data_8CND # _model_server_result.job_id wgkwpKaqybfgK_lvNOW2Zg _model_server_result.datetime_utc '2024-10-15 14:32:07' _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 8cnd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1805}' # _entry.id 8CND # _exptl.entry_id 8CND _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 8CND _cell.length_a 86.81 _cell.length_b 149.195 _cell.length_c 154.918 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CND _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,G _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc2 A SG CYS 147 A CYS 1200 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc3 A SG CYS 230 A CYS 1283 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc4 A SG CYS 233 A CYS 1286 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc5 A ND1 HIS 238 A HIS 1291 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.921 ? metalc ? metalc6 A SG CYS 241 A CYS 1294 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc7 A SG CYS 255 A CYS 1308 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc8 A SG CYS 258 A CYS 1311 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc9 A SG CYS 600 A CYS 1709 1_555 D ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc10 A SG CYS 610 A CYS 1719 1_555 E ZN ZN . A ZN 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc11 A SG CYS 613 A CYS 1722 1_555 E ZN ZN . A ZN 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc12 A O CYS 619 A CYS 1728 1_555 D ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc13 A NE2 HIS 628 A HIS 1738 1_555 E ZN ZN . A ZN 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc14 A ND1 HIS 630 A HIS 1740 1_555 E ZN ZN . A ZN 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? # _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 8CND _atom_sites.fract_transf_matrix[1][1] 0.011519 _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] 0.006703 _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] 0.006455 _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 . G 2 ZN A 1 1806 1 ZN ZN . # 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 -6.718 47.787 9.122 1 104.26 ? O1 01K 1805 A 1 HETATM 2 P P2 01K . . . F 3 -5.279 47.663 8.592 1 104.34 ? P2 01K 1805 A 1 HETATM 3 O O3 01K . . . F 3 -4.745 46.197 8.922 1 103.32 ? O3 01K 1805 A 1 HETATM 4 P P4 01K . . . F 3 -5.418 44.778 9.172 1 102.19 ? P4 01K 1805 A 1 HETATM 5 O O5 01K . . . F 3 -5.679 44.714 10.768 1 101.7 ? O5 01K 1805 A 1 HETATM 6 C C6 01K . . . F 3 -6.752 45.448 11.38 1 101.36 ? C6 01K 1805 A 1 HETATM 7 C C7 01K . . . F 3 -6.37 45.867 12.797 1 100.89 ? C7 01K 1805 A 1 HETATM 8 C C8 01K . . . F 3 -7.511 46.705 13.386 1 100.88 ? C8 01K 1805 A 1 HETATM 9 C C9 01K . . . F 3 -6.185 44.598 13.637 1 100.98 ? C9 01K 1805 A 1 HETATM 10 C C10 01K . . . F 3 -5.066 46.71 12.809 1 100.2 ? C10 01K 1805 A 1 HETATM 11 O O11 01K . . . F 3 -5.106 47.763 11.854 1 99.98 ? O11 01K 1805 A 1 HETATM 12 C C12 01K . . . F 3 -4.681 47.229 14.199 1 99.86 ? C12 01K 1805 A 1 HETATM 13 N N13 01K . . . F 3 -4.231 48.485 14.282 1 100 ? N13 01K 1805 A 1 HETATM 14 C C14 01K . . . F 3 -5.069 49.602 14.693 1 100.3 ? C14 01K 1805 A 1 HETATM 15 C C15 01K . . . F 3 -5.392 49.571 16.174 1 100.58 ? C15 01K 1805 A 1 HETATM 16 C C16 01K . . . F 3 -6.715 48.895 16.452 1 101.12 ? C16 01K 1805 A 1 HETATM 17 N N17 01K . . . F 3 -7.787 49.684 16.459 1 100.88 ? N17 01K 1805 A 1 HETATM 18 C C18 01K . . . F 3 -8.91 49.474 17.363 1 100.81 ? C18 01K 1805 A 1 HETATM 19 C C19 01K . . . F 3 -9.896 48.437 16.853 1 100.63 ? C19 01K 1805 A 1 HETATM 20 S S20 01K . . . F 3 -11.445 48.361 17.797 1 100.48 ? S20 01K 1805 A 1 HETATM 21 C C21 01K . . . F 3 -10.823 48.359 19.505 1 100.66 ? C21 01K 1805 A 1 HETATM 22 C C22 01K . . . F 3 -11.708 49.028 20.537 1 100.87 ? C22 01K 1805 A 1 HETATM 23 N NZ 01K . . . F 3 -11.393 50.284 20.838 1 101.08 ? NZ 01K 1805 A 1 HETATM 24 C CE 01K . . . F 3 -12.014 51.003 21.94 1 101.32 ? CE 01K 1805 A 1 HETATM 25 C CD 01K . . . F 3 -12.147 52.481 21.652 1 101.82 ? CD 01K 1805 A 1 HETATM 26 C CG 01K . . . F 3 -11.082 53.325 22.338 1 102.36 ? CG 01K 1805 A 1 HETATM 27 C CB 01K . . . F 3 -11.523 54.766 22.605 1 102.83 ? CB 01K 1805 A 1 HETATM 28 C CA 01K . . . F 3 -10.735 55.501 23.695 1 103.24 ? CA 01K 1805 A 1 HETATM 29 N N 01K . . . F 3 -11.39 56.757 24.034 1 103.18 ? N 01K 1805 A 1 HETATM 30 C C 01K . . . F 3 -10.543 54.607 24.924 1 103.72 ? C 01K 1805 A 1 HETATM 31 O O 01K . . . F 3 -9.416 54.185 25.206 1 103.84 ? O 01K 1805 A 1 HETATM 32 O O33 01K . . . F 3 -6.782 47.685 16.663 1 101.57 ? O33 01K 1805 A 1 HETATM 33 O O34 01K . . . F 3 -4.73 46.485 15.172 1 99.6 ? O34 01K 1805 A 1 HETATM 34 O O35 01K . . . F 3 -4.565 43.675 8.725 1 102.13 ? O35 01K 1805 A 1 HETATM 35 O O36 01K . . . F 3 -6.732 44.786 8.417 1 102.14 ? O36 01K 1805 A 1 HETATM 36 O O37 01K . . . F 3 -4.315 48.668 9.115 1 104.59 ? O37 01K 1805 A 1 HETATM 37 O O38 01K . . . F 3 -5.443 47.709 6.984 1 104.49 ? O38 01K 1805 A 1 HETATM 38 C C40 01K . . . F 3 -4.437 47.362 4.848 1 104.27 ? C40 01K 1805 A 1 HETATM 39 C C41 01K . . . F 3 -2.921 47.539 4.855 1 104.47 ? C41 01K 1805 A 1 HETATM 40 O O45 01K . . . F 3 -1.223 46.166 1.66 1 105.96 ? O45 01K 1805 A 1 HETATM 41 O O46 01K . . . F 3 -2.902 44.874 3.037 1 105.8 ? O46 01K 1805 A 1 HETATM 42 C C54 01K . . . F 3 -4.41 52.135 4.962 1 104.4 ? C54 01K 1805 A 1 HETATM 43 C C63 01K . . . F 3 -11.648 58.863 25.182 1 102.98 ? C63 01K 1805 A 1 HETATM 44 C C61 01K . . . F 3 -10.779 57.719 24.743 1 102.95 ? C61 01K 1805 A 1 HETATM 45 O O62 01K . . . F 3 -9.584 57.661 25.03 1 102.96 ? O62 01K 1805 A 1 HETATM 46 N N64 01K . . . F 3 -11.631 54.293 25.615 1 103.79 ? N64 01K 1805 A 1 HETATM 47 O O32 01K . . . F 3 -12.645 48.431 21.061 1 100.99 ? O32 01K 1805 A 1 HETATM 48 C C39 01K . . . F 3 -5.005 46.682 6.067 1 104.37 ? C39 01K 1805 A 1 HETATM 49 O O60 01K . . . F 3 -4.987 48.692 4.744 1 104.12 ? O60 01K 1805 A 1 HETATM 50 O O42 01K . . . F 3 -2.46 47.326 3.507 1 105.36 ? O42 01K 1805 A 1 HETATM 51 P P43 01K . . . F 3 -1.784 45.938 3.075 1 105.99 ? P43 01K 1805 A 1 HETATM 52 O O44 01K . . . F 3 -0.732 45.647 4.091 1 106.43 ? O44 01K 1805 A 1 HETATM 53 C C47 01K . . . F 3 -2.713 48.986 5.298 1 104.19 ? C47 01K 1805 A 1 HETATM 54 O O48 01K . . . F 3 -1.527 49.553 4.753 1 103.98 ? O48 01K 1805 A 1 HETATM 55 C C49 01K . . . F 3 -3.948 49.651 4.694 1 104.15 ? C49 01K 1805 A 1 HETATM 56 N N50 01K . . . F 3 -4.385 50.838 5.418 1 104.08 ? N50 01K 1805 A 1 HETATM 57 C C51 01K . . . F 3 -4.801 50.895 6.72 1 103.94 ? C51 01K 1805 A 1 HETATM 58 N N52 01K . . . F 3 -5.083 52.103 7.14 1 104.1 ? N52 01K 1805 A 1 HETATM 59 C C53 01K . . . F 3 -4.831 52.902 6.035 1 104.31 ? C53 01K 1805 A 1 HETATM 60 N N55 01K . . . F 3 -4.034 52.583 3.76 1 104.69 ? N55 01K 1805 A 1 HETATM 61 C C56 01K . . . F 3 -4.096 53.918 3.702 1 104.72 ? C56 01K 1805 A 1 HETATM 62 N N57 01K . . . F 3 -4.467 54.782 4.651 1 104.57 ? N57 01K 1805 A 1 HETATM 63 C C58 01K . . . F 3 -4.84 54.3 5.856 1 104.45 ? C58 01K 1805 A 1 HETATM 64 N N59 01K . . . F 3 -5.111 55.172 6.832 1 104.49 ? N59 01K 1805 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 64 #