data_2F56 # _model_server_result.job_id hKlVw47WiJuTT6BElw_Txw _model_server_result.datetime_utc '2024-11-27 00:50:38' _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 2f56 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":209}' # _entry.id 2F56 # _exptl.entry_id 2F56 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 60.055 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description UREA _entity.pdbx_number_of_molecules 11 _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 2F56 _cell.length_a 59.28 _cell.length_b 59.28 _cell.length_c 81.55 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2F56 _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32' # 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 PISA monomeric 1 author_and_software_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,P 1 1 B,G,H,I,J,K,L,Q 2 1 C,M,N,O,R 3 1 A,D,E,F,P 4 1 C,M,N,O,R 4 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' 2_564 -y,x-y+1,z-1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -29.64 51.337986 -27.183333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 N N N ? 2 O 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 C ND1 HIS 16 C HIS 16 1_555 M ZN ZN . C ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc2 C NZ LYS 60 C LYS 60 2_564 M ZN ZN . C ZN 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc3 M ZN ZN . C ZN 300 1_555 R O HOH . C HOH 452 2_564 ? ? ? ? ? ? ? ? ? ? ? ? 1.902 ? # _chem_comp.formula 'C H4 N2 O' _chem_comp.formula_weight 60.055 _chem_comp.id URE _chem_comp.mon_nstd_flag . _chem_comp.name UREA _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 C O URE doub 326 n n C N1 URE sing 327 n n C N2 URE sing 328 n n N1 HN11 URE sing 329 n n N1 HN12 URE sing 330 n n N2 HN21 URE sing 331 n n N2 HN22 URE sing 332 n n # _atom_sites.entry_id 2F56 _atom_sites.fract_transf_matrix[1][1] 0.016869 _atom_sites.fract_transf_matrix[1][2] 0.009739 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019479 _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] 0.012262 _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 D 2 URE A 1 206 206 URE URE . E 2 URE A 1 209 209 URE URE . F 2 URE A 1 210 210 URE URE . G 2 URE B 1 202 202 URE URE . H 2 URE B 1 203 203 URE URE . I 2 URE B 1 204 204 URE URE . J 2 URE B 1 205 205 URE URE . K 2 URE B 1 207 207 URE URE . L 2 URE B 1 208 208 URE URE . M 3 ZN C 1 300 300 ZN ZN . N 2 URE C 1 201 201 URE URE . O 2 URE C 1 211 211 URE URE . P 4 HOH A 1 304 304 HOH HOH . P 4 HOH A 2 306 306 HOH HOH . P 4 HOH A 3 307 307 HOH HOH . P 4 HOH A 4 308 308 HOH HOH . P 4 HOH A 5 317 317 HOH HOH . P 4 HOH A 6 320 320 HOH HOH . P 4 HOH A 7 324 324 HOH HOH . P 4 HOH A 8 326 326 HOH HOH . P 4 HOH A 9 327 327 HOH HOH . P 4 HOH A 10 328 328 HOH HOH . P 4 HOH A 11 331 331 HOH HOH . P 4 HOH A 12 336 336 HOH HOH . P 4 HOH A 13 338 338 HOH HOH . P 4 HOH A 14 339 339 HOH HOH . P 4 HOH A 15 340 340 HOH HOH . P 4 HOH A 16 344 344 HOH HOH . P 4 HOH A 17 346 346 HOH HOH . P 4 HOH A 18 350 350 HOH HOH . P 4 HOH A 19 351 351 HOH HOH . P 4 HOH A 20 355 355 HOH HOH . P 4 HOH A 21 356 356 HOH HOH . P 4 HOH A 22 362 362 HOH HOH . P 4 HOH A 23 367 367 HOH HOH . P 4 HOH A 24 373 373 HOH HOH . P 4 HOH A 25 376 376 HOH HOH . P 4 HOH A 26 378 378 HOH HOH . P 4 HOH A 27 382 382 HOH HOH . P 4 HOH A 28 389 389 HOH HOH . P 4 HOH A 29 392 392 HOH HOH . P 4 HOH A 30 394 394 HOH HOH . P 4 HOH A 31 398 398 HOH HOH . P 4 HOH A 32 400 400 HOH HOH . P 4 HOH A 33 401 401 HOH HOH . P 4 HOH A 34 405 405 HOH HOH . P 4 HOH A 35 410 410 HOH HOH . P 4 HOH A 36 411 411 HOH HOH . P 4 HOH A 37 416 416 HOH HOH . P 4 HOH A 38 426 426 HOH HOH . P 4 HOH A 39 429 429 HOH HOH . P 4 HOH A 40 432 432 HOH HOH . P 4 HOH A 41 434 434 HOH HOH . P 4 HOH A 42 439 439 HOH HOH . P 4 HOH A 43 441 441 HOH HOH . P 4 HOH A 44 442 442 HOH HOH . P 4 HOH A 45 446 446 HOH HOH . P 4 HOH A 46 448 448 HOH HOH . P 4 HOH A 47 450 450 HOH HOH . P 4 HOH A 48 453 453 HOH HOH . P 4 HOH A 49 456 456 HOH HOH . P 4 HOH A 50 458 458 HOH HOH . P 4 HOH A 51 463 463 HOH HOH . P 4 HOH A 52 464 464 HOH HOH . P 4 HOH A 53 466 466 HOH HOH . P 4 HOH A 54 467 467 HOH HOH . P 4 HOH A 55 469 469 HOH HOH . P 4 HOH A 56 474 474 HOH HOH . P 4 HOH A 57 477 477 HOH HOH . P 4 HOH A 58 483 483 HOH HOH . P 4 HOH A 59 485 485 HOH HOH . P 4 HOH A 60 487 487 HOH HOH . P 4 HOH A 61 488 488 HOH HOH . P 4 HOH A 62 493 493 HOH HOH . P 4 HOH A 63 497 497 HOH HOH . P 4 HOH A 64 498 498 HOH HOH . P 4 HOH A 65 500 500 HOH HOH . P 4 HOH A 66 510 510 HOH HOH . P 4 HOH A 67 511 511 HOH HOH . P 4 HOH A 68 512 512 HOH HOH . P 4 HOH A 69 513 513 HOH HOH . P 4 HOH A 70 516 516 HOH HOH . P 4 HOH A 71 518 518 HOH HOH . P 4 HOH A 72 519 519 HOH HOH . P 4 HOH A 73 525 525 HOH HOH . P 4 HOH A 74 526 526 HOH HOH . P 4 HOH A 75 534 534 HOH HOH . P 4 HOH A 76 537 537 HOH HOH . Q 4 HOH B 1 301 301 HOH HOH . Q 4 HOH B 2 302 302 HOH HOH . Q 4 HOH B 3 303 303 HOH HOH . Q 4 HOH B 4 305 305 HOH HOH . Q 4 HOH B 5 311 311 HOH HOH . Q 4 HOH B 6 316 316 HOH HOH . Q 4 HOH B 7 318 318 HOH HOH . Q 4 HOH B 8 321 321 HOH HOH . Q 4 HOH B 9 322 322 HOH HOH . Q 4 HOH B 10 323 323 HOH HOH . Q 4 HOH B 11 325 325 HOH HOH . Q 4 HOH B 12 329 329 HOH HOH . Q 4 HOH B 13 332 332 HOH HOH . Q 4 HOH B 14 333 333 HOH HOH . Q 4 HOH B 15 341 341 HOH HOH . Q 4 HOH B 16 345 345 HOH HOH . Q 4 HOH B 17 348 348 HOH HOH . Q 4 HOH B 18 349 349 HOH HOH . Q 4 HOH B 19 361 361 HOH HOH . Q 4 HOH B 20 364 364 HOH HOH . Q 4 HOH B 21 368 368 HOH HOH . Q 4 HOH B 22 371 371 HOH HOH . Q 4 HOH B 23 372 372 HOH HOH . Q 4 HOH B 24 375 375 HOH HOH . Q 4 HOH B 25 377 377 HOH HOH . Q 4 HOH B 26 379 379 HOH HOH . Q 4 HOH B 27 380 380 HOH HOH . Q 4 HOH B 28 384 384 HOH HOH . Q 4 HOH B 29 385 385 HOH HOH . Q 4 HOH B 30 387 387 HOH HOH . Q 4 HOH B 31 388 388 HOH HOH . Q 4 HOH B 32 393 393 HOH HOH . Q 4 HOH B 33 396 396 HOH HOH . Q 4 HOH B 34 404 404 HOH HOH . Q 4 HOH B 35 406 406 HOH HOH . Q 4 HOH B 36 407 407 HOH HOH . Q 4 HOH B 37 408 408 HOH HOH . Q 4 HOH B 38 409 409 HOH HOH . Q 4 HOH B 39 415 415 HOH HOH . Q 4 HOH B 40 418 418 HOH HOH . Q 4 HOH B 41 420 420 HOH HOH . Q 4 HOH B 42 421 421 HOH HOH . Q 4 HOH B 43 422 422 HOH HOH . Q 4 HOH B 44 428 428 HOH HOH . Q 4 HOH B 45 430 430 HOH HOH . Q 4 HOH B 46 431 431 HOH HOH . Q 4 HOH B 47 436 436 HOH HOH . Q 4 HOH B 48 440 440 HOH HOH . Q 4 HOH B 49 444 444 HOH HOH . Q 4 HOH B 50 445 445 HOH HOH . Q 4 HOH B 51 447 447 HOH HOH . Q 4 HOH B 52 451 451 HOH HOH . Q 4 HOH B 53 454 454 HOH HOH . Q 4 HOH B 54 457 457 HOH HOH . Q 4 HOH B 55 462 462 HOH HOH . Q 4 HOH B 56 470 470 HOH HOH . Q 4 HOH B 57 471 471 HOH HOH . Q 4 HOH B 58 473 473 HOH HOH . Q 4 HOH B 59 478 478 HOH HOH . Q 4 HOH B 60 480 480 HOH HOH . Q 4 HOH B 61 481 481 HOH HOH . Q 4 HOH B 62 486 486 HOH HOH . Q 4 HOH B 63 489 489 HOH HOH . Q 4 HOH B 64 491 491 HOH HOH . Q 4 HOH B 65 494 494 HOH HOH . Q 4 HOH B 66 499 499 HOH HOH . Q 4 HOH B 67 514 514 HOH HOH . Q 4 HOH B 68 515 515 HOH HOH . Q 4 HOH B 69 521 521 HOH HOH . Q 4 HOH B 70 527 527 HOH HOH . Q 4 HOH B 71 530 530 HOH HOH . Q 4 HOH B 72 531 531 HOH HOH . Q 4 HOH B 73 532 532 HOH HOH . Q 4 HOH B 74 535 535 HOH HOH . R 4 HOH C 1 309 309 HOH HOH . R 4 HOH C 2 310 310 HOH HOH . R 4 HOH C 3 312 312 HOH HOH . R 4 HOH C 4 313 313 HOH HOH . R 4 HOH C 5 314 314 HOH HOH . R 4 HOH C 6 315 315 HOH HOH . R 4 HOH C 7 319 319 HOH HOH . R 4 HOH C 8 330 330 HOH HOH . R 4 HOH C 9 334 334 HOH HOH . R 4 HOH C 10 335 335 HOH HOH . R 4 HOH C 11 337 337 HOH HOH . R 4 HOH C 12 342 342 HOH HOH . R 4 HOH C 13 343 343 HOH HOH . R 4 HOH C 14 347 347 HOH HOH . R 4 HOH C 15 352 352 HOH HOH . R 4 HOH C 16 353 353 HOH HOH . R 4 HOH C 17 354 354 HOH HOH . R 4 HOH C 18 357 357 HOH HOH . R 4 HOH C 19 358 358 HOH HOH . R 4 HOH C 20 359 359 HOH HOH . R 4 HOH C 21 360 360 HOH HOH . R 4 HOH C 22 363 363 HOH HOH . R 4 HOH C 23 365 365 HOH HOH . R 4 HOH C 24 366 366 HOH HOH . R 4 HOH C 25 369 369 HOH HOH . R 4 HOH C 26 370 370 HOH HOH . R 4 HOH C 27 374 374 HOH HOH . R 4 HOH C 28 381 381 HOH HOH . R 4 HOH C 29 383 383 HOH HOH . R 4 HOH C 30 386 386 HOH HOH . R 4 HOH C 31 390 390 HOH HOH . R 4 HOH C 32 391 391 HOH HOH . R 4 HOH C 33 395 395 HOH HOH . R 4 HOH C 34 397 397 HOH HOH . R 4 HOH C 35 399 399 HOH HOH . R 4 HOH C 36 402 402 HOH HOH . R 4 HOH C 37 403 403 HOH HOH . R 4 HOH C 38 412 412 HOH HOH . R 4 HOH C 39 413 413 HOH HOH . R 4 HOH C 40 414 414 HOH HOH . R 4 HOH C 41 417 417 HOH HOH . R 4 HOH C 42 419 419 HOH HOH . R 4 HOH C 43 423 423 HOH HOH . R 4 HOH C 44 425 425 HOH HOH . R 4 HOH C 45 427 427 HOH HOH . R 4 HOH C 46 433 433 HOH HOH . R 4 HOH C 47 435 435 HOH HOH . R 4 HOH C 48 437 437 HOH HOH . R 4 HOH C 49 438 438 HOH HOH . R 4 HOH C 50 443 443 HOH HOH . R 4 HOH C 51 449 449 HOH HOH . R 4 HOH C 52 452 452 HOH HOH . R 4 HOH C 53 455 455 HOH HOH . R 4 HOH C 54 459 459 HOH HOH . R 4 HOH C 55 460 460 HOH HOH . R 4 HOH C 56 461 461 HOH HOH . R 4 HOH C 57 465 465 HOH HOH . R 4 HOH C 58 468 468 HOH HOH . R 4 HOH C 59 472 472 HOH HOH . R 4 HOH C 60 475 475 HOH HOH . R 4 HOH C 61 476 476 HOH HOH . R 4 HOH C 62 479 479 HOH HOH . R 4 HOH C 63 482 482 HOH HOH . R 4 HOH C 64 484 484 HOH HOH . R 4 HOH C 65 490 490 HOH HOH . R 4 HOH C 66 492 492 HOH HOH . R 4 HOH C 67 495 495 HOH HOH . R 4 HOH C 68 496 496 HOH HOH . R 4 HOH C 69 501 501 HOH HOH . R 4 HOH C 70 502 502 HOH HOH . R 4 HOH C 71 503 503 HOH HOH . R 4 HOH C 72 504 504 HOH HOH . R 4 HOH C 73 505 505 HOH HOH . R 4 HOH C 74 506 506 HOH HOH . R 4 HOH C 75 507 507 HOH HOH . R 4 HOH C 76 508 508 HOH HOH . R 4 HOH C 77 509 509 HOH HOH . R 4 HOH C 78 517 517 HOH HOH . R 4 HOH C 79 520 520 HOH HOH . R 4 HOH C 80 522 522 HOH HOH . R 4 HOH C 81 523 523 HOH HOH . R 4 HOH C 82 524 524 HOH HOH . R 4 HOH C 83 528 528 HOH HOH . R 4 HOH C 84 529 529 HOH HOH . R 4 HOH C 85 533 533 HOH HOH . R 4 HOH C 86 536 536 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 C C URE . . . E 2 -17.291 14.472 -14.209 0.5 42.07 ? C URE 209 A 1 HETATM 2 O O URE . . . E 2 -16.4 14.014 -13.457 0.5 33.27 ? O URE 209 A 1 HETATM 3 N N1 URE . . . E 2 -18.546 14.067 -14.026 0.5 55.21 ? N1 URE 209 A 1 HETATM 4 N N2 URE . . . E 2 -16.94 15.362 -15.132 0.5 40.04 ? N2 URE 209 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 426 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 4 #