data_5LSX # _model_server_result.job_id DHu6F7bYxl_YzGOpeXKaPg _model_server_result.datetime_utc '2024-11-14 18:03:16' _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 5lsx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1804}' # _entry.id 5LSX # _exptl.entry_id 5LSX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 473.525 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(phenylmethyl)azanium' _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 5LSX _cell.length_a 49.244 _cell.length_b 77.305 _cell.length_c 78.843 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LSX _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,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 E _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 83 A CYS 1499 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc2 A SG CYS 85 A CYS 1501 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc3 A SG CYS 100 A CYS 1516 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc4 A SG CYS 100 A CYS 1516 1_555 D ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc5 A SG CYS 104 A CYS 1520 1_555 C ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc6 A SG CYS 113 A CYS 1529 1_555 D ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc7 A SG CYS 117 A CYS 1533 1_555 D ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc8 A SG CYS 123 A CYS 1539 1_555 D ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc9 A SG CYS 215 A CYS 1631 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc10 A SG CYS 262 A CYS 1678 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc11 A SG CYS 264 A CYS 1680 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc12 A SG CYS 269 A CYS 1685 1_555 B ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? # _chem_comp.formula 'C22 H31 N7 O5 2' _chem_comp.formula_weight 473.525 _chem_comp.id 76O _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(phenylmethyl)azanium' _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 O22 C20 76O doub 1 n n N19 C18 76O sing 2 n n C20 C18 76O sing 3 n n C20 O21 76O sing 4 n n C18 C17 76O sing 5 n n N3 C4 76O doub 6 n y N3 C2 76O sing 7 n y N1 C2 76O sing 8 n n C17 C16 76O sing 9 n n C4 N5 76O sing 10 n y C2 C10 76O doub 11 n y N5 C6 76O doub 12 n y C10 C6 76O sing 13 n y C10 N9 76O sing 14 n y C6 N7 76O sing 15 n y N9 C8 76O doub 16 n y N7 C8 76O sing 17 n y N7 C11 76O sing 18 n n C11 O12 76O sing 19 n n C11 C33 76O sing 20 n n O12 C13 76O sing 21 n n C16 C15 76O sing 22 n n O34 C33 76O sing 23 n n C33 C31 76O sing 24 n n C15 N23 76O sing 25 n n C15 C14 76O sing 26 n n C13 C31 76O sing 27 n n C13 C14 76O sing 28 n n C31 O32 76O sing 29 n n N23 C24 76O sing 30 n n C24 C25 76O sing 31 n n C30 C25 76O doub 32 n y C30 C29 76O sing 33 n y C25 C26 76O sing 34 n y C29 C28 76O doub 35 n y C26 C27 76O doub 36 n y C28 C27 76O sing 37 n y C8 H49 76O sing 38 n n C11 H35 76O sing 39 n n C13 H36 76O sing 40 n n C14 H51 76O sing 41 n n C14 H50 76O sing 42 n n C15 H37 76O sing 43 n n C16 H52 76O sing 44 n n C16 H53 76O sing 45 n n C24 H56 76O sing 46 n n C24 H57 76O sing 47 n n C26 H58 76O sing 48 n n C27 H59 76O sing 49 n n C28 H60 76O sing 50 n n C31 H44 76O sing 51 n n N1 H47 76O sing 52 n n N1 H46 76O sing 53 n n C4 H48 76O sing 54 n n C17 H54 76O sing 55 n n C17 H55 76O sing 56 n n C18 H38 76O sing 57 n n N19 H39 76O sing 58 n n N19 H41 76O sing 59 n n N19 H40 76O sing 60 n n O21 H1 76O sing 61 n n N23 H43 76O sing 62 n n N23 H42 76O sing 63 n n C29 H61 76O sing 64 n n C30 H62 76O sing 65 n n O32 H63 76O sing 66 n n C33 H45 76O sing 67 n n O34 H64 76O sing 68 n n # _atom_sites.entry_id 5LSX _atom_sites.fract_transf_matrix[1][1] 0.020307 _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] 0.012936 _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] 0.012683 _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 1 ZN ZN . C 2 ZN A 1 1802 2 ZN ZN . D 2 ZN A 1 1803 3 ZN ZN . E 3 76O A 1 1804 1 76O L01 . F 4 HOH A 1 1901 2 HOH HOH . F 4 HOH A 2 1902 1 HOH HOH . F 4 HOH A 3 1903 6 HOH HOH . F 4 HOH A 4 1904 7 HOH HOH . F 4 HOH A 5 1905 3 HOH HOH . F 4 HOH A 6 1906 5 HOH HOH . F 4 HOH A 7 1907 4 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 C2 76O . . . E 3 -1.121 31.63 -18.725 0.88 73.93 ? C2 76O 1804 A 1 HETATM 2 C C6 76O . . . E 3 1.026 30.726 -18.328 0.88 74.16 ? C6 76O 1804 A 1 HETATM 3 C C8 76O . . . E 3 0.539 28.619 -17.921 0.88 80.03 ? C8 76O 1804 A 1 HETATM 4 C C10 76O . . . E 3 -0.33 30.516 -18.411 0.88 69.44 ? C10 76O 1804 A 1 HETATM 5 C C11 76O . . . E 3 2.994 29.233 -17.821 0.88 78.73 ? C11 76O 1804 A 1 HETATM 6 C C13 76O . . . E 3 3.83 27.732 -16.228 0.88 88.32 ? C13 76O 1804 A 1 HETATM 7 C C14 76O . . . E 3 3.34 26.503 -15.491 0.88 95.95 ? C14 76O 1804 A 1 HETATM 8 C C15 76O . . . E 3 2.996 25.302 -16.373 0.88 87.73 ? C15 76O 1804 A 1 HETATM 9 C C16 76O . . . E 3 4.082 24.911 -17.376 0.88 90.28 ? C16 76O 1804 A 1 HETATM 10 C C24 76O . . . E 3 1.513 24.239 -14.626 0.88 101.55 ? C24 76O 1804 A 1 HETATM 11 C C25 76O . . . E 3 1.219 22.962 -13.885 0.88 89.2 ? C25 76O 1804 A 1 HETATM 12 C C26 76O . . . E 3 1.649 22.79 -12.579 0.88 87.14 ? C26 76O 1804 A 1 HETATM 13 C C27 76O . . . E 3 1.379 21.623 -11.904 0.88 82.4 ? C27 76O 1804 A 1 HETATM 14 C C28 76O . . . E 3 0.68 20.618 -12.522 0.88 84.13 ? C28 76O 1804 A 1 HETATM 15 C C31 76O . . . E 3 3.603 29.066 -15.512 0.88 94.74 ? C31 76O 1804 A 1 HETATM 16 N N1 76O . . . E 3 -2.446 31.571 -18.838 0.88 89.87 ? N1 76O 1804 A 1 HETATM 17 N N3 76O . . . E 3 -0.508 32.825 -18.924 0.88 77.03 ? N3 76O 1804 A 1 HETATM 18 C C4 76O . . . E 3 0.835 32.878 -18.809 0.88 74.53 ? C4 76O 1804 A 1 HETATM 19 N N5 76O . . . E 3 1.672 31.888 -18.517 0.88 67.03 ? N5 76O 1804 A 1 HETATM 20 N N7 76O . . . E 3 1.579 29.513 -18.015 0.88 77.27 ? N7 76O 1804 A 1 HETATM 21 N N9 76O . . . E 3 -0.63 29.189 -18.154 0.88 80.21 ? N9 76O 1804 A 1 HETATM 22 O O12 76O . . . E 3 3.125 27.859 -17.46 0.88 80.59 ? O12 76O 1804 A 1 HETATM 23 C C17 76O . . . E 3 3.613 24.827 -18.814 0.88 88.14 ? C17 76O 1804 A 1 HETATM 24 C C18 76O . . . E 3 4.369 25.745 -19.773 0.88 99.5 ? C18 76O 1804 A 1 HETATM 25 N N19 76O . . . E 3 3.498 26.107 -20.93 0.88 107.52 1 N19 76O 1804 A 1 HETATM 26 C C20 76O . . . E 3 5.666 25.101 -20.288 0.88 85.3 ? C20 76O 1804 A 1 HETATM 27 O O21 76O . . . E 3 6.294 24.371 -19.49 0.88 85.2 ? O21 76O 1804 A 1 HETATM 28 O O22 76O . . . E 3 6.008 25.349 -21.466 0.88 83.77 -1 O22 76O 1804 A 1 HETATM 29 N N23 76O . . . E 3 2.718 24.112 -15.495 0.88 89.15 1 N23 76O 1804 A 1 HETATM 30 C C29 76O . . . E 3 0.248 20.774 -13.815 0.88 83.72 ? C29 76O 1804 A 1 HETATM 31 C C30 76O . . . E 3 0.515 21.939 -14.496 0.88 82.42 ? C30 76O 1804 A 1 HETATM 32 O O32 76O . . . E 3 4.629 29.304 -14.561 0.88 84.11 ? O32 76O 1804 A 1 HETATM 33 C C33 76O . . . E 3 3.648 30.052 -16.689 0.88 91.58 ? C33 76O 1804 A 1 HETATM 34 O O34 76O . . . E 3 4.981 30.412 -17.013 0.88 98.94 ? O34 76O 1804 A 1 HETATM 35 H H49 76O . . . E 3 0.651 27.707 -17.714 0.88 78.68 ? H49 76O 1804 A 1 HETATM 36 H H35 76O . . . E 3 3.453 29.41 -18.673 0.88 81.7 ? H35 76O 1804 A 1 HETATM 37 H H36 76O . . . E 3 4.782 27.62 -16.403 0.88 88.51 ? H36 76O 1804 A 1 HETATM 38 H H51 76O . . . E 3 2.543 26.75 -14.978 0.88 92.66 ? H51 76O 1804 A 1 HETATM 39 H H50 76O . . . E 3 4.028 26.231 -14.856 0.88 91.52 ? H50 76O 1804 A 1 HETATM 40 H H37 76O . . . E 3 2.171 25.512 -16.869 0.88 89.51 ? H37 76O 1804 A 1 HETATM 41 H H52 76O . . . E 3 4.81 25.562 -17.321 0.88 89.89 ? H52 76O 1804 A 1 HETATM 42 H H53 76O . . . E 3 4.442 24.048 -17.12 0.88 88.64 ? H53 76O 1804 A 1 HETATM 43 H H56 76O . . . E 3 0.741 24.479 -15.183 0.88 95.17 ? H56 76O 1804 A 1 HETATM 44 H H57 76O . . . E 3 1.659 24.961 -13.982 0.88 94.91 ? H57 76O 1804 A 1 HETATM 45 H H58 76O . . . E 3 2.13 23.477 -12.15 0.88 86.56 ? H58 76O 1804 A 1 HETATM 46 H H59 76O . . . E 3 1.676 21.513 -11.015 0.88 84.16 ? H59 76O 1804 A 1 HETATM 47 H H60 76O . . . E 3 0.497 19.821 -12.059 0.88 84.05 ? H60 76O 1804 A 1 HETATM 48 H H44 76O . . . E 3 2.721 29.088 -15.074 0.88 91.12 ? H44 76O 1804 A 1 HETATM 49 H H47 76O . . . E 3 -2.906 32.304 -19.038 0.88 84.38 ? H47 76O 1804 A 1 HETATM 50 H H46 76O . . . E 3 -2.866 30.799 -18.711 0.88 83.39 ? H46 76O 1804 A 1 HETATM 51 H H48 76O . . . E 3 1.229 33.723 -18.954 0.88 73.23 ? H48 76O 1804 A 1 HETATM 52 H H54 76O . . . E 3 3.712 23.904 -19.121 0.88 90.15 ? H54 76O 1804 A 1 HETATM 53 H H55 76O . . . E 3 2.663 25.052 -18.848 0.88 91.01 ? H55 76O 1804 A 1 HETATM 54 H H38 76O . . . E 3 4.602 26.579 -19.302 0.88 94.99 ? H38 76O 1804 A 1 HETATM 55 H H39 76O . . . E 3 3.956 26.134 -21.64 0.88 99.76 ? H39 76O 1804 A 1 HETATM 56 H H41 76O . . . E 3 2.831 25.489 -21.032 0.88 102.19 ? H41 76O 1804 A 1 HETATM 57 H H40 76O . . . E 3 3.124 26.923 -20.789 0.88 102.76 ? H40 76O 1804 A 1 HETATM 58 H H43 76O . . . E 3 2.613 23.372 -16.029 0.88 91.21 ? H43 76O 1804 A 1 HETATM 59 H H42 76O . . . E 3 3.447 23.965 -14.963 0.88 91.46 ? H42 76O 1804 A 1 HETATM 60 H H61 76O . . . E 3 -0.231 20.083 -14.237 0.88 82.95 ? H61 76O 1804 A 1 HETATM 61 H H62 76O . . . E 3 0.215 22.041 -15.385 0.88 84.77 ? H62 76O 1804 A 1 HETATM 62 H H63 76O . . . E 3 5.173 28.622 -14.572 0 133.03 ? H63 76O 1804 A 1 HETATM 63 H H45 76O . . . E 3 3.129 30.859 -16.475 0.88 89.19 ? H45 76O 1804 A 1 HETATM 64 H H64 76O . . . E 3 5.515 29.996 -16.477 0 133.03 ? H64 76O 1804 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 64 #