data_1RKD
#
_model_server_result.job_id            jzg7dVTaCH8YR8e9Z82DIQ 
_model_server_result.datetime_utc      '2024-11-28 05:25:45' 
_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":"B","auth_seq_id":311}' 
#
_entry.id    1RKD 
#
_exptl.entry_id    1RKD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              150.13 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            alpha-D-ribofuranose 
_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                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C5 H10 O5' 
_chem_comp.formula_weight    150.13 
_chem_comp.id                RIB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              alpha-D-ribofuranose 
_chem_comp.type              'd-saccharide, alpha linking' 
_chem_comp.pdbx_synonyms     alpha-D-ribose;D-ribose;ribose 
#
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
O5 C5 RIB sing 325 n n 
O5 HO5 RIB sing 326 n n 
C5 C4 RIB sing 327 n n 
C5 H51 RIB sing 328 n n 
C5 H52 RIB sing 329 n n 
C4 O4 RIB sing 330 n n 
C4 C3 RIB sing 331 n n 
C4 H4 RIB sing 332 n n 
O4 C1 RIB sing 333 n n 
C3 O3 RIB sing 334 n n 
C3 C2 RIB sing 335 n n 
C3 H3 RIB sing 336 n n 
O3 HO3 RIB sing 337 n n 
C2 O2 RIB sing 338 n n 
C2 C1 RIB sing 339 n n 
C2 H2 RIB sing 340 n n 
O2 HO2 RIB sing 341 n n 
C1 O1 RIB sing 342 n n 
C1 H1 RIB sing 343 n n 
O1 HO1 RIB sing 344 n n 
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.identifier
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
RIB DRibfa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
RIB a-D-ribofuranose 'COMMON NAME' GMML 1 
RIB a-D-Ribf 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
RIB Rib 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_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 O O5 RIB . . . B 2 -22.638 14.721 43.822 1 22.48 ? O5 RIB 311 A 1 
HETATM 2 C C5 RIB . . . B 2 -21.843 14.285 44.944 1 21.5 ? C5 RIB 311 A 1 
HETATM 3 C C4 RIB . . . B 2 -20.428 14.057 44.341 1 22.23 ? C4 RIB 311 A 1 
HETATM 4 O O4 RIB . . . B 2 -19.948 15.274 43.768 1 22.86 ? O4 RIB 311 A 1 
HETATM 5 C C3 RIB . . . B 2 -19.396 13.613 45.381 1 20.99 ? C3 RIB 311 A 1 
HETATM 6 O O3 RIB . . . B 2 -19.441 12.184 45.5 1 19.13 ? O3 RIB 311 A 1 
HETATM 7 C C2 RIB . . . B 2 -18.089 14.222 44.874 1 21.45 ? C2 RIB 311 A 1 
HETATM 8 O O2 RIB . . . B 2 -17.199 13.2 44.431 1 17.8 ? O2 RIB 311 A 1 
HETATM 9 C C1 RIB . . . B 2 -18.512 15.123 43.696 1 23.61 ? C1 RIB 311 A 1 
HETATM 10 O O1 RIB . . . B 2 -18.241 14.414 42.529 1 27.06 ? O1 RIB 311 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           10 
#