data_8CNA # _model_server_result.job_id H_pqoU4DlN1ltXMKxWBH4A _model_server_result.datetime_utc '2024-11-29 10:32:00' _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 8cna # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1805}' # _entry.id 8CNA # _exptl.entry_id 8CNA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 994.794 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R,20R)-20-carbamoyl-3-hydroxy-2,2-dimethyl-4,8,14,22-tetraoxo-12-thia-5,9,15,21-tetraazatricos-1-yl dihydrogen 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 90 _cell.entry_id 8CNA _cell.length_a 86.825 _cell.length_b 144.504 _cell.length_c 154.62 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CNA _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 # _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 3 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A SG CYS 146 A CYS 1199 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc2 A SG CYS 147 A CYS 1200 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc3 A SG CYS 230 A CYS 1283 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc4 A SG CYS 233 A CYS 1286 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc5 A ND1 HIS 238 A HIS 1291 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc6 A SG CYS 241 A CYS 1294 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc7 A SG CYS 255 A CYS 1308 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc8 A SG CYS 258 A CYS 1311 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc9 A SG CYS 600 A CYS 1710 1_555 D ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc10 A SG CYS 610 A CYS 1720 1_555 E ZN ZN . A ZN 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc11 A SG CYS 613 A CYS 1723 1_555 E ZN ZN . A ZN 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc12 A O CYS 619 A CYS 1729 1_555 D ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc13 A ND1 HIS 630 A HIS 1740 1_555 E ZN ZN . A ZN 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? # _chem_comp.formula 'C31 H53 N10 O19 P3 S' _chem_comp.formula_weight 994.794 _chem_comp.id 01K _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R,20R)-20-carbamoyl-3-hydroxy-2,2-dimethyl-4,8,14,22-tetraoxo-12-thia-5,9,15,21-tetraazatricos-1-yl dihydrogen diphosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Lysine-COENZYME A derivative' # 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 P2 O1 01K sing 1 n n O1 HO1 01K sing 2 n n O37 P2 01K doub 3 n n O38 P2 01K sing 4 n n O3 P2 01K sing 5 n n P4 O3 01K sing 6 n n O35 P4 01K doub 7 n n O5 P4 01K sing 8 n n P4 O36 01K sing 9 n n O5 C6 01K sing 10 n n C7 C6 01K sing 11 n n C6 H6 01K sing 12 n n C6 H6A 01K sing 13 n n C10 C7 01K sing 14 n n C9 C7 01K sing 15 n n C7 C8 01K sing 16 n n C8 H8 01K sing 17 n n C8 H8A 01K sing 18 n n C8 H8B 01K sing 19 n n C9 H9 01K sing 20 n n C9 H9A 01K sing 21 n n C9 H9B 01K sing 22 n n C12 C10 01K sing 23 n n C10 O11 01K sing 24 n n C10 H10 01K sing 25 n n O11 HO11 01K sing 26 n n O34 C12 01K doub 27 n n C12 N13 01K sing 28 n n C14 N13 01K sing 29 n n N13 HN13 01K sing 30 n n C14 C15 01K sing 31 n n C14 H14 01K sing 32 n n C14 H14A 01K sing 33 n n C15 C16 01K sing 34 n n C15 H15 01K sing 35 n n C15 H15A 01K sing 36 n n C16 N17 01K sing 37 n n C16 O33 01K doub 38 n n N17 C18 01K sing 39 n n N17 HN17 01K sing 40 n n C18 C19 01K sing 41 n n C18 H18 01K sing 42 n n C18 H18A 01K sing 43 n n C19 S20 01K sing 44 n n C19 H19 01K sing 45 n n C19 H19A 01K sing 46 n n C21 S20 01K sing 47 n n C22 C21 01K sing 48 n n C21 H21 01K sing 49 n n C21 H21A 01K sing 50 n n O32 C22 01K doub 51 n n C22 NZ 01K sing 52 n n CE NZ 01K sing 53 n n NZ HNZ 01K sing 54 n n CE CD 01K sing 55 n n CE HE 01K sing 56 n n CE HEA 01K sing 57 n n CG CD 01K sing 58 n n CD HD 01K sing 59 n n CD HDA 01K sing 60 n n CG CB 01K sing 61 n n CG HG 01K sing 62 n n CG HGA 01K sing 63 n n CA CB 01K sing 64 n n CB HB 01K sing 65 n n CB HBA 01K sing 66 n n C CA 01K sing 67 n n CA N 01K sing 68 n n CA HA 01K sing 69 n n N C61 01K sing 70 n n N HN 01K sing 71 n n O C 01K doub 72 n n N64 C 01K sing 73 n n O36 HO36 01K sing 74 n n O38 C39 01K sing 75 n n C41 C40 01K sing 76 n n C40 C39 01K sing 77 n n C40 O60 01K sing 78 n n C40 H40 01K sing 79 n n C47 C41 01K sing 80 n n C41 O42 01K sing 81 n n C41 H41 01K sing 82 n n P43 O45 01K sing 83 n n O45 HO45 01K sing 84 n n P43 O46 01K sing 85 n n O46 HO46 01K sing 86 n n N50 C54 01K sing 87 n y C53 C54 01K doub 88 n y C54 N55 01K sing 89 n y C63 C61 01K sing 90 n n C63 H63 01K sing 91 n n C63 H63A 01K sing 92 n n C63 H63B 01K sing 93 n n C61 O62 01K doub 94 n n N64 HN64 01K sing 95 n n N64 HN6A 01K sing 96 n n C39 H39 01K sing 97 n n C39 H39A 01K sing 98 n n C49 O60 01K sing 99 n n P43 O42 01K sing 100 n n O44 P43 01K doub 101 n n O48 C47 01K sing 102 n n C47 C49 01K sing 103 n n C47 H47 01K sing 104 n n O48 HO48 01K sing 105 n n C49 N50 01K sing 106 n n C49 H49 01K sing 107 n n C51 N50 01K sing 108 n y C51 N52 01K doub 109 n y C51 H51 01K sing 110 n n N52 C53 01K sing 111 n y C53 C58 01K sing 112 n y N55 C56 01K doub 113 n y C56 N57 01K sing 114 n y C56 H56 01K sing 115 n n C58 N57 01K doub 116 n y N59 C58 01K sing 117 n n N59 HN59 01K sing 118 n n N59 HN5A 01K sing 119 n n # _atom_sites.entry_id 8CNA _atom_sites.fract_transf_matrix[1][1] 0.011517 _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] 0.00692 _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] 0.006467 _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 ZN A 1 1801 1801 ZN ZN . C 2 ZN A 1 1802 1802 ZN ZN . D 2 ZN A 1 1803 1803 ZN ZN . E 2 ZN A 1 1804 1804 ZN ZN . F 3 01K A 1 1805 1901 01K 01K . # 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 O1 01K . . . F 3 -7.064 45.97 8.345 1 117.03 ? O1 01K 1805 A 1 HETATM 2 P P2 01K . . . F 3 -5.588 45.567 8.11 1 117.41 ? P2 01K 1805 A 1 HETATM 3 O O3 01K . . . F 3 -5.548 43.976 8.025 1 114.04 ? O3 01K 1805 A 1 HETATM 4 P P4 01K . . . F 3 -5.163 42.859 9.09 1 108.09 ? P4 01K 1805 A 1 HETATM 5 O O5 01K . . . F 3 -5.548 43.608 10.519 1 109.6 ? O5 01K 1805 A 1 HETATM 6 C C6 01K . . . F 3 -6.263 43.045 11.643 1 101.63 ? C6 01K 1805 A 1 HETATM 7 C C7 01K . . . F 3 -6.311 44.037 12.802 1 87.34 ? C7 01K 1805 A 1 HETATM 8 C C8 01K . . . F 3 -7.673 44.747 12.796 1 89.57 ? C8 01K 1805 A 1 HETATM 9 C C9 01K . . . F 3 -6.18 43.256 14.115 1 74.34 ? C9 01K 1805 A 1 HETATM 10 C C10 01K . . . F 3 -5.173 45.085 12.675 1 83.5 ? C10 01K 1805 A 1 HETATM 11 O O11 01K . . . F 3 -5.532 46.098 11.741 1 89.3 ? O11 01K 1805 A 1 HETATM 12 C C12 01K . . . F 3 -4.601 45.725 13.942 1 75.21 ? C12 01K 1805 A 1 HETATM 13 N N13 01K . . . F 3 -4.767 47.049 14.071 1 76.51 ? N13 01K 1805 A 1 HETATM 14 C C14 01K . . . F 3 -4.221 47.828 15.179 1 67.25 ? C14 01K 1805 A 1 HETATM 15 C C15 01K . . . F 3 -5.016 47.634 16.449 1 58.71 ? C15 01K 1805 A 1 HETATM 16 C C16 01K . . . F 3 -6.5 47.588 16.172 1 65.91 ? C16 01K 1805 A 1 HETATM 17 N N17 01K . . . F 3 -7.302 47.963 17.168 1 67.89 ? N17 01K 1805 A 1 HETATM 18 C C18 01K . . . F 3 -8.753 47.868 17.068 1 67.37 ? C18 01K 1805 A 1 HETATM 19 C C19 01K . . . F 3 -9.269 46.621 17.76 1 77.1 ? C19 01K 1805 A 1 HETATM 20 S S20 01K . . . F 3 -10.994 46.173 17.405 1 81.36 ? S20 01K 1805 A 1 HETATM 21 C C21 01K . . . F 3 -11.909 47.405 18.372 1 80.81 ? C21 01K 1805 A 1 HETATM 22 C C22 01K . . . F 3 -11.757 47.383 19.878 1 73.45 ? C22 01K 1805 A 1 HETATM 23 N NZ 01K . . . F 3 -12.57 48.197 20.549 1 53.56 ? NZ 01K 1805 A 1 HETATM 24 C CE 01K . . . F 3 -12.316 48.614 21.921 1 38.11 ? CE 01K 1805 A 1 HETATM 25 C CD 01K . . . F 3 -11.752 50.024 22.007 1 43.27 ? CD 01K 1805 A 1 HETATM 26 C CG 01K . . . F 3 -11.087 50.271 23.351 1 69.44 ? CG 01K 1805 A 1 HETATM 27 C CB 01K . . . F 3 -11.354 51.642 23.971 1 89.48 ? CB 01K 1805 A 1 HETATM 28 C CA 01K . . . F 3 -10.156 52.604 24.001 1 107.87 ? CA 01K 1805 A 1 HETATM 29 N N 01K . . . F 3 -10.59 53.921 24.467 1 113.19 ? N 01K 1805 A 1 HETATM 30 C C 01K . . . F 3 -8.979 51.976 24.758 1 107.3 ? C 01K 1805 A 1 HETATM 31 O O 01K . . . F 3 -7.821 52.223 24.409 1 111.63 ? O 01K 1805 A 1 HETATM 32 O O33 01K . . . F 3 -6.933 47.213 15.086 1 66.14 ? O33 01K 1805 A 1 HETATM 33 O O34 01K . . . F 3 -3.976 45.047 14.753 1 71.05 ? O34 01K 1805 A 1 HETATM 34 O O35 01K . . . F 3 -3.722 42.508 8.945 1 111.62 ? O35 01K 1805 A 1 HETATM 35 O O36 01K . . . F 3 -6.154 41.69 8.906 1 102.91 ? O36 01K 1805 A 1 HETATM 36 O O37 01K . . . F 3 -4.648 46.097 9.126 1 115.93 ? O37 01K 1805 A 1 HETATM 37 O O38 01K . . . F 3 -5.151 46.084 6.637 1 107.74 ? O38 01K 1805 A 1 HETATM 38 C C40 01K . . . F 3 -4.378 46.21 4.404 1 75.83 ? C40 01K 1805 A 1 HETATM 39 C C41 01K . . . F 3 -2.86 46.409 4.363 1 77.16 ? C41 01K 1805 A 1 HETATM 40 O O45 01K . . . F 3 -1.848 44.87 0.903 1 88.06 ? O45 01K 1805 A 1 HETATM 41 O O46 01K . . . F 3 -2.853 43.71 2.912 1 86.43 ? O46 01K 1805 A 1 HETATM 42 C C54 01K . . . F 3 -4.342 50.994 5.005 1 87.34 ? C54 01K 1805 A 1 HETATM 43 C C63 01K . . . F 3 -10.571 56.34 24.516 1 96.72 ? C63 01K 1805 A 1 HETATM 44 C C61 01K . . . F 3 -9.836 55.036 24.375 1 107.35 ? C61 01K 1805 A 1 HETATM 45 O O62 01K . . . F 3 -8.622 54.993 24.187 1 111.14 ? O62 01K 1805 A 1 HETATM 46 N N64 01K . . . F 3 -9.272 51.142 25.748 1 96.37 ? N64 01K 1805 A 1 HETATM 47 O O32 01K . . . F 3 -10.898 46.697 20.424 1 83.15 ? O32 01K 1805 A 1 HETATM 48 C C39 01K . . . F 3 -4.862 45.269 5.479 1 85.69 ? C39 01K 1805 A 1 HETATM 49 O O60 01K . . . F 3 -4.952 47.515 4.633 1 78.12 ? O60 01K 1805 A 1 HETATM 50 O O42 01K . . . F 3 -2.367 46.178 3.024 1 87.53 ? O42 01K 1805 A 1 HETATM 51 P P43 01K . . . F 3 -1.807 44.755 2.437 1 88.6 ? P43 01K 1805 A 1 HETATM 52 O O44 01K . . . F 3 -0.419 44.484 2.925 1 90.07 ? O44 01K 1805 A 1 HETATM 53 C C47 01K . . . F 3 -2.623 47.86 4.791 1 73.81 ? C47 01K 1805 A 1 HETATM 54 O O48 01K . . . F 3 -1.592 48.385 3.961 1 69.4 ? O48 01K 1805 A 1 HETATM 55 C C49 01K . . . F 3 -3.969 48.517 4.466 1 78.31 ? C49 01K 1805 A 1 HETATM 56 N N50 01K . . . F 3 -4.319 49.654 5.331 1 83.55 ? N50 01K 1805 A 1 HETATM 57 C C51 01K . . . F 3 -4.683 49.577 6.647 1 85.28 ? C51 01K 1805 A 1 HETATM 58 N N52 01K . . . F 3 -4.936 50.743 7.198 1 87.86 ? N52 01K 1805 A 1 HETATM 59 C C53 01K . . . F 3 -4.725 51.644 6.173 1 86.3 ? C53 01K 1805 A 1 HETATM 60 N N55 01K . . . F 3 -4.053 51.559 3.832 1 88.33 ? N55 01K 1805 A 1 HETATM 61 C C56 01K . . . F 3 -4.18 52.89 3.889 1 76.85 ? C56 01K 1805 A 1 HETATM 62 N N57 01K . . . F 3 -4.54 53.653 4.925 1 69.21 ? N57 01K 1805 A 1 HETATM 63 C C58 01K . . . F 3 -4.82 53.056 6.105 1 76.85 ? C58 01K 1805 A 1 HETATM 64 N N59 01K . . . F 3 -5.151 53.831 7.147 1 73.61 ? N59 01K 1805 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 64 #