data_8GJX # _model_server_result.job_id kryRJnNQzDIElhyLh7Hl-w _model_server_result.datetime_utc '2024-11-25 04:48:04' _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 8gjx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8GJX # _exptl.entry_id 8GJX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 635.372 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'3'-cUA" _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 90 _cell.entry_id 8GJX _cell.length_a 110.879 _cell.length_b 110.879 _cell.length_c 35.553 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GJX _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall 'P 4w' _symmetry.space_group_name_H-M 'P 41' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C19 H23 N7 O14 P2' _chem_comp.formula_weight 635.372 _chem_comp.id ZNT _chem_comp.mon_nstd_flag . _chem_comp.name "2'3'-cUA" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-[(2R,5R,7R,8R,10S,12aR,14R,15R,15aS,16R)-14-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxooctahydro-2H,10H,12H-5,8-methano-2lambda~5~,10lambda~5~-furo[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-7-yl]pyrimidine-2,4(1H,3H)-dione # 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 O30 P11 ZNT doub 376 n n O29 P11 ZNT sing 377 n n O31 C32 ZNT sing 378 n n O31 C08 ZNT sing 379 n n P11 O10 ZNT sing 380 n n P11 O12 ZNT sing 381 n n C42 N41 ZNT doub 382 n y C42 N33 ZNT sing 383 n y O10 C09 ZNT sing 384 n n N41 C40 ZNT sing 385 n y C09 C08 ZNT sing 386 n n N33 C32 ZNT sing 387 n n N33 C34 ZNT sing 388 n y C32 C02 ZNT sing 389 n n C08 C03 ZNT sing 390 n n C40 C34 ZNT doub 391 n y C40 C38 ZNT sing 392 n y C34 N35 ZNT sing 393 n y N39 C38 ZNT sing 394 n n O12 C13 ZNT sing 395 n n C38 N37 ZNT doub 396 n y N35 C36 ZNT doub 397 n y N37 C36 ZNT sing 398 n y C02 C03 ZNT sing 399 n n C02 O01 ZNT sing 400 n n C03 O04 ZNT sing 401 n n O28 C22 ZNT doub 402 n n C13 C14 ZNT sing 403 n n C13 C20 ZNT sing 404 n n O15 C14 ZNT sing 405 n n C22 N23 ZNT sing 406 n n C22 N21 ZNT sing 407 n n N23 C24 ZNT sing 408 n n O04 P05 ZNT sing 409 n n C14 C16 ZNT sing 410 n n O27 C24 ZNT doub 411 n n C24 C25 ZNT sing 412 n n N21 C20 ZNT sing 413 n n N21 C26 ZNT sing 414 n n C20 O19 ZNT sing 415 n n C25 C26 ZNT doub 416 n n O07 P05 ZNT doub 417 n n P05 O18 ZNT sing 418 n n P05 O06 ZNT sing 419 n n C16 O19 ZNT sing 420 n n C16 C17 ZNT sing 421 n n O18 C17 ZNT sing 422 n n C13 H1 ZNT sing 423 n n C17 H2 ZNT sing 424 n n C17 H3 ZNT sing 425 n n C20 H4 ZNT sing 426 n n C26 H5 ZNT sing 427 n n C02 H6 ZNT sing 428 n n C03 H7 ZNT sing 429 n n C08 H8 ZNT sing 430 n n C09 H9 ZNT sing 431 n n C09 H10 ZNT sing 432 n n C14 H11 ZNT sing 433 n n C16 H12 ZNT sing 434 n n C25 H13 ZNT sing 435 n n C32 H14 ZNT sing 436 n n C36 H15 ZNT sing 437 n n C42 H16 ZNT sing 438 n n N23 H17 ZNT sing 439 n n N39 H18 ZNT sing 440 n n N39 H19 ZNT sing 441 n n O01 H20 ZNT sing 442 n n O06 H21 ZNT sing 443 n n O15 H22 ZNT sing 444 n n O29 H23 ZNT sing 445 n n # _atom_sites.entry_id 8GJX _atom_sites.fract_transf_matrix[1][1] 0.009019 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009019 _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] 0.028127 _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 ZNT B 1 401 401 ZNT LIG . D 3 HOH A 1 401 22 HOH HOH . D 3 HOH A 2 402 36 HOH HOH . D 3 HOH A 3 403 40 HOH HOH . D 3 HOH A 4 404 15 HOH HOH . D 3 HOH A 5 405 2 HOH HOH . D 3 HOH A 6 406 23 HOH HOH . D 3 HOH A 7 407 3 HOH HOH . D 3 HOH A 8 408 52 HOH HOH . D 3 HOH A 9 409 12 HOH HOH . D 3 HOH A 10 410 43 HOH HOH . D 3 HOH A 11 411 7 HOH HOH . D 3 HOH A 12 412 10 HOH HOH . D 3 HOH A 13 413 19 HOH HOH . D 3 HOH A 14 414 27 HOH HOH . D 3 HOH A 15 415 9 HOH HOH . D 3 HOH A 16 416 44 HOH HOH . D 3 HOH A 17 417 55 HOH HOH . D 3 HOH A 18 418 54 HOH HOH . D 3 HOH A 19 419 29 HOH HOH . D 3 HOH A 20 420 30 HOH HOH . D 3 HOH A 21 421 53 HOH HOH . D 3 HOH A 22 422 20 HOH HOH . D 3 HOH A 23 423 13 HOH HOH . D 3 HOH A 24 424 33 HOH HOH . D 3 HOH A 25 425 31 HOH HOH . D 3 HOH A 26 426 28 HOH HOH . D 3 HOH A 27 427 48 HOH HOH . D 3 HOH A 28 428 34 HOH HOH . D 3 HOH A 29 429 25 HOH HOH . E 3 HOH B 1 501 50 HOH HOH . E 3 HOH B 2 502 38 HOH HOH . E 3 HOH B 3 503 39 HOH HOH . E 3 HOH B 4 504 24 HOH HOH . E 3 HOH B 5 505 11 HOH HOH . E 3 HOH B 6 506 4 HOH HOH . E 3 HOH B 7 507 8 HOH HOH . E 3 HOH B 8 508 47 HOH HOH . E 3 HOH B 9 509 41 HOH HOH . E 3 HOH B 10 510 17 HOH HOH . E 3 HOH B 11 511 6 HOH HOH . E 3 HOH B 12 512 18 HOH HOH . E 3 HOH B 13 513 49 HOH HOH . E 3 HOH B 14 514 1 HOH HOH . E 3 HOH B 15 515 14 HOH HOH . E 3 HOH B 16 516 42 HOH HOH . E 3 HOH B 17 517 26 HOH HOH . E 3 HOH B 18 518 16 HOH HOH . E 3 HOH B 19 519 5 HOH HOH . E 3 HOH B 20 520 45 HOH HOH . E 3 HOH B 21 521 37 HOH HOH . E 3 HOH B 22 522 46 HOH HOH . E 3 HOH B 23 523 21 HOH HOH . E 3 HOH B 24 524 32 HOH HOH . E 3 HOH B 25 525 51 HOH HOH . E 3 HOH B 26 526 56 HOH HOH . E 3 HOH B 27 527 35 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 C13 ZNT . A . C 2 -22.626 35.536 -1.447 0.51 35.97 ? C13 ZNT 401 B 1 HETATM 2 C C13 ZNT . B . C 2 -19.934 32.837 -2.301 0.49 34.93 ? C13 ZNT 401 B 1 HETATM 3 C C17 ZNT . A . C 2 -22.159 34.013 1.382 0.51 31.41 ? C17 ZNT 401 B 1 HETATM 4 C C17 ZNT . B . C 2 -21.528 33.292 -5.079 0.49 33.89 ? C17 ZNT 401 B 1 HETATM 5 C C20 ZNT . A . C 2 -23.114 36.692 -0.621 0.51 36.51 ? C20 ZNT 401 B 1 HETATM 6 C C20 ZNT . B . C 2 -18.783 32.369 -3.143 0.49 34.45 ? C20 ZNT 401 B 1 HETATM 7 C C22 ZNT . A . C 2 -22.592 39.068 -1.306 0.51 33.95 ? C22 ZNT 401 B 1 HETATM 8 C C22 ZNT . B . C 2 -16.404 32.876 -2.474 0.49 31.88 ? C22 ZNT 401 B 1 HETATM 9 C C24 ZNT . A . C 2 -20.199 39.901 -0.697 0.51 36.41 ? C24 ZNT 401 B 1 HETATM 10 C C24 ZNT . B . C 2 -15.58 35.283 -3.036 0.49 37.1 ? C24 ZNT 401 B 1 HETATM 11 C C26 ZNT . A . C 2 -20.862 37.55 -0.079 0.51 34.64 ? C26 ZNT 401 B 1 HETATM 12 C C26 ZNT . B . C 2 -17.937 34.634 -3.642 0.49 34.84 ? C26 ZNT 401 B 1 HETATM 13 C C02 ZNT . A . C 2 -17.923 32.533 -2.107 0.51 33.07 ? C02 ZNT 401 B 1 HETATM 14 C C02 ZNT . B . C 2 -22.749 37.672 -1.693 0.49 33.2 ? C02 ZNT 401 B 1 HETATM 15 C C03 ZNT . A . C 2 -19.302 33.028 -2.057 0.51 36.27 ? C03 ZNT 401 B 1 HETATM 16 C C03 ZNT . B . C 2 -22.337 36.266 -1.723 0.49 37.79 ? C03 ZNT 401 B 1 HETATM 17 C C08 ZNT . A . C 2 -19.815 32.561 -3.366 0.51 33.75 ? C08 ZNT 401 B 1 HETATM 18 C C08 ZNT . B . C 2 -22.83 35.792 -0.409 0.49 34.94 ? C08 ZNT 401 B 1 HETATM 19 C C09 ZNT . A . C 2 -21.059 33.298 -3.762 0.51 36.44 ? C09 ZNT 401 B 1 HETATM 20 C C09 ZNT . B . C 2 -22.122 34.545 0.026 0.49 32.92 ? C09 ZNT 401 B 1 HETATM 21 C C14 ZNT . A . C 2 -23.143 34.347 -0.813 0.51 35.86 ? C14 ZNT 401 B 1 HETATM 22 C C14 ZNT . B . C 2 -21.115 32.28 -2.915 0.49 37.45 ? C14 ZNT 401 B 1 HETATM 23 C C16 ZNT . A . C 2 -23.253 34.651 0.597 0.51 29.42 ? C16 ZNT 401 B 1 HETATM 24 C C16 ZNT . B . C 2 -20.832 32.208 -4.331 0.49 31.45 ? C16 ZNT 401 B 1 HETATM 25 C C25 ZNT . A . C 2 -19.87 38.618 -0.094 0.51 32.04 ? C25 ZNT 401 B 1 HETATM 26 C C25 ZNT . B . C 2 -16.87 35.627 -3.616 0.49 34.15 ? C25 ZNT 401 B 1 HETATM 27 C C32 ZNT . A . C 2 -17.509 32.817 -3.522 0.51 31.85 ? C32 ZNT 401 B 1 HETATM 28 C C32 ZNT . B . C 2 -22.448 38.085 -0.282 0.49 32.82 ? C32 ZNT 401 B 1 HETATM 29 C C34 ZNT . A . C 2 -15.606 34.325 -2.976 0.51 37.78 ? C34 ZNT 401 B 1 HETATM 30 C C34 ZNT . B . C 2 -20.738 39.846 -0.715 0.49 36.9 ? C34 ZNT 401 B 1 HETATM 31 C C36 ZNT . A . C 2 -13.553 34.069 -1.925 0.51 34.77 ? C36 ZNT 401 B 1 HETATM 32 C C36 ZNT . B . C 2 -20.741 41.959 -1.678 0.49 34.55 ? C36 ZNT 401 B 1 HETATM 33 C C38 ZNT . A . C 2 -14.092 36.189 -2.701 0.51 41.81 ? C38 ZNT 401 B 1 HETATM 34 C C38 ZNT . B . C 2 -18.716 41.158 -0.875 0.49 40.58 ? C38 ZNT 401 B 1 HETATM 35 C C40 ZNT . A . C 2 -15.322 35.668 -3.167 0.51 37.89 ? C40 ZNT 401 B 1 HETATM 36 C C40 ZNT . B . C 2 -19.379 39.975 -0.478 0.49 38.34 ? C40 ZNT 401 B 1 HETATM 37 C C42 ZNT . A . C 2 -17.295 35.231 -4.013 0.51 34.42 ? C42 ZNT 401 B 1 HETATM 38 C C42 ZNT . B . C 2 -20.045 38.028 0.267 0.49 32.8 ? C42 ZNT 401 B 1 HETATM 39 N N21 ZNT . A . C 2 -22.188 37.748 -0.661 0.51 33.32 ? N21 ZNT 401 B 1 HETATM 40 N N21 ZNT . B . C 2 -17.73 33.295 -3.093 0.49 33.29 ? N21 ZNT 401 B 1 HETATM 41 N N23 ZNT . A . C 2 -21.501 40.13 -1.282 0.51 40.98 ? N23 ZNT 401 B 1 HETATM 42 N N23 ZNT . B . C 2 -15.344 33.968 -2.485 0.49 38.89 ? N23 ZNT 401 B 1 HETATM 43 N N33 ZNT . A . C 2 -16.83 34.094 -3.518 0.51 35.86 ? N33 ZNT 401 B 1 HETATM 44 N N33 ZNT . B . C 2 -21.111 38.631 -0.236 0.49 34.18 ? N33 ZNT 401 B 1 HETATM 45 N N35 ZNT . A . C 2 -14.699 33.555 -2.353 0.51 39.34 ? N35 ZNT 401 B 1 HETATM 46 N N35 ZNT . B . C 2 -21.388 40.857 -1.315 0.49 39.44 ? N35 ZNT 401 B 1 HETATM 47 N N37 ZNT . A . C 2 -13.256 35.353 -2.095 0.51 39.49 ? N37 ZNT 401 B 1 HETATM 48 N N37 ZNT . B . C 2 -19.437 42.106 -1.463 0.49 36.36 ? N37 ZNT 401 B 1 HETATM 49 N N39 ZNT . A . C 2 -13.742 37.594 -2.875 0.51 34.86 ? N39 ZNT 401 B 1 HETATM 50 N N39 ZNT . B . C 2 -17.287 41.338 -0.649 0.49 35.59 ? N39 ZNT 401 B 1 HETATM 51 N N41 ZNT . A . C 2 -16.388 36.192 -3.809 0.51 33.07 ? N41 ZNT 401 B 1 HETATM 52 N N41 ZNT . B . C 2 -18.988 38.833 0.127 0.49 36.24 ? N41 ZNT 401 B 1 HETATM 53 O O01 ZNT . A . C 2 -17.907 31.138 -1.848 0.51 29.29 ? O01 ZNT 401 B 1 HETATM 54 O O01 ZNT . B . C 2 -24.144 37.759 -1.947 0.49 29.18 ? O01 ZNT 401 B 1 HETATM 55 O O04 ZNT . A . C 2 -19.995 32.437 -0.942 0.51 35.05 ? O04 ZNT 401 B 1 HETATM 56 O O04 ZNT . B . C 2 -22.987 35.592 -2.816 0.49 36.65 ? O04 ZNT 401 B 1 HETATM 57 O O06 ZNT . A . C 2 -19.65 32.165 1.699 0.51 31.38 -1 O06 ZNT 401 B 1 HETATM 58 O O06 ZNT . B . C 2 -23.295 35.861 -5.458 0.49 36.44 -1 O06 ZNT 401 B 1 HETATM 59 O O07 ZNT . A . C 2 -18.453 33.843 0.488 0.51 30.51 ? O07 ZNT 401 B 1 HETATM 60 O O07 ZNT . B . C 2 -21.55 37.035 -4.322 0.49 45.78 ? O07 ZNT 401 B 1 HETATM 61 O O10 ZNT . A . C 2 -20.747 34.664 -3.897 0.51 33.69 ? O10 ZNT 401 B 1 HETATM 62 O O10 ZNT . B . C 2 -20.738 34.795 0.042 0.49 32.96 ? O10 ZNT 401 B 1 HETATM 63 O O12 ZNT . A . C 2 -23.114 35.641 -2.79 0.51 35.18 ? O12 ZNT 401 B 1 HETATM 64 O O12 ZNT . B . C 2 -19.792 32.369 -0.957 0.49 35.13 ? O12 ZNT 401 B 1 HETATM 65 O O15 ZNT . A . C 2 -24.478 34.017 -1.348 0.51 34.2 ? O15 ZNT 401 B 1 HETATM 66 O O15 ZNT . B . C 2 -21.38 30.926 -2.391 0.49 35.28 ? O15 ZNT 401 B 1 HETATM 67 O O18 ZNT . A . C 2 -20.878 34.376 0.866 0.51 33.66 ? O18 ZNT 401 B 1 HETATM 68 O O18 ZNT . B . C 2 -21.112 34.58 -4.622 0.49 34.62 ? O18 ZNT 401 B 1 HETATM 69 O O19 ZNT . A . C 2 -23.208 36.155 0.743 0.51 34.62 ? O19 ZNT 401 B 1 HETATM 70 O O19 ZNT . B . C 2 -19.333 32.309 -4.502 0.49 34.92 ? O19 ZNT 401 B 1 HETATM 71 O O27 ZNT . A . C 2 -19.393 40.766 -0.709 0.51 42.84 ? O27 ZNT 401 B 1 HETATM 72 O O27 ZNT . B . C 2 -14.716 36.089 -3.015 0.49 41.85 ? O27 ZNT 401 B 1 HETATM 73 O O28 ZNT . A . C 2 -23.659 39.255 -1.783 0.51 33.72 ? O28 ZNT 401 B 1 HETATM 74 O O28 ZNT . B . C 2 -16.214 31.797 -2.024 0.49 31.23 ? O28 ZNT 401 B 1 HETATM 75 O O29 ZNT . A . C 2 -21.547 37.173 -4.296 0.51 37.52 -1 O29 ZNT 401 B 1 HETATM 76 O O29 ZNT . B . C 2 -18.288 33.91 0.6 0.49 32.4 -1 O29 ZNT 401 B 1 HETATM 77 O O30 ZNT . A . C 2 -22.77 35.349 -5.247 0.51 32.26 ? O30 ZNT 401 B 1 HETATM 78 O O30 ZNT . B . C 2 -20.211 32.774 1.469 0.49 30.08 ? O30 ZNT 401 B 1 HETATM 79 O O31 ZNT . A . C 2 -18.713 32.859 -4.287 0.51 33.36 ? O31 ZNT 401 B 1 HETATM 80 O O31 ZNT . B . C 2 -22.532 36.9 0.504 0.49 32.12 ? O31 ZNT 401 B 1 HETATM 81 P P05 ZNT . A . C 2 -19.797 33.149 0.559 0.51 29.97 ? P05 ZNT 401 B 1 HETATM 82 P P05 ZNT . B . C 2 -22.293 35.715 -4.333 0.49 34.67 ? P05 ZNT 401 B 1 HETATM 83 P P11 ZNT . A . C 2 -21.999 35.762 -4.012 0.51 32.82 ? P11 ZNT 401 B 1 HETATM 84 P P11 ZNT . B . C 2 -19.698 33.505 0.247 0.49 30.61 ? P11 ZNT 401 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 84 #