data_5T3D # _model_server_result.job_id SlZ3xLNrMgxAz8nrm8fjsg _model_server_result.datetime_utc '2024-11-13 11:52:51' _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 5t3d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1301}' # _entry.id 5T3D # _exptl.entry_id 5T3D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 773.773 _entity.id 2 _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 90 _cell.angle_gamma 90 _cell.entry_id 5T3D _cell.length_a 127.711 _cell.length_b 127.711 _cell.length_c 186.94 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5T3D _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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 _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 B _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 B _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 1.569 _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 5T3D _atom_sites.fract_transf_matrix[1][1] 0.00783 _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] 0.00783 _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] 0.005349 _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 75C A 1 1301 701 75C 4T8 . C 3 HOH A 1 1401 17 HOH HOH . C 3 HOH A 2 1402 16 HOH HOH . C 3 HOH A 3 1403 10 HOH HOH . C 3 HOH A 4 1404 18 HOH HOH . C 3 HOH A 5 1405 1 HOH HOH . C 3 HOH A 6 1406 7 HOH HOH . C 3 HOH A 7 1407 4 HOH HOH . C 3 HOH A 8 1408 8 HOH HOH . C 3 HOH A 9 1409 9 HOH HOH . C 3 HOH A 10 1410 13 HOH HOH . C 3 HOH A 11 1411 20 HOH HOH . C 3 HOH A 12 1412 2 HOH HOH . C 3 HOH A 13 1413 15 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 . . . B 2 47.512 122.363 69.526 1 62.99 ? O1 75C 1301 A 1 HETATM 2 C C1 75C . . . B 2 62.636 126.869 74.368 1 34.89 ? C1 75C 1301 A 1 HETATM 3 C C2 75C . . . B 2 63.498 128.777 73.219 1 32.49 ? C2 75C 1301 A 1 HETATM 4 C C3 75C . . . B 2 61.331 127.75 75.816 1 38.27 ? C3 75C 1301 A 1 HETATM 5 O O2 75C . . . B 2 62.552 124.245 79.2 1 42.38 ? O2 75C 1301 A 1 HETATM 6 C C4 75C . . . B 2 57.086 128.963 79.206 1 44.25 ? C4 75C 1301 A 1 HETATM 7 N N1 75C . . . B 2 58.416 125.489 78.819 1 36.91 ? N1 75C 1301 A 1 HETATM 8 S S1 75C . . . B 2 57.566 126.319 79.826 1 51.93 ? S1 75C 1301 A 1 HETATM 9 C C5 75C . . . B 2 58.04 127.916 79.774 1 42.8 ? C5 75C 1301 A 1 HETATM 10 N N2 75C . . . B 2 64.212 127.951 72.456 1 33.77 ? N2 75C 1301 A 1 HETATM 11 C C6 75C . . . B 2 64.15 126.643 72.635 1 36.78 ? C6 75C 1301 A 1 HETATM 12 N N3 75C . . . B 2 58.667 130.596 80.172 1 45.4 ? N3 75C 1301 A 1 HETATM 13 O O3 75C . . . B 2 62.512 123.256 76.556 1 28.67 ? O3 75C 1301 A 1 HETATM 14 C C7 75C . . . B 2 59.801 125.946 78.859 1 35.47 ? C7 75C 1301 A 1 HETATM 15 N N4 75C . . . B 2 63.374 126.066 73.551 1 36.74 ? N4 75C 1301 A 1 HETATM 16 C C8 75C . . . B 2 62.684 128.237 74.21 1 39.46 ? C8 75C 1301 A 1 HETATM 17 N N5 75C . . . B 2 63.559 130.121 73.028 1 28.01 ? N5 75C 1301 A 1 HETATM 18 N N6 75C . . . B 2 61.85 128.76 75.12 1 42.4 ? N6 75C 1301 A 1 HETATM 19 N N7 75C . . . B 2 61.809 126.604 75.363 1 31.22 ? N7 75C 1301 A 1 HETATM 20 C C9 75C . . . B 2 57.759 130.31 79.096 1 43.96 ? C9 75C 1301 A 1 HETATM 21 C C10 75C . . . B 2 58.683 130.379 77.919 1 44.53 ? C10 75C 1301 A 1 HETATM 22 S S2 75C . . . B 2 56.654 128.613 77.532 1 54.23 ? S2 75C 1301 A 1 HETATM 23 P P1 75C . . . B 2 46.637 123.918 69.048 1 47.82 ? P1 75C 1301 A 1 HETATM 24 C C11 75C . . . B 2 55.279 129.525 76.969 1 56.75 ? C11 75C 1301 A 1 HETATM 25 O O4 75C . . . B 2 56.242 125.94 79.542 1 40.2 ? O4 75C 1301 A 1 HETATM 26 C C12 75C . . . B 2 53.986 128.831 77.313 1 54.28 ? C12 75C 1301 A 1 HETATM 27 O O5 75C . . . B 2 57.868 125.711 81.042 1 73.13 ? O5 75C 1301 A 1 HETATM 28 O O6 75C . . . B 2 45.117 124.433 69.86 1 43.93 ? O6 75C 1301 A 1 HETATM 29 N N8 75C . . . B 2 53.296 128.422 76.085 1 55.48 ? N8 75C 1301 A 1 HETATM 30 C C13 75C . . . B 2 52.59 129.04 75.235 1 43.76 ? C13 75C 1301 A 1 HETATM 31 O O7 75C . . . B 2 52.351 130.235 75.294 1 32.45 ? O7 75C 1301 A 1 HETATM 32 O O8 75C . . . B 2 47.644 125.256 69.255 1 24.55 ? O8 75C 1301 A 1 HETATM 33 C C14 75C . . . B 2 52.023 128.19 74.098 1 45.35 ? C14 75C 1301 A 1 HETATM 34 C C15 75C . . . B 2 50.78 128.872 73.471 1 37.37 ? C15 75C 1301 A 1 HETATM 35 N N9 75C . . . B 2 50.099 127.968 72.528 1 27.67 ? N9 75C 1301 A 1 HETATM 36 C C16 75C . . . B 2 48.869 128.025 72.219 1 40.19 ? C16 75C 1301 A 1 HETATM 37 O O9 75C . . . B 2 48.069 128.82 72.725 1 54.12 ? O9 75C 1301 A 1 HETATM 38 C C17 75C . . . B 2 48.363 127.017 71.212 1 34.39 ? C17 75C 1301 A 1 HETATM 39 O O10 75C . . . B 2 49.365 125.986 71.041 1 38.39 ? O10 75C 1301 A 1 HETATM 40 C C18 75C . . . B 2 48.044 127.583 69.802 1 31.93 ? C18 75C 1301 A 1 HETATM 41 C C19 75C . . . B 2 47.106 126.573 69.075 1 18.51 ? C19 75C 1301 A 1 HETATM 42 C C20 75C . . . B 2 47.4 128.961 69.698 1 15.83 ? C20 75C 1301 A 1 HETATM 43 C C21 75C . . . B 2 49.414 127.867 69.172 1 20.59 ? C21 75C 1301 A 1 HETATM 44 O O11 75C . . . B 2 58.838 131.774 77.649 1 42.11 ? O11 75C 1301 A 1 HETATM 45 C C22 75C . . . B 2 61.519 125.233 75.808 1 26.42 ? C22 75C 1301 A 1 HETATM 46 C C23 75C . . . B 2 62.6 124.686 76.723 1 28.48 ? C23 75C 1301 A 1 HETATM 47 C C24 75C . . . B 2 62.135 125.098 78.12 1 42.64 ? C24 75C 1301 A 1 HETATM 48 C C25 75C . . . B 2 60.616 124.999 77.981 1 44.03 ? C25 75C 1301 A 1 HETATM 49 O O12 75C . . . B 2 60.324 125.187 76.585 1 33.55 ? O12 75C 1301 A 1 # _model_server_stats.io_time_ms 107 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 49 #