data_5JA2 # _model_server_result.job_id iCiIz953vHxpi4pVtBjS8A _model_server_result.datetime_utc '2024-11-04 23:26:29' _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 5ja2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1301}' # _entry.id 5JA2 # _exptl.entry_id 5JA2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 773.773 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}amino)-5'-deoxyadenosine" _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 97.62 _cell.angle_gamma 90 _cell.entry_id 5JA2 _cell.length_a 159.27 _cell.length_b 57.69 _cell.length_c 182.424 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JA2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 1 2 1' # _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,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 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 OG _struct_conn.ptnr1_label_comp_id SER _struct_conn.ptnr1_label_seq_id 1008 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id SER _struct_conn.ptnr1_auth_seq_id 1006 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id P1 _struct_conn.ptnr2_label_comp_id 75C _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id 75C _struct_conn.ptnr2_auth_seq_id 1301 _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 ? _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 1.615 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C25 H44 N9 O13 P S2' _chem_comp.formula_weight 773.773 _chem_comp.id 75C _chem_comp.mon_nstd_flag . _chem_comp.name "5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}amino)-5'-deoxyadenosine" _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 C20 C18 75C sing 1 n n O6 P1 75C sing 2 n n O9 C16 75C doub 3 n n O8 P1 75C sing 4 n n O8 C19 75C sing 5 n n C18 C17 75C sing 6 n n C18 C19 75C sing 7 n n C18 C21 75C sing 8 n n P1 O1 75C doub 9 n n C16 C17 75C sing 10 n n C16 N9 75C sing 11 n n C17 O10 75C sing 12 n n N9 C15 75C sing 13 n n C15 C14 75C sing 14 n n O7 C13 75C doub 15 n n C14 C13 75C sing 16 n n C13 N8 75C sing 17 n n N8 C12 75C sing 18 n n C12 C11 75C sing 19 n n C11 S2 75C sing 20 n n C4 S2 75C sing 21 n n C4 C9 75C sing 22 n n C4 C5 75C sing 23 n n C9 C10 75C sing 24 n n C9 N3 75C sing 25 n n O11 C10 75C sing 26 n n O4 S1 75C doub 27 n n C5 S1 75C sing 28 n n S1 N1 75C sing 29 n n S1 O5 75C doub 30 n n N1 C7 75C sing 31 n n C7 C25 75C sing 32 n n N6 C3 75C doub 33 n y N6 C8 75C sing 34 n y C3 N7 75C sing 35 n y O12 C25 75C sing 36 n n O12 C22 75C sing 37 n n N5 C2 75C sing 38 n n C25 C24 75C sing 39 n n C8 C2 75C doub 40 n y C8 C1 75C sing 41 n y N7 C22 75C sing 42 n n N7 C1 75C sing 43 n y C2 N2 75C sing 44 n y C22 C23 75C sing 45 n n C1 N4 75C doub 46 n y N2 C6 75C doub 47 n y C24 C23 75C sing 48 n n C24 O2 75C sing 49 n n N4 C6 75C sing 50 n y C23 O3 75C sing 51 n n C3 H2 75C sing 52 n n O2 H3 75C sing 53 n n C4 H4 75C sing 54 n n N1 H5 75C sing 55 n n C5 H6 75C sing 56 n n C5 H7 75C sing 57 n n C6 H8 75C sing 58 n n N3 H9 75C sing 59 n n N3 H10 75C sing 60 n n O3 H12 75C sing 61 n n C7 H13 75C sing 62 n n C7 H14 75C sing 63 n n N5 H15 75C sing 64 n n N5 H16 75C sing 65 n n C9 H17 75C sing 66 n n C10 H18 75C sing 67 n n C10 H19 75C sing 68 n n C11 H20 75C sing 69 n n C11 H21 75C sing 70 n n C12 H22 75C sing 71 n n C12 H23 75C sing 72 n n O6 H24 75C sing 73 n n N8 H25 75C sing 74 n n C14 H26 75C sing 75 n n C14 H27 75C sing 76 n n C15 H28 75C sing 77 n n C15 H29 75C sing 78 n n N9 H30 75C sing 79 n n C17 H31 75C sing 80 n n O10 H32 75C sing 81 n n C19 H33 75C sing 82 n n C19 H34 75C sing 83 n n C20 H35 75C sing 84 n n C20 H36 75C sing 85 n n C20 H37 75C sing 86 n n C21 H38 75C sing 87 n n C21 H39 75C sing 88 n n C21 H40 75C sing 89 n n O11 H41 75C sing 90 n n C22 H42 75C sing 91 n n C23 H43 75C sing 92 n n C24 H44 75C sing 93 n n C25 H45 75C sing 94 n n P1 O13 75C sing 95 n n O13 H1 75C sing 96 n n # _atom_sites.entry_id 5JA2 _atom_sites.fract_transf_matrix[1][1] 0.006279 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00084 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017334 _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] 0.005531 _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 3 75C A 1 1301 701 75C 4T8 . D 4 BU9 A 1 1302 1 BU9 BTD . E 4 BU9 A 1 1303 2 BU9 BTD . F 5 HOH A 1 1401 11 HOH HOH . F 5 HOH A 2 1402 15 HOH HOH . F 5 HOH A 3 1403 10 HOH HOH . F 5 HOH A 4 1404 4 HOH HOH . F 5 HOH A 5 1405 1 HOH HOH . F 5 HOH A 6 1406 3 HOH HOH . F 5 HOH A 7 1407 17 HOH HOH . F 5 HOH A 8 1408 18 HOH HOH . F 5 HOH A 9 1409 6 HOH HOH . F 5 HOH A 10 1410 7 HOH HOH . F 5 HOH A 11 1411 16 HOH HOH . F 5 HOH A 12 1412 9 HOH HOH . F 5 HOH A 13 1413 14 HOH HOH . F 5 HOH A 14 1414 13 HOH HOH . F 5 HOH A 15 1415 8 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 O O1 75C . . . C 3 -46.871 -23.026 -25.851 1 83.68 ? O1 75C 1301 A 1 HETATM 2 C C1 75C . . . C 3 -58.195 -22.532 -14.821 1 29.4 ? C1 75C 1301 A 1 HETATM 3 C C2 75C . . . C 3 -59.713 -20.709 -15.082 1 38.1 ? C2 75C 1301 A 1 HETATM 4 C C3 75C . . . C 3 -59.069 -24.049 -16.101 1 34.6 ? C3 75C 1301 A 1 HETATM 5 O O2 75C . . . C 3 -57.034 -27.799 -13.146 1 55.31 ? O2 75C 1301 A 1 HETATM 6 C C4 75C . . . C 3 -59.221 -27.935 -20.147 1 57.88 ? C4 75C 1301 A 1 HETATM 7 N N1 75C . . . C 3 -56.998 -27.876 -17.702 1 52.93 ? N1 75C 1301 A 1 HETATM 8 S S1 75C . . . C 3 -57.452 -29.185 -18.512 1 48.61 ? S1 75C 1301 A 1 HETATM 9 C C5 75C . . . C 3 -59.021 -28.978 -19.039 1 60.78 ? C5 75C 1301 A 1 HETATM 10 N N2 75C . . . C 3 -58.952 -19.99 -14.231 1 35.29 ? N2 75C 1301 A 1 HETATM 11 C C6 75C . . . C 3 -57.848 -20.523 -13.69 1 36.4 ? C6 75C 1301 A 1 HETATM 12 N N3 75C . . . C 3 -61.497 -28.176 -19.275 1 41.34 ? N3 75C 1301 A 1 HETATM 13 O O3 75C . . . C 3 -56.222 -25.428 -12.731 1 46.38 ? O3 75C 1301 A 1 HETATM 14 C C7 75C . . . C 3 -57.7 -27.86 -16.408 1 52.27 ? C7 75C 1301 A 1 HETATM 15 N N4 75C . . . C 3 -57.463 -21.773 -13.975 1 33.7 ? N4 75C 1301 A 1 HETATM 16 C C8 75C . . . C 3 -59.339 -22.008 -15.393 1 34.72 ? C8 75C 1301 A 1 HETATM 17 N N5 75C . . . C 3 -60.829 -20.168 -15.627 1 39.18 ? N5 75C 1301 A 1 HETATM 18 N N6 75C . . . C 3 -59.867 -22.962 -16.185 1 35.45 ? N6 75C 1301 A 1 HETATM 19 N N7 75C . . . C 3 -58.052 -23.779 -15.272 1 34.57 ? N7 75C 1301 A 1 HETATM 20 C C9 75C . . . C 3 -60.619 -27.29 -20.076 1 42.36 ? C9 75C 1301 A 1 HETATM 21 C C10 75C . . . C 3 -60.696 -25.861 -19.562 1 26.42 ? C10 75C 1301 A 1 HETATM 22 S S2 75C . . . C 3 -57.942 -26.718 -20.133 1 50.81 ? S2 75C 1301 A 1 HETATM 23 P P1 75C . . . C 3 -46.856 -22.954 -27.682 1 69.81 ? P1 75C 1301 A 1 HETATM 24 C C11 75C . . . C 3 -57.724 -25.997 -21.728 1 53.76 ? C11 75C 1301 A 1 HETATM 25 O O4 75C . . . C 3 -56.53 -29.428 -19.587 1 58.37 ? O4 75C 1301 A 1 HETATM 26 C C12 75C . . . C 3 -57.283 -27.018 -22.771 1 35.26 ? C12 75C 1301 A 1 HETATM 27 O O5 75C . . . C 3 -57.4 -30.301 -17.615 1 57.38 ? O5 75C 1301 A 1 HETATM 28 O O6 75C . . . C 3 -46.424 -24.456 -28.643 1 73.02 ? O6 75C 1301 A 1 HETATM 29 N N8 75C . . . C 3 -56.061 -26.466 -23.346 1 31.18 ? N8 75C 1301 A 1 HETATM 30 C C13 75C . . . C 3 -55.92 -25.744 -24.374 1 33.14 ? C13 75C 1301 A 1 HETATM 31 O O7 75C . . . C 3 -56.851 -25.392 -25.078 1 35.66 ? O7 75C 1301 A 1 HETATM 32 O O8 75C . . . C 3 -48.416 -22.415 -28.214 1 38.94 ? O8 75C 1301 A 1 HETATM 33 C C14 75C . . . C 3 -54.507 -25.323 -24.713 1 31.87 ? C14 75C 1301 A 1 HETATM 34 C C15 75C . . . C 3 -54.492 -24.55 -26.026 1 33.47 ? C15 75C 1301 A 1 HETATM 35 N N9 75C . . . C 3 -53.092 -24.23 -26.27 1 37.32 ? N9 75C 1301 A 1 HETATM 36 C C16 75C . . . C 3 -52.548 -23.987 -27.385 1 41.17 ? C16 75C 1301 A 1 HETATM 37 O O9 75C . . . C 3 -53.161 -24.011 -28.443 1 47.24 ? O9 75C 1301 A 1 HETATM 38 C C17 75C . . . C 3 -51.076 -23.685 -27.35 1 31.21 ? C17 75C 1301 A 1 HETATM 39 O O10 75C . . . C 3 -50.598 -23.913 -26.02 1 35.63 ? O10 75C 1301 A 1 HETATM 40 C C18 75C . . . C 3 -50.771 -22.241 -27.738 1 27.44 ? C18 75C 1301 A 1 HETATM 41 C C19 75C . . . C 3 -49.361 -21.894 -27.279 1 35.09 ? C19 75C 1301 A 1 HETATM 42 C C20 75C . . . C 3 -50.86 -22.057 -29.246 1 23.15 ? C20 75C 1301 A 1 HETATM 43 C C21 75C . . . C 3 -51.763 -21.297 -27.07 1 18.02 ? C21 75C 1301 A 1 HETATM 44 O O11 75C . . . C 3 -62.01 -25.407 -19.908 1 30.79 ? O11 75C 1301 A 1 HETATM 45 C C22 75C . . . C 3 -56.953 -24.704 -14.905 1 43.05 ? C22 75C 1301 A 1 HETATM 46 C C23 75C . . . C 3 -57.325 -25.456 -13.639 1 44.18 ? C23 75C 1301 A 1 HETATM 47 C C24 75C . . . C 3 -57.598 -26.877 -14.081 1 46.37 ? C24 75C 1301 A 1 HETATM 48 C C25 75C . . . C 3 -56.913 -26.997 -15.43 1 48.32 ? C25 75C 1301 A 1 HETATM 49 O O12 75C . . . C 3 -56.768 -25.671 -15.942 1 50.45 ? O12 75C 1301 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 49 #