 707 707 GOL GOL . K 4 NA A 1 708 1 NA NA . L 4 NA A 1 709 2 NA NA . M 4 NA A 1 710 3 NA NA . N 5 PAU A 1 603 603 PAU PAU . O 6 HOH A 1 320 320 HOH HOH . O 6 HOH A 2 321 321 HOH HOH . O 6 HOH A 3 322 322 HOH HOH . O 6 HOH A 4 323 323 HOH HOH . O 6 HOH A 5 324 324 HOH HOH . O 6 HOH A 6 325 325 HOH HOH . O 6 HOH A 7 326 326 HOH HOH . O 6 HOH A 8 327 327 HOH HOH . O 6 HOH A 9 328 328 HOH HOH . O 6 HOH A 10 329 329 HOH HOH . O 6 HOH A 11 330 330 HOH HOH . O 6 HOH A 12 331 331 HOH HOH . O 6 HOH A 13 332 332 HOH HOH . O 6 HOH A 14 333 333 HOH HOH . O 6 HOH A 15 334 334 HOH HOH . O 6 HOH A 16 335 335 HOH HOH . O 6 HOH A 17 336 336 HOH HOH . O 6 HOH A 18 337 337 HOH HOH . O 6 HOH A 19 338 338 HOH HOH . O 6 HOH A 20 339 339 HOH HOH . O 6 HOH A 21 340 340 HOH HOH . O 6 HOH A 22 341 341 HOH HOH . O 6 HOH A 23 342 342 HOH HOH . O 6 HOH A 24 343 343 HOH HOH . O 6 HOH A 25 344 344 HOH HOH . O 6 HOH A 26 345 345 HOH HOH . O 6 HOH A 27 346 346 HOH HOH . O 6 HOH A 28 347 347 HOH HOH . O 6 HOH A 29 348 348 HOH HOH . O 6 HOH A 30 349 349 HOH HOH . O 6 HOH A 31 350 350 HOH HOH . O 6 HOH A 32 351 351 HOH HOH . O 6 HOH A 33 352 352 HOH HOH . O 6 HOH A 34 353 353 HOH HOH . O 6 HOH A 35 354 354 HOH HOH . O 6 HOH A 36 355 355 HOH HOH . O 6 HOH A 37 356 356 HOH HOH . O 6 HOH A 38 357 357 HOH HOH . O 6 HOH A 39 358 358 HOH HOH . O 6 HOH A 40 359 359 HOH HOH . O 6 HOH A 41 360 360 HOH HOH . O 6 HOH A 42 361 361 HOH HOH . O 6 HOH A 43 362 362 HOH HOH . O 6 HOH A 44 363 363 HOH HOH . O 6 HOH A 45 364 364 HOH HOH . O 6 HOH A 46 365 365 HOH HOH . O 6 HOH A 47 366 366 HOH HOH . O 6 HOH A 48 367 367 HOH HOH . O 6 HOH A 49 368 368 HOH HOH . O 6 HOH A 50 369 369 HOH HOH . O 6 HOH A 51 370 370 HOH HOH . O 6 HOH A 52 371 371 HOH HOH . O 6 HOH A 53 372 372 HOH HOH . O 6 HOH A 54 373 373 HOH HOH . O 6 HOH A 55 374 374 HOH HOH . O 6 HOH A 56 375 375 HOH HOH . O 6 HOH A 57 376 376 HOH HOH . O 6 HOH A 58 377 377 HOH HOH . O 6 HOH A 59 378 378 HOH HOH . O 6 HOH A 60 379 379 HOH HOH . O 6 HOH A 61 380 380 HOH HOH . O 6 HOH A 62 381 381 HOH HOH . O 6 HOH A 63 382 382 HOH HOH . O 6 HOH A 64 383 383 HOH HOH . O 6 HOH A 65 384 384 HOH HOH . O 6 HOH A 66 385 385 HOH HOH . O 6 HOH A 67 386 386 HOH HOH . O 6 HOH A 68 387 387 HOH HOH . O 6 HOH A 69 388 388 HOH HOH . O 6 HOH A 70 389 389 HOH HOH . O 6 HOH A 71 390 390 HOH HOH . O 6 HOH A 72 391 391 HOH HOH . O 6 HOH A 73 392 392 HOH HOH . O 6 HOH A 74 393 393 HOH HOH . O 6 HOH A 75 394 394 HOH HOH . O 6 HOH A 76 395 395 HOH HOH . O 6 HOH A 77 396 396 HOH HOH . O 6 HOH A 78 397 397 HOH HOH . O 6 HOH A 79 398 398 HOH HOH . O 6 HOH A 80 399 399 HOH HOH . O 6 HOH A 81 400 400 HOH HOH . O 6 HOH A 82 401 401 HOH HOH . O 6 HOH A 83 402 402 HOH HOH . O 6 HOH A 84 403 403 HOH HOH . O 6 HOH A 85 404 404 HOH HOH . O 6 HOH A 86 405 405 HOH HOH . O 6 HOH A 87 406 406 HOH HOH . O 6 HOH A 88 407 407 HOH HOH . O 6 HOH A 89 408 408 HOH HOH . O 6 HOH A 90 409 409 HOH HOH . O 6 HOH A 91 410 410 HOH HOH . O 6 HOH A 92 411 411 HOH HOH . O 6 HOH A 93 412 412 HOH HOH . O 6 HOH A 94 413 413 HOH HOH . O 6 HOH A 95 414 414 HOH HOH . O 6 HOH A 96 415 415 HOH HOH . O 6 HOH A 97 416 416 HOH HOH . O 6 HOH A 98 417 417 HOH HOH . O 6 HOH A 99 418 418 HOH HOH . O 6 HOH A 100 419 419 HOH HOH . O 6 HOH A 101 420 420 HOH HOH . O 6 HOH A 102 421 421 HOH HOH . O 6 HOH A 103 422 422 HOH HOH . O 6 HOH A 104 423 423 HOH HOH . O 6 HOH A 105 424 424 HOH HOH . O 6 HOH A 106 425 425 HOH HOH . O 6 HOH A 107 426 426 HOH HOH . O 6 HOH A 108 427 427 HOH HOH . O 6 HOH A 109 428 428 HOH HOH . O 6 HOH A 110 429 429 HOH HOH . O 6 HOH A 111 430 430 HOH HOH . O 6 HOH A 112 431 431 HOH HOH . O 6 HOH A 113 432 432 HOH HOH . O 6 HOH A 114 433 433 HOH HOH . O 6 HOH A 115 434 434 HOH HOH . O 6 HOH A 116 435 435 HOH HOH . O 6 HOH A 117 436 436 HOH HOH . O 6 HOH A 118 437 437 HOH HOH . O 6 HOH A 119 438 438 HOH HOH . O 6 HOH A 120 439 439 HOH HOH . O 6 HOH A 121 440 440 HOH HOH . O 6 HOH A 122 441 441 HOH HOH . O 6 HOH A 123 442 442 HOH HOH . O 6 HOH A 124 443 443 HOH HOH . O 6 HOH A 125 444 444 HOH HOH . O 6 HOH A 126 445 445 HOH HOH . O 6 HOH A 127 446 446 HOH HOH . O 6 HOH A 128 447 447 HOH HOH . O 6 HOH A 129 448 448 HOH HOH . O 6 HOH A 130 449 449 HOH HOH . O 6 HOH A 131 450 450 HOH HOH . O 6 HOH A 132 451 451 HOH HOH . O 6 HOH A 133 452 452 HOH HOH . O 6 HOH A 134 453 453 HOH HOH . O 6 HOH A 135 454 454 HOH HOH . O 6 HOH A 136 455 455 HOH HOH . O 6 HOH A 137 456 456 HOH HOH . O 6 HOH A 138 457 457 HOH HOH . O 6 HOH A 139 458 458 HOH HOH . O 6 HOH A 140 459 459 HOH HOH . O 6 HOH A 141 460 460 HOH HOH . O 6 HOH A 142 461 461 HOH HOH . O 6 HOH A 143 462 462 HOH HOH . O 6 HOH A 144 463 463 HOH HOH . O 6 HOH A 145 464 464 HOH HOH . O 6 HOH A 146 465 465 HOH HOH . O 6 HOH A 147 466 466 HOH HOH . O 6 HOH A 148 467 467 HOH HOH . O 6 HOH A 149 468 468 HOH HOH . O 6 HOH A 150 469 469 HOH HOH . O 6 HOH A 151 470 470 HOH HOH . O 6 HOH A 152 471 471 HOH HOH . O 6 HOH A 153 472 472 HOH HOH . O 6 HOH A 154 473 473 HOH HOH . O 6 HOH A 155 474 474 HOH HOH . O 6 HOH A 156 475 475 HOH HOH . O 6 HOH A 157 476 476 HOH HOH . O 6 HOH A 158 477 477 HOH HOH . O 6 HOH A 159 478 478 HOH HOH . O 6 HOH A 160 479 479 HOH HOH . O 6 HOH A 161 480 480 HOH HOH . O 6 HOH A 162 481 481 HOH HOH . O 6 HOH A 163 482 482 HOH HOH . O 6 HOH A 164 483 483 HOH HOH . O 6 HOH A 165 484 484 HOH HOH . O 6 HOH A 166 485 485 HOH HOH . O 6 HOH A 167 486 486 HOH HOH . O 6 HOH A 168 487 487 HOH HOH . O 6 HOH A 169 488 488 HOH HOH . O 6 HOH A 170 489 489 HOH HOH . O 6 HOH A 171 490 490 HOH HOH . O 6 HOH A 172 491 491 HOH HOH . O 6 HOH A 173 492 492 HOH HOH . O 6 HOH A 174 493 493 HOH HOH . O 6 HOH A 175 494 494 HOH HOH . O 6 HOH A 176 495 495 HOH HOH . O 6 HOH A 177 496 496 HOH HOH . O 6 HOH A 178 497 497 HOH HOH . O 6 HOH A 179 498 498 HOH HOH . O 6 HOH A 180 499 499 HOH HOH . O 6 HOH A 181 500 500 HOH HOH . O 6 HOH A 182 501 501 HOH HOH . O 6 HOH A 183 502 502 HOH HOH . O 6 HOH A 184 503 503 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 . . . B 2 15.226 58.993 62.101 1 46.53 ? PB ADP 315 A 1 HETATM 2 O O1B ADP . . . B 2 14.603 58.905 63.441 1 46.53 ? O1B ADP 315 A 1 HETATM 3 O O2B ADP . . . B 2 16.672 58.289 62.058 1 46.53 ? O2B ADP 315 A 1 HETATM 4 O O3B ADP . . . B 2 15.456 60.515 61.635 1 46.53 ? O3B ADP 315 A 1 HETATM 5 P PA ADP . . . B 2 12.898 57.701 61.208 1 46.53 ? PA ADP 315 A 1 HETATM 6 O O1A ADP . . . B 2 12.539 57.004 62.462 1 46.53 ? O1A ADP 315 A 1 HETATM 7 O O2A ADP . . . B 2 12.048 57.513 59.855 1 46.53 ? O2A ADP 315 A 1 HETATM 8 O O3A ADP . . . B 2 14.368 58.297 60.93 1 46.53 ? O3A ADP 315 A 1 HETATM 9 O O5' ADP . . . B 2 12.303 59.164 61.514 1 46.53 ? O5' ADP 315 A 1 HETATM 10 C C5' ADP . . . B 2 11.006 59.539 61.046 1 46.53 ? C5' ADP 315 A 1 HETATM 11 C C4' ADP . . . B 2 10.76 61.035 61.258 1 46.53 ? C4' ADP 315 A 1 HETATM 12 O O4' ADP . . . B 2 9.341 61.26 61.25 1 46.53 ? O4' ADP 315 A 1 HETATM 13 C C3' ADP . . . B 2 11.154 61.416 62.686 1 46.53 ? C3' ADP 315 A 1 HETATM 14 O O3' ADP . . . B 2 10.95 62.816 62.903 1 46.53 ? O3' ADP 315 A 1 HETATM 15 C C2' ADP . . . B 2 10.075 60.633 63.429 1 46.53 ? C2' ADP 315 A 1 HETATM 16 O O2' ADP . . . B 2 9.901 61.198 64.73 1 46.53 ? O2' ADP 315 A 1 HETATM 17 C C1' ADP . . . B 2 8.851 60.958 62.57 1 46.53 ? C1' ADP 315 A 1 HETATM 18 N N9 ADP . . . B 2 7.947 59.787 62.554 1 46.53 ? N9 ADP 315 A 1 HETATM 19 C C8 ADP . . . B 2 8.319 58.513 62.462 1 46.53 ? C8 ADP 315 A 1 HETATM 20 N N7 ADP . . . B 2 7.244 57.729 62.466 1 46.53 ? N7 ADP 315 A 1 HETATM 21 C C5 ADP . . . B 2 6.173 58.51 62.561 1 46.53 ? C5 ADP 315 A 1 HETATM 22 C C6 ADP . . . B 2 4.805 58.273 62.596 1 46.53 ? C6 ADP 315 A 1 HETATM 23 N N6 ADP . . . B 2 4.329 57.033 62.538 1 46.53 ? N6 ADP 315 A 1 HETATM 24 N N1 ADP . . . B 2 3.97 59.319 62.687 1 46.53 ? N1 ADP 315 A 1 HETATM 25 C C2 ADP . . . B 2 4.431 60.555 62.745 1 46.53 ? C2 ADP 315 A 1 HETATM 26 N N3 ADP . . . B 2 5.728 60.819 62.714 1 46.53 ? N3 ADP 315 A 1 HETATM 27 C C4 ADP . . . B 2 6.616 59.826 62.621 1 46.53 ? C4 ADP 315 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #