data_2XRL # _model_server_result.job_id zmjGmkTx15EYze2fHPw1ng _model_server_result.datetime_utc '2024-11-23 22:29:38' _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 2xrl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1211}' # _entry.id 2XRL # _exptl.entry_id 2XRL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 444.435 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE _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 2XRL _cell.length_a 67.888 _cell.length_b 67.888 _cell.length_c 180.438 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XRL _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 67.888 67.888 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 NE2 HIS 99 A HIS 100 1_555 E MG MG . A MG 1212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc2 D O11 DXT . A DXT 1211 1_555 E MG MG . A MG 1212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc3 D O12 DXT . A DXT 1211 1_555 E MG MG . A MG 1212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc4 E MG MG . A MG 1212 1_555 F O HOH . A HOH 1213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc5 E MG MG . A MG 1212 1_555 F O HOH . A HOH 1214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc6 E MG MG . A MG 1212 1_555 F O HOH . A HOH 1215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? # _chem_comp.formula 'C22 H24 N2 O8' _chem_comp.formula_weight 444.435 _chem_comp.id DXT _chem_comp.mon_nstd_flag . _chem_comp.name (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DOXYTETRACYCLINE;DOXYCYCLINE # 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 C1 C4B DXT sing 70 n n C1 O1 DXT doub 71 n n C1 C2 DXT sing 72 n n C2 C21 DXT sing 73 n n C2 C3 DXT doub 74 n n O21 C21 DXT doub 75 n n C21 N21 DXT sing 76 n n N21 H211 DXT sing 77 n n N21 H212 DXT sing 78 n n C3 O3 DXT sing 79 n n C3 C4 DXT sing 80 n n O3 HO3 DXT sing 81 n n C4 H4 DXT sing 82 n n C4 N4 DXT sing 83 n n C4 C4A DXT sing 84 n n N4 C41 DXT sing 85 n n N4 C42 DXT sing 86 n n C41 H411 DXT sing 87 n n C41 H412 DXT sing 88 n n C41 H413 DXT sing 89 n n C42 H421 DXT sing 90 n n C42 H422 DXT sing 91 n n C42 H423 DXT sing 92 n n C4A C4B DXT sing 93 n n C4A H4A DXT sing 94 n n C4A C5 DXT sing 95 n n C5 H5 DXT sing 96 n n C5 O5 DXT sing 97 n n C5 C5A DXT sing 98 n n O5 HO5 DXT sing 99 n n C5A C5B DXT sing 100 n n C5A H5A DXT sing 101 n n C5A C6 DXT sing 102 n n C6 H6 DXT sing 103 n n C6 C6A DXT sing 104 n n C6 C61 DXT sing 105 n n C61 H611 DXT sing 106 n n C61 H612 DXT sing 107 n n C61 H613 DXT sing 108 n n C6A C6B DXT sing 109 n y C6A C7 DXT doub 110 n y C7 H7 DXT sing 111 n n C7 C8 DXT sing 112 n y C8 H8 DXT sing 113 n n C8 C9 DXT doub 114 n y C9 C10 DXT sing 115 n y C9 H9 DXT sing 116 n n C10 O10 DXT sing 117 n n C10 C6B DXT doub 118 n y O10 H10 DXT sing 119 n n C6B C11 DXT sing 120 n n C11 O11 DXT doub 121 n n C11 C5B DXT sing 122 n n C5B C12 DXT doub 123 n n C12 O12 DXT sing 124 n n C12 C4B DXT sing 125 n n O12 H12 DXT sing 126 n n C4B O13 DXT sing 127 n n O13 H13 DXT sing 128 n n # _atom_sites.entry_id 2XRL _atom_sites.fract_transf_matrix[1][1] 0.01473 _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] 0.01473 _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] 0.005542 _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 CL A 1 1209 1209 CL CL . C 2 CL A 1 1210 1210 CL CL . D 3 DXT A 1 1211 1211 DXT DXT . E 4 MG A 1 1212 1212 MG MG . F 5 HOH A 1 1213 1213 HOH HOH . F 5 HOH A 2 1214 1214 HOH HOH . F 5 HOH A 3 1215 1215 HOH HOH . F 5 HOH A 4 2001 2001 HOH HOH . F 5 HOH A 5 2002 2002 HOH HOH . F 5 HOH A 6 2003 2003 HOH HOH . F 5 HOH A 7 2004 2004 HOH HOH . F 5 HOH A 8 2005 2005 HOH HOH . F 5 HOH A 9 2006 2006 HOH HOH . F 5 HOH A 10 2007 2007 HOH HOH . F 5 HOH A 11 2008 2008 HOH HOH . F 5 HOH A 12 2009 2009 HOH HOH . F 5 HOH A 13 2010 2010 HOH HOH . F 5 HOH A 14 2011 2011 HOH HOH . F 5 HOH A 15 2012 2012 HOH HOH . F 5 HOH A 16 2013 2013 HOH HOH . F 5 HOH A 17 2014 2014 HOH HOH . F 5 HOH A 18 2015 2015 HOH HOH . F 5 HOH A 19 2016 2016 HOH HOH . F 5 HOH A 20 2017 2017 HOH HOH . F 5 HOH A 21 2018 2018 HOH HOH . F 5 HOH A 22 2019 2019 HOH HOH . F 5 HOH A 23 2020 2020 HOH HOH . F 5 HOH A 24 2021 2021 HOH HOH . F 5 HOH A 25 2022 2022 HOH HOH . F 5 HOH A 26 2023 2023 HOH HOH . F 5 HOH A 27 2024 2024 HOH HOH . F 5 HOH A 28 2025 2025 HOH HOH . F 5 HOH A 29 2026 2026 HOH HOH . F 5 HOH A 30 2027 2027 HOH HOH . F 5 HOH A 31 2028 2028 HOH HOH . F 5 HOH A 32 2029 2029 HOH HOH . F 5 HOH A 33 2030 2030 HOH HOH . F 5 HOH A 34 2031 2031 HOH HOH . F 5 HOH A 35 2032 2032 HOH HOH . F 5 HOH A 36 2033 2033 HOH HOH . F 5 HOH A 37 2034 2034 HOH HOH . F 5 HOH A 38 2035 2035 HOH HOH . F 5 HOH A 39 2036 2036 HOH HOH . F 5 HOH A 40 2037 2037 HOH HOH . F 5 HOH A 41 2038 2038 HOH HOH . F 5 HOH A 42 2039 2039 HOH HOH . F 5 HOH A 43 2040 2040 HOH HOH . F 5 HOH A 44 2041 2041 HOH HOH . F 5 HOH A 45 2042 2042 HOH HOH . F 5 HOH A 46 2043 2043 HOH HOH . F 5 HOH A 47 2044 2044 HOH HOH . F 5 HOH A 48 2045 2045 HOH HOH . F 5 HOH A 49 2046 2046 HOH HOH . F 5 HOH A 50 2047 2047 HOH HOH . F 5 HOH A 51 2048 2048 HOH HOH . F 5 HOH A 52 2049 2049 HOH HOH . F 5 HOH A 53 2050 2050 HOH HOH . F 5 HOH A 54 2051 2051 HOH HOH . F 5 HOH A 55 2052 2052 HOH HOH . F 5 HOH A 56 2053 2053 HOH HOH . F 5 HOH A 57 2054 2054 HOH HOH . F 5 HOH A 58 2055 2055 HOH HOH . F 5 HOH A 59 2056 2056 HOH HOH . F 5 HOH A 60 2057 2057 HOH HOH . F 5 HOH A 61 2058 2058 HOH HOH . F 5 HOH A 62 2059 2059 HOH HOH . F 5 HOH A 63 2061 2061 HOH HOH . F 5 HOH A 64 2062 2062 HOH HOH . F 5 HOH A 65 2063 2063 HOH HOH . F 5 HOH A 66 2064 2064 HOH HOH . F 5 HOH A 67 2065 2065 HOH HOH . F 5 HOH A 68 2066 2066 HOH HOH . F 5 HOH A 69 2067 2067 HOH HOH . F 5 HOH A 70 2068 2068 HOH HOH . F 5 HOH A 71 2069 2069 HOH HOH . F 5 HOH A 72 2070 2070 HOH HOH . F 5 HOH A 73 2071 2071 HOH HOH . F 5 HOH A 74 2072 2072 HOH HOH . F 5 HOH A 75 2073 2073 HOH HOH . F 5 HOH A 76 2074 2074 HOH HOH . F 5 HOH A 77 2075 2075 HOH HOH . F 5 HOH A 78 2076 2076 HOH HOH . F 5 HOH A 79 2077 2077 HOH HOH . F 5 HOH A 80 2078 2078 HOH HOH . F 5 HOH A 81 2079 2079 HOH HOH . F 5 HOH A 82 2081 2081 HOH HOH . F 5 HOH A 83 2082 2082 HOH HOH . F 5 HOH A 84 2083 2083 HOH HOH . F 5 HOH A 85 2084 2084 HOH HOH . F 5 HOH A 86 2085 2085 HOH HOH . F 5 HOH A 87 2086 2086 HOH HOH . F 5 HOH A 88 2087 2087 HOH HOH . F 5 HOH A 89 2088 2088 HOH HOH . F 5 HOH A 90 2089 2089 HOH HOH . F 5 HOH A 91 2090 2090 HOH HOH . F 5 HOH A 92 2091 2091 HOH HOH . F 5 HOH A 93 2092 2092 HOH HOH . F 5 HOH A 94 2093 2093 HOH HOH . F 5 HOH A 95 2094 2094 HOH HOH . F 5 HOH A 96 2095 2095 HOH HOH . F 5 HOH A 97 2096 2096 HOH HOH . F 5 HOH A 98 2097 2097 HOH HOH . F 5 HOH A 99 2098 2098 HOH HOH . F 5 HOH A 100 2099 2099 HOH HOH . F 5 HOH A 101 2100 2100 HOH HOH . F 5 HOH A 102 2101 2101 HOH HOH . F 5 HOH A 103 2102 2102 HOH HOH . F 5 HOH A 104 2103 2103 HOH HOH . F 5 HOH A 105 2104 2104 HOH HOH . F 5 HOH A 106 2105 2105 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 C1 DXT . . . D 3 19.797 33.888 34.466 1 50.29 ? C1 DXT 1211 A 1 HETATM 2 O O1 DXT . . . D 3 19.176 34.357 33.435 1 49.59 ? O1 DXT 1211 A 1 HETATM 3 C C2 DXT . . . D 3 19.368 32.727 35.143 1 49.34 ? C2 DXT 1211 A 1 HETATM 4 O O21 DXT . . . D 3 17.531 31.276 35.532 1 47.83 ? O21 DXT 1211 A 1 HETATM 5 C C21 DXT . . . D 3 18.122 32.136 34.801 1 52.93 ? C21 DXT 1211 A 1 HETATM 6 N N21 DXT . . . D 3 17.489 32.428 33.657 1 49.96 ? N21 DXT 1211 A 1 HETATM 7 C C3 DXT . . . D 3 19.913 32.424 36.349 1 47.17 ? C3 DXT 1211 A 1 HETATM 8 O O3 DXT . . . D 3 19.7 31.294 36.965 1 49.59 ? O3 DXT 1211 A 1 HETATM 9 C C4 DXT . . . D 3 20.765 33.372 37.12 1 44.28 ? C4 DXT 1211 A 1 HETATM 10 N N4 DXT . . . D 3 21.839 32.598 37.865 1 46.88 ? N4 DXT 1211 A 1 HETATM 11 C C41 DXT . . . D 3 22.33 33.462 39.004 1 45.78 ? C41 DXT 1211 A 1 HETATM 12 C C42 DXT . . . D 3 23.052 32.114 37.108 1 45.81 ? C42 DXT 1211 A 1 HETATM 13 C C4A DXT . . . D 3 21.273 34.636 36.375 1 44.54 ? C4A DXT 1211 A 1 HETATM 14 C C5 DXT . . . D 3 20.448 35.884 36.747 1 48.09 ? C5 DXT 1211 A 1 HETATM 15 O O5 DXT . . . D 3 20.217 35.99 38.141 1 47.29 ? O5 DXT 1211 A 1 HETATM 16 C C5A DXT . . . D 3 20.797 37.168 36.001 1 49.05 ? C5A DXT 1211 A 1 HETATM 17 C C6 DXT . . . D 3 19.908 38.404 36.047 1 50.22 ? C6 DXT 1211 A 1 HETATM 18 C C61 DXT . . . D 3 19.318 38.622 37.459 1 52.84 ? C61 DXT 1211 A 1 HETATM 19 C C6A DXT . . . D 3 20.716 39.566 35.494 1 51.48 ? C6A DXT 1211 A 1 HETATM 20 C C7 DXT . . . D 3 20.673 40.859 36.021 1 55.48 ? C7 DXT 1211 A 1 HETATM 21 C C8 DXT . . . D 3 21.414 41.929 35.486 1 55.59 ? C8 DXT 1211 A 1 HETATM 22 C C9 DXT . . . D 3 22.271 41.741 34.402 1 59.07 ? C9 DXT 1211 A 1 HETATM 23 C C10 DXT . . . D 3 22.338 40.474 33.804 1 58.17 ? C10 DXT 1211 A 1 HETATM 24 O O10 DXT . . . D 3 23.144 40.33 32.712 1 55.24 ? O10 DXT 1211 A 1 HETATM 25 C C6B DXT . . . D 3 21.581 39.39 34.393 1 54.6 ? C6B DXT 1211 A 1 HETATM 26 C C11 DXT . . . D 3 21.652 38.015 33.81 1 52.8 ? C11 DXT 1211 A 1 HETATM 27 O O11 DXT . . . D 3 22.205 37.914 32.665 1 50.49 ? O11 DXT 1211 A 1 HETATM 28 C C5B DXT . . . D 3 21.365 36.936 34.594 1 48 ? C5B DXT 1211 A 1 HETATM 29 C C12 DXT . . . D 3 21.549 35.706 34.129 1 45.28 ? C12 DXT 1211 A 1 HETATM 30 O O12 DXT . . . D 3 22.042 35.51 32.962 1 49.63 ? O12 DXT 1211 A 1 HETATM 31 C C4B DXT . . . D 3 21.19 34.432 34.878 1 46.3 ? C4B DXT 1211 A 1 HETATM 32 O O13 DXT . . . D 3 22.146 33.414 34.504 1 45.83 ? O13 DXT 1211 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #