data_1RKD
#
_model_server_result.job_id            QLo7bHzi3rwkeenRCtoqMg 
_model_server_result.datetime_utc      '2024-11-24 11:42:26' 
_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          1rkd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":310}' 
#
_entry.id    1RKD 
#
_exptl.entry_id    1RKD 
_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            1RKD 
_cell.length_a            95.4 
_cell.length_b            95.4 
_cell.length_c            154.87 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RKD 
_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,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' 9_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 103.246667 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_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                     1RKD 
_atom_sites.fract_transf_matrix[1][1]    0.010482 
_atom_sites.fract_transf_matrix[1][2]    0.006052 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012104 
_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]    0.006457 
_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 RIB A 1 311 311 RIB RIB . 
C 3 PO4 A 1 312 312 PO4 PO4 . 
D 3 PO4 A 1 313 313 PO4 PO4 . 
E 4 ADP A 1 310 310 ADP ADP . 
F 5 HOH A 1 314 314 HOH HOH . 
F 5 HOH A 2 315 315 HOH HOH . 
F 5 HOH A 3 316 316 HOH HOH . 
F 5 HOH A 4 317 317 HOH HOH . 
F 5 HOH A 5 318 318 HOH HOH . 
F 5 HOH A 6 319 319 HOH HOH . 
F 5 HOH A 7 320 320 HOH HOH . 
F 5 HOH A 8 321 321 HOH HOH . 
F 5 HOH A 9 322 322 HOH HOH . 
F 5 HOH A 10 323 323 HOH HOH . 
F 5 HOH A 11 324 324 HOH HOH . 
F 5 HOH A 12 325 325 HOH HOH . 
F 5 HOH A 13 326 326 HOH HOH . 
F 5 HOH A 14 327 327 HOH HOH . 
F 5 HOH A 15 328 328 HOH HOH . 
F 5 HOH A 16 329 329 HOH HOH . 
F 5 HOH A 17 330 330 HOH HOH . 
F 5 HOH A 18 331 331 HOH HOH . 
F 5 HOH A 19 332 332 HOH HOH . 
F 5 HOH A 20 333 333 HOH HOH . 
F 5 HOH A 21 334 334 HOH HOH . 
F 5 HOH A 22 335 335 HOH HOH . 
F 5 HOH A 23 336 336 HOH HOH . 
F 5 HOH A 24 337 337 HOH HOH . 
F 5 HOH A 25 338 338 HOH HOH . 
F 5 HOH A 26 339 339 HOH HOH . 
F 5 HOH A 27 340 340 HOH HOH . 
F 5 HOH A 28 341 341 HOH HOH . 
F 5 HOH A 29 342 342 HOH HOH . 
F 5 HOH A 30 343 343 HOH HOH . 
F 5 HOH A 31 344 344 HOH HOH . 
F 5 HOH A 32 345 345 HOH HOH . 
F 5 HOH A 33 346 346 HOH HOH . 
F 5 HOH A 34 347 347 HOH HOH . 
F 5 HOH A 35 348 348 HOH HOH . 
F 5 HOH A 36 349 349 HOH HOH . 
F 5 HOH A 37 350 350 HOH HOH . 
F 5 HOH A 38 351 351 HOH HOH . 
F 5 HOH A 39 352 352 HOH HOH . 
F 5 HOH A 40 353 353 HOH HOH . 
F 5 HOH A 41 354 354 HOH HOH . 
F 5 HOH A 42 355 355 HOH HOH . 
F 5 HOH A 43 356 356 HOH HOH . 
F 5 HOH A 44 357 357 HOH HOH . 
F 5 HOH A 45 358 358 HOH HOH . 
F 5 HOH A 46 359 359 HOH HOH . 
F 5 HOH A 47 360 360 HOH HOH . 
F 5 HOH A 48 361 361 HOH HOH . 
F 5 HOH A 49 362 362 HOH HOH . 
F 5 HOH A 50 363 363 HOH HOH . 
F 5 HOH A 51 364 364 HOH HOH . 
F 5 HOH A 52 365 365 HOH HOH . 
F 5 HOH A 53 366 366 HOH HOH . 
F 5 HOH A 54 367 367 HOH HOH . 
F 5 HOH A 55 368 368 HOH HOH . 
F 5 HOH A 56 369 369 HOH HOH . 
F 5 HOH A 57 370 370 HOH HOH . 
F 5 HOH A 58 371 371 HOH HOH . 
F 5 HOH A 59 372 372 HOH HOH . 
F 5 HOH A 60 373 373 HOH HOH . 
F 5 HOH A 61 374 374 HOH HOH . 
F 5 HOH A 62 375 375 HOH HOH . 
F 5 HOH A 63 376 376 HOH HOH . 
F 5 HOH A 64 377 377 HOH HOH . 
F 5 HOH A 65 378 378 HOH HOH . 
F 5 HOH A 66 379 379 HOH HOH . 
F 5 HOH A 67 380 380 HOH HOH . 
F 5 HOH A 68 381 381 HOH HOH . 
F 5 HOH A 69 382 382 HOH HOH . 
F 5 HOH A 70 383 383 HOH HOH . 
F 5 HOH A 71 384 384 HOH HOH . 
F 5 HOH A 72 385 385 HOH HOH . 
F 5 HOH A 73 386 386 HOH HOH . 
F 5 HOH A 74 387 387 HOH HOH . 
F 5 HOH A 75 388 388 HOH HOH . 
F 5 HOH A 76 389 389 HOH HOH . 
F 5 HOH A 77 390 390 HOH HOH . 
F 5 HOH A 78 391 391 HOH HOH . 
F 5 HOH A 79 392 392 HOH HOH . 
F 5 HOH A 80 393 393 HOH HOH . 
F 5 HOH A 81 394 394 HOH HOH . 
F 5 HOH A 82 395 395 HOH HOH . 
F 5 HOH A 83 396 396 HOH HOH . 
F 5 HOH A 84 397 397 HOH HOH . 
F 5 HOH A 85 398 398 HOH HOH . 
F 5 HOH A 86 399 399 HOH HOH . 
F 5 HOH A 87 400 400 HOH HOH . 
F 5 HOH A 88 401 401 HOH HOH . 
F 5 HOH A 89 402 402 HOH HOH . 
F 5 HOH A 90 403 403 HOH HOH . 
F 5 HOH A 91 404 404 HOH HOH . 
F 5 HOH A 92 405 405 HOH HOH . 
F 5 HOH A 93 406 406 HOH HOH . 
F 5 HOH A 94 407 407 HOH HOH . 
F 5 HOH A 95 408 408 HOH HOH . 
F 5 HOH A 96 409 409 HOH HOH . 
F 5 HOH A 97 410 410 HOH HOH . 
F 5 HOH A 98 411 411 HOH HOH . 
F 5 HOH A 99 412 412 HOH HOH . 
F 5 HOH A 100 413 413 HOH HOH . 
F 5 HOH A 101 414 414 HOH HOH . 
F 5 HOH A 102 415 415 HOH HOH . 
F 5 HOH A 103 416 416 HOH HOH . 
F 5 HOH A 104 417 417 HOH HOH . 
F 5 HOH A 105 418 418 HOH HOH . 
F 5 HOH A 106 419 419 HOH HOH . 
F 5 HOH A 107 420 420 HOH HOH . 
F 5 HOH A 108 421 421 HOH HOH . 
F 5 HOH A 109 422 422 HOH HOH . 
F 5 HOH A 110 423 423 HOH HOH . 
F 5 HOH A 111 424 424 HOH HOH . 
F 5 HOH A 112 425 425 HOH HOH . 
F 5 HOH A 113 426 426 HOH HOH . 
F 5 HOH A 114 427 427 HOH HOH . 
F 5 HOH A 115 428 428 HOH HOH . 
F 5 HOH A 116 429 429 HOH HOH . 
F 5 HOH A 117 430 430 HOH HOH . 
F 5 HOH A 118 431 431 HOH HOH . 
F 5 HOH A 119 432 432 HOH HOH . 
F 5 HOH A 120 433 433 HOH HOH . 
F 5 HOH A 121 434 434 HOH HOH . 
F 5 HOH A 122 435 435 HOH HOH . 
F 5 HOH A 123 436 436 HOH HOH . 
F 5 HOH A 124 437 437 HOH HOH . 
F 5 HOH A 125 438 438 HOH HOH . 
F 5 HOH A 126 439 439 HOH HOH . 
F 5 HOH A 127 440 440 HOH HOH . 
F 5 HOH A 128 441 441 HOH HOH . 
F 5 HOH A 129 442 442 HOH HOH . 
F 5 HOH A 130 443 443 HOH HOH . 
F 5 HOH A 131 444 444 HOH HOH . 
F 5 HOH A 132 445 445 HOH HOH . 
F 5 HOH A 133 446 446 HOH HOH . 
F 5 HOH A 134 447 447 HOH HOH . 
F 5 HOH A 135 448 448 HOH HOH . 
F 5 HOH A 136 449 449 HOH HOH . 
F 5 HOH A 137 450 450 HOH HOH . 
F 5 HOH A 138 451 451 HOH HOH . 
F 5 HOH A 139 452 452 HOH HOH . 
F 5 HOH A 140 453 453 HOH HOH . 
F 5 HOH A 141 454 454 HOH HOH . 
F 5 HOH A 142 455 455 HOH HOH . 
F 5 HOH A 143 456 456 HOH HOH . 
F 5 HOH A 144 457 457 HOH HOH . 
F 5 HOH A 145 458 458 HOH HOH . 
F 5 HOH A 146 459 459 HOH HOH . 
F 5 HOH A 147 460 460 HOH HOH . 
F 5 HOH A 148 461 461 HOH HOH . 
F 5 HOH A 149 462 462 HOH HOH . 
F 5 HOH A 150 463 463 HOH HOH . 
F 5 HOH A 151 464 464 HOH HOH . 
F 5 HOH A 152 465 465 HOH HOH . 
F 5 HOH A 153 466 466 HOH HOH . 
F 5 HOH A 154 467 467 HOH HOH . 
F 5 HOH A 155 468 468 HOH HOH . 
F 5 HOH A 156 469 469 HOH HOH . 
F 5 HOH A 157 470 470 HOH HOH . 
F 5 HOH A 158 471 471 HOH HOH . 
F 5 HOH A 159 472 472 HOH HOH . 
F 5 HOH A 160 473 473 HOH HOH . 
F 5 HOH A 161 474 474 HOH HOH . 
F 5 HOH A 162 475 475 HOH HOH . 
F 5 HOH A 163 476 476 HOH HOH . 
F 5 HOH A 164 477 477 HOH HOH . 
F 5 HOH A 165 478 478 HOH HOH . 
F 5 HOH A 166 479 479 HOH HOH . 
F 5 HOH A 167 480 480 HOH HOH . 
F 5 HOH A 168 481 481 HOH HOH . 
F 5 HOH A 169 482 482 HOH HOH . 
F 5 HOH A 170 483 483 HOH HOH . 
F 5 HOH A 171 484 484 HOH HOH . 
F 5 HOH A 172 485 485 HOH HOH . 
F 5 HOH A 173 486 486 HOH HOH . 
F 5 HOH A 174 487 487 HOH HOH . 
F 5 HOH A 175 488 488 HOH HOH . 
F 5 HOH A 176 489 489 HOH HOH . 
F 5 HOH A 177 490 490 HOH HOH . 
F 5 HOH A 178 491 491 HOH HOH . 
F 5 HOH A 179 492 492 HOH HOH . 
F 5 HOH A 180 493 493 HOH HOH . 
F 5 HOH A 181 494 494 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 . . . E 4 -28.706 18.845 43.498 1 54.12 ? PB ADP 310 A 1 
HETATM 2 O O1B ADP . . . E 4 -28.353 18.162 44.769 1 51.02 ? O1B ADP 310 A 1 
HETATM 3 O O2B ADP . . . E 4 -28.268 20.266 43.547 1 50.8 ? O2B ADP 310 A 1 
HETATM 4 O O3B ADP . . . E 4 -28.269 18.038 42.203 1 54.41 ? O3B ADP 310 A 1 
HETATM 5 P PA ADP . . . E 4 -31.451 19.54 44.155 1 41.85 ? PA ADP 310 A 1 
HETATM 6 O O1A ADP . . . E 4 -30.982 20.336 45.306 1 42.97 ? O1A ADP 310 A 1 
HETATM 7 O O2A ADP . . . E 4 -32.306 20.457 43.308 1 40.26 ? O2A ADP 310 A 1 
HETATM 8 O O3A ADP . . . E 4 -30.299 18.833 43.291 1 44.53 ? O3A ADP 310 A 1 
HETATM 9 O O5' ADP . . . E 4 -32.245 18.23 44.605 1 39.19 ? O5' ADP 310 A 1 
HETATM 10 C C5' ADP . . . E 4 -32.373 17.105 43.694 1 30.92 ? C5' ADP 310 A 1 
HETATM 11 C C4' ADP . . . E 4 -33.491 16.18 44.153 1 35.56 ? C4' ADP 310 A 1 
HETATM 12 O O4' ADP . . . E 4 -33.165 15.741 45.493 1 34.28 ? O4' ADP 310 A 1 
HETATM 13 C C3' ADP . . . E 4 -34.86 16.864 44.319 1 37.01 ? C3' ADP 310 A 1 
HETATM 14 O O3' ADP . . . E 4 -35.571 17.032 43.082 1 39.27 ? O3' ADP 310 A 1 
HETATM 15 C C2' ADP . . . E 4 -35.513 15.883 45.335 1 35.45 ? C2' ADP 310 A 1 
HETATM 16 O O2' ADP . . . E 4 -35.832 14.622 44.729 1 35.05 ? O2' ADP 310 A 1 
HETATM 17 C C1' ADP . . . E 4 -34.301 15.67 46.292 1 37.64 ? C1' ADP 310 A 1 
HETATM 18 N N9 ADP . . . E 4 -34.345 16.661 47.339 1 39.26 ? N9 ADP 310 A 1 
HETATM 19 C C8 ADP . . . E 4 -33.509 17.716 47.525 1 42.22 ? C8 ADP 310 A 1 
HETATM 20 N N7 ADP . . . E 4 -33.59 18.332 48.649 1 42.83 ? N7 ADP 310 A 1 
HETATM 21 C C5 ADP . . . E 4 -34.545 17.676 49.28 1 43.09 ? C5 ADP 310 A 1 
HETATM 22 C C6 ADP . . . E 4 -35.059 17.915 50.525 1 43.23 ? C6 ADP 310 A 1 
HETATM 23 N N6 ADP . . . E 4 -34.636 18.867 51.36 1 45.73 ? N6 ADP 310 A 1 
HETATM 24 N N1 ADP . . . E 4 -36.052 17.096 50.93 1 41.79 ? N1 ADP 310 A 1 
HETATM 25 C C2 ADP . . . E 4 -36.48 16.091 50.087 1 44.23 ? C2 ADP 310 A 1 
HETATM 26 N N3 ADP . . . E 4 -36.067 15.802 48.878 1 43.28 ? N3 ADP 310 A 1 
HETATM 27 C C4 ADP . . . E 4 -35.073 16.646 48.526 1 41.91 ? C4 ADP 310 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           1106 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           27 
#