data_8GJZ # _model_server_result.job_id hk4NSr7rTQP5vBA2EcEpGg _model_server_result.datetime_utc '2024-11-28 19:36:56' _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 8gjz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8GJZ # _exptl.entry_id 8GJZ _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 120 _cell.entry_id 8GJZ _cell.length_a 113.429 _cell.length_b 113.429 _cell.length_c 259.272 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GJZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall 'P 65 2 (x,y,z+1/12)' _symmetry.space_group_name_H-M 'P 65 2 2' # _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 _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NH1 _struct_conn.ptnr1_label_comp_id ARG _struct_conn.ptnr1_label_seq_id 82 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ARG _struct_conn.ptnr1_auth_seq_id 261 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id O29 _struct_conn.ptnr2_label_comp_id ZNT _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id ZNT _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _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 A _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 1.298 _struct_conn.pdbx_value_order ? # _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 8GJZ _atom_sites.fract_transf_matrix[1][1] 0.008816 _atom_sites.fract_transf_matrix[1][2] 0.00509 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01018 _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] 0.003857 _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 A 1 401 401 ZNT LIG . D 3 HOH A 1 501 2 HOH HOH . D 3 HOH A 2 502 1 HOH HOH . D 3 HOH A 3 503 4 HOH HOH . D 3 HOH A 4 504 5 HOH HOH . D 3 HOH A 5 505 6 HOH HOH . D 3 HOH A 6 506 3 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 -23.055 48.722 -1.228 0.5 57.73 ? C13 ZNT 401 A 1 HETATM 2 C C13 ZNT . B . C 2 -27.645 48.157 -1.848 0.5 60.95 ? C13 ZNT 401 A 1 HETATM 3 C C17 ZNT . A . C 2 -23.891 46.236 0.776 0.5 61.13 ? C17 ZNT 401 A 1 HETATM 4 C C17 ZNT . B . C 2 -27.014 51.41 -1.49 0.5 67.33 ? C17 ZNT 401 A 1 HETATM 5 C C20 ZNT . A . C 2 -21.771 47.978 -1.443 0.5 63.81 ? C20 ZNT 401 A 1 HETATM 6 C C20 ZNT . B . C 2 -28.968 48.662 -2.359 0.5 60.87 ? C20 ZNT 401 A 1 HETATM 7 C C22 ZNT . A . C 2 -20.409 48.165 -3.552 0.5 69.79 ? C22 ZNT 401 A 1 HETATM 8 C C22 ZNT . B . C 2 -30.174 47.627 -4.316 0.5 66.5 ? C22 ZNT 401 A 1 HETATM 9 C C24 ZNT . A . C 2 -21.401 46.962 -5.636 0.5 72.96 ? C24 ZNT 401 A 1 HETATM 10 C C24 ZNT . B . C 2 -29.232 48.25 -6.663 0.5 68.1 ? C24 ZNT 401 A 1 HETATM 11 C C26 ZNT . A . C 2 -22.66 46.855 -3.454 0.5 70.19 ? C26 ZNT 401 A 1 HETATM 12 C C26 ZNT . B . C 2 -28.123 49.212 -4.614 0.5 56.54 ? C26 ZNT 401 A 1 HETATM 13 C C02 ZNT . A . C 2 -28.453 48.042 -1.92 0.5 61.89 ? C02 ZNT 401 A 1 HETATM 14 C C02 ZNT . B . C 2 -21.891 49.062 -0.891 0.5 66.76 ? C02 ZNT 401 A 1 HETATM 15 C C03 ZNT . A . C 2 -27.136 48.429 -1.397 0.5 58.99 ? C03 ZNT 401 A 1 HETATM 16 C C03 ZNT . B . C 2 -23.324 48.835 -0.714 0.5 57.79 ? C03 ZNT 401 A 1 HETATM 17 C C08 ZNT . A . C 2 -27.328 49.85 -1.015 0.5 60.02 ? C08 ZNT 401 A 1 HETATM 18 C C08 ZNT . B . C 2 -23.282 47.832 0.377 0.5 58.61 ? C08 ZNT 401 A 1 HETATM 19 C C09 ZNT . A . C 2 -26.051 50.626 -1.127 0.5 63.37 ? C09 ZNT 401 A 1 HETATM 20 C C09 ZNT . B . C 2 -24.568 47.075 0.509 0.5 71.17 ? C09 ZNT 401 A 1 HETATM 21 C C14 ZNT . A . C 2 -23.382 48.501 0.161 0.5 57.89 ? C14 ZNT 401 A 1 HETATM 22 C C14 ZNT . B . C 2 -27.211 49.092 -0.834 0.5 59.25 ? C14 ZNT 401 A 1 HETATM 23 C C16 ZNT . A . C 2 -22.809 47.223 0.528 0.5 57.47 ? C16 ZNT 401 A 1 HETATM 24 C C16 ZNT . B . C 2 -27.927 50.335 -1.017 0.5 63.31 ? C16 ZNT 401 A 1 HETATM 25 C C25 ZNT . A . C 2 -22.548 46.505 -4.864 0.5 71.01 ? C25 ZNT 401 A 1 HETATM 26 C C25 ZNT . B . C 2 -28.198 49.084 -6.064 0.5 62.26 ? C25 ZNT 401 A 1 HETATM 27 C C32 ZNT . A . C 2 -28.982 49.291 -2.564 0.5 61.1 ? C32 ZNT 401 A 1 HETATM 28 C C32 ZNT . B . C 2 -21.405 47.651 -0.973 0.5 66.79 ? C32 ZNT 401 A 1 HETATM 29 C C34 ZNT . A . C 2 -29.39 48.556 -4.906 0.5 62.72 ? C34 ZNT 401 A 1 HETATM 30 C C34 ZNT . B . C 2 -20.993 47.691 -3.417 0.5 64.77 ? C34 ZNT 401 A 1 HETATM 31 C C36 ZNT . A . C 2 -30.921 47.174 -5.967 0.5 62.92 ? C36 ZNT 401 A 1 HETATM 32 C C36 ZNT . B . C 2 -19.542 48.83 -4.824 0.5 83.79 ? C36 ZNT 401 A 1 HETATM 33 C C38 ZNT . A . C 2 -29.31 48.194 -7.291 0.5 69.46 ? C38 ZNT 401 A 1 HETATM 34 C C38 ZNT . B . C 2 -21.023 47.336 -5.803 0.5 75.44 ? C38 ZNT 401 A 1 HETATM 35 C C40 ZNT . A . C 2 -28.79 48.805 -6.128 0.5 64.4 ? C40 ZNT 401 A 1 HETATM 36 C C40 ZNT . B . C 2 -21.531 47.048 -4.518 0.5 68.39 ? C40 ZNT 401 A 1 HETATM 37 C C42 ZNT . A . C 2 -27.717 49.918 -4.582 0.5 54.98 ? C42 ZNT 401 A 1 HETATM 38 C C42 ZNT . B . C 2 -22.562 46.345 -2.721 0.5 70.3 ? C42 ZNT 401 A 1 HETATM 39 N N21 ZNT . A . C 2 -21.63 47.657 -2.8 0.5 61.77 ? N21 ZNT 401 A 1 HETATM 40 N N21 ZNT . B . C 2 -29.069 48.51 -3.751 0.5 61.47 ? N21 ZNT 401 A 1 HETATM 41 N N23 ZNT . A . C 2 -20.367 47.758 -5.017 0.5 78.65 ? N23 ZNT 401 A 1 HETATM 42 N N23 ZNT . B . C 2 -30.185 47.547 -5.836 0.5 63.9 ? N23 ZNT 401 A 1 HETATM 43 N N33 ZNT . A . C 2 -28.696 49.263 -3.979 0.5 57.57 ? N33 ZNT 401 A 1 HETATM 44 N N33 ZNT . B . C 2 -21.653 47.223 -2.328 0.5 63.42 ? N33 ZNT 401 A 1 HETATM 45 N N35 ZNT . A . C 2 -30.453 47.736 -4.859 0.5 65.38 ? N35 ZNT 401 A 1 HETATM 46 N N35 ZNT . B . C 2 -20.001 48.576 -3.603 0.5 74.81 ? N35 ZNT 401 A 1 HETATM 47 N N37 ZNT . A . C 2 -30.364 47.397 -7.153 0.5 64.58 ? N37 ZNT 401 A 1 HETATM 48 N N37 ZNT . B . C 2 -20.041 48.225 -5.897 0.5 84.37 ? N37 ZNT 401 A 1 HETATM 49 N N39 ZNT . A . C 2 -28.71 48.429 -8.599 0.5 68.73 ? N39 ZNT 401 A 1 HETATM 50 N N39 ZNT . B . C 2 -21.56 46.68 -6.989 0.5 75.99 ? N39 ZNT 401 A 1 HETATM 51 N N41 ZNT . A . C 2 -27.764 49.648 -5.889 0.5 58.55 ? N41 ZNT 401 A 1 HETATM 52 N N41 ZNT . B . C 2 -22.493 46.226 -4.049 0.5 71.96 ? N41 ZNT 401 A 1 HETATM 53 O O01 ZNT . A . C 2 -29.309 47.653 -0.854 0.5 51.32 ? O01 ZNT 401 A 1 HETATM 54 O O01 ZNT . B . C 2 -21.372 49.704 0.264 0.5 80.81 ? O01 ZNT 401 A 1 HETATM 55 O O04 ZNT . A . C 2 -26.811 47.627 -0.245 0.5 56.09 ? O04 ZNT 401 A 1 HETATM 56 O O04 ZNT . B . C 2 -23.962 50.073 -0.358 0.5 59.08 ? O04 ZNT 401 A 1 HETATM 57 O O06 ZNT . A . C 2 -26.922 45.029 0.382 0.5 55.09 ? O06 ZNT 401 A 1 HETATM 58 O O06 ZNT . B . C 2 -24.01 52.541 -1.393 0.5 67.44 ? O06 ZNT 401 A 1 HETATM 59 O O07 ZNT . A . C 2 -26.595 45.715 -1.895 0.5 59.67 ? O07 ZNT 401 A 1 HETATM 60 O O07 ZNT . B . C 2 -23.492 50.66 -2.776 0.5 63.92 ? O07 ZNT 401 A 1 HETATM 61 O O10 ZNT . A . C 2 -25.502 50.434 -2.411 0.5 67.58 ? O10 ZNT 401 A 1 HETATM 62 O O10 ZNT . B . C 2 -25.061 46.77 -0.774 0.5 71.2 ? O10 ZNT 401 A 1 HETATM 63 O O12 ZNT . A . C 2 -22.893 50.12 -1.506 0.5 59.05 ? O12 ZNT 401 A 1 HETATM 64 O O12 ZNT . B . C 2 -27.82 46.852 -1.275 0.5 67.67 ? O12 ZNT 401 A 1 HETATM 65 O O15 ZNT . A . C 2 -22.815 49.572 1 0.5 50.85 ? O15 ZNT 401 A 1 HETATM 66 O O15 ZNT . B . C 2 -27.491 48.555 0.511 0.5 67.54 ? O15 ZNT 401 A 1 HETATM 67 O O18 ZNT . A . C 2 -24.569 45.961 -0.45 0.5 69.44 ? O18 ZNT 401 A 1 HETATM 68 O O18 ZNT . B . C 2 -25.913 50.838 -2.2 0.5 69.6 ? O18 ZNT 401 A 1 HETATM 69 O O19 ZNT . A . C 2 -21.942 46.774 -0.625 0.5 64.02 ? O19 ZNT 401 A 1 HETATM 70 O O19 ZNT . B . C 2 -29.012 50.092 -2.036 0.5 63.51 ? O19 ZNT 401 A 1 HETATM 71 O O27 ZNT . A . C 2 -21.313 46.676 -6.779 0.5 76 ? O27 ZNT 401 A 1 HETATM 72 O O27 ZNT . B . C 2 -29.291 48.148 -7.839 0.5 70.81 ? O27 ZNT 401 A 1 HETATM 73 O O28 ZNT . A . C 2 -19.566 48.817 -3.039 0.5 75.48 ? O28 ZNT 401 A 1 HETATM 74 O O28 ZNT . B . C 2 -30.952 47.053 -3.632 0.5 65.75 ? O28 ZNT 401 A 1 HETATM 75 O O29 ZNT . A . C 2 -23.414 50.62 -4.071 0.5 80.6 ? O29 ZNT 401 A 1 HETATM 76 O O29 ZNT . B . C 2 -26.391 44.641 -1.659 0.5 68.01 ? O29 ZNT 401 A 1 HETATM 77 O O30 ZNT . A . C 2 -23.796 52.293 -2.406 0.5 60.3 ? O30 ZNT 401 A 1 HETATM 78 O O30 ZNT . B . C 2 -26.77 45.484 0.547 0.5 52.24 ? O30 ZNT 401 A 1 HETATM 79 O O31 ZNT . A . C 2 -28.317 50.389 -1.953 0.5 63.66 ? O31 ZNT 401 A 1 HETATM 80 O O31 ZNT . B . C 2 -22.207 46.926 -0.044 0.5 61.07 ? O31 ZNT 401 A 1 HETATM 81 P P05 ZNT . A . C 2 -26.23 46.073 -0.469 0.5 49.2 ? P05 ZNT 401 A 1 HETATM 82 P P05 ZNT . B . C 2 -24.372 51.089 -1.622 0.5 67.23 ? P05 ZNT 401 A 1 HETATM 83 P P11 ZNT . A . C 2 -23.89 50.801 -2.647 0.5 61.22 ? P11 ZNT 401 A 1 HETATM 84 P P11 ZNT . B . C 2 -26.497 45.927 -0.876 0.5 51.62 ? P11 ZNT 401 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 84 #