data_1XWK # _model_server_result.job_id N1LqxPwfVN5lvaVucBjtHw _model_server_result.datetime_utc '2024-10-13 12:17:20' _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 1xwk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":219}' # _entry.id 1XWK # _exptl.entry_id 1XWK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 473.415 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'GLUTATHIONE S-(2,4 DINITROBENZENE)' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 121.08 _cell.angle_gamma 90 _cell.entry_id 1XWK _cell.length_a 175.83 _cell.length_b 51.94 _cell.length_c 93.84 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XWK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,F,G,I 1 1 B,E,H 2 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' 2_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 175.83 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C16 H19 N5 O10 S' _chem_comp.formula_weight 473.415 _chem_comp.id GDN _chem_comp.mon_nstd_flag . _chem_comp.name 'GLUTATHIONE S-(2,4 DINITROBENZENE)' _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 N1 CA1 GDN sing 83 n n N1 HN1 GDN sing 84 n n N1 HN2A GDN sing 85 n n CA1 C1 GDN sing 86 n n CA1 CB1 GDN sing 87 n n CA1 HA1 GDN sing 88 n n C1 O11 GDN doub 89 n n C1 O12 GDN sing 90 n n O12 H12 GDN sing 91 n n CB1 CG1 GDN sing 92 n n CB1 HB11 GDN sing 93 n n CB1 HB12 GDN sing 94 n n CG1 CD1 GDN sing 95 n n CG1 HG11 GDN sing 96 n n CG1 HG12 GDN sing 97 n n CD1 OE1 GDN doub 98 n n CD1 N2 GDN sing 99 n n N2 CA2 GDN sing 100 n n N2 HN2 GDN sing 101 n n CA2 C2 GDN sing 102 n n CA2 CB2 GDN sing 103 n n CA2 HA2 GDN sing 104 n n C2 O2 GDN doub 105 n n C2 N3 GDN sing 106 n n CB2 SG2 GDN sing 107 n n CB2 HB21 GDN sing 108 n n CB2 HB22 GDN sing 109 n n SG2 C1' GDN sing 110 n n N3 CA3 GDN sing 111 n n N3 HN3 GDN sing 112 n n CA3 C3 GDN sing 113 n n CA3 HA31 GDN sing 114 n n CA3 HA32 GDN sing 115 n n C3 O31 GDN doub 116 n n C3 O32 GDN sing 117 n n O32 H32 GDN sing 118 n n C1' C2' GDN doub 119 n y C1' C6' GDN sing 120 n y C2' C3' GDN sing 121 n y C2' N2' GDN sing 122 n n C3' C4' GDN doub 123 n y C3' H3' GDN sing 124 n n C4' C5' GDN sing 125 n y C4' N4' GDN sing 126 n n C5' C6' GDN doub 127 n y C5' H5' GDN sing 128 n n C6' H6' GDN sing 129 n n N2' O2A GDN sing 130 n n N2' O2B GDN doub 131 n n N4' O4A GDN sing 132 n n N4' O4B GDN doub 133 n n # _atom_sites.entry_id 1XWK _atom_sites.fract_transf_matrix[1][1] 0.005687 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003428 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019253 _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] 0.012443 _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 D 2 GDN A 1 218 218 GDN GDN . E 2 GDN B 1 219 218 GDN GDN . F 2 GDN C 1 220 218 GDN GDN . G 3 HOH A 1 219 1 HOH HOH . G 3 HOH A 2 220 2 HOH HOH . G 3 HOH A 3 221 3 HOH HOH . G 3 HOH A 4 222 4 HOH HOH . G 3 HOH A 5 223 5 HOH HOH . G 3 HOH A 6 224 6 HOH HOH . G 3 HOH A 7 225 10 HOH HOH . G 3 HOH A 8 226 14 HOH HOH . G 3 HOH A 9 227 16 HOH HOH . G 3 HOH A 10 228 17 HOH HOH . G 3 HOH A 11 229 18 HOH HOH . G 3 HOH A 12 230 24 HOH HOH . G 3 HOH A 13 231 36 HOH HOH . G 3 HOH A 14 232 41 HOH HOH . G 3 HOH A 15 233 46 HOH HOH . G 3 HOH A 16 234 50 HOH HOH . G 3 HOH A 17 235 54 HOH HOH . G 3 HOH A 18 236 56 HOH HOH . G 3 HOH A 19 237 58 HOH HOH . G 3 HOH A 20 238 65 HOH HOH . G 3 HOH A 21 239 66 HOH HOH . G 3 HOH A 22 240 68 HOH HOH . G 3 HOH A 23 241 71 HOH HOH . G 3 HOH A 24 242 74 HOH HOH . G 3 HOH A 25 243 77 HOH HOH . G 3 HOH A 26 244 80 HOH HOH . G 3 HOH A 27 245 86 HOH HOH . G 3 HOH A 28 246 87 HOH HOH . G 3 HOH A 29 247 89 HOH HOH . G 3 HOH A 30 248 90 HOH HOH . G 3 HOH A 31 249 91 HOH HOH . G 3 HOH A 32 250 92 HOH HOH . G 3 HOH A 33 251 95 HOH HOH . G 3 HOH A 34 252 96 HOH HOH . G 3 HOH A 35 253 97 HOH HOH . G 3 HOH A 36 254 100 HOH HOH . G 3 HOH A 37 255 103 HOH HOH . G 3 HOH A 38 256 106 HOH HOH . G 3 HOH A 39 257 109 HOH HOH . G 3 HOH A 40 258 110 HOH HOH . G 3 HOH A 41 259 111 HOH HOH . G 3 HOH A 42 260 113 HOH HOH . G 3 HOH A 43 261 116 HOH HOH . G 3 HOH A 44 262 121 HOH HOH . G 3 HOH A 45 263 122 HOH HOH . G 3 HOH A 46 264 130 HOH HOH . G 3 HOH A 47 265 131 HOH HOH . G 3 HOH A 48 266 135 HOH HOH . G 3 HOH A 49 267 136 HOH HOH . G 3 HOH A 50 268 137 HOH HOH . G 3 HOH A 51 269 138 HOH HOH . G 3 HOH A 52 270 139 HOH HOH . G 3 HOH A 53 271 140 HOH HOH . G 3 HOH A 54 272 141 HOH HOH . G 3 HOH A 55 273 150 HOH HOH . G 3 HOH A 56 274 155 HOH HOH . H 3 HOH B 1 220 7 HOH HOH . H 3 HOH B 2 221 8 HOH HOH . H 3 HOH B 3 222 11 HOH HOH . H 3 HOH B 4 223 13 HOH HOH . H 3 HOH B 5 224 15 HOH HOH . H 3 HOH B 6 225 23 HOH HOH . H 3 HOH B 7 226 29 HOH HOH . H 3 HOH B 8 227 30 HOH HOH . H 3 HOH B 9 228 31 HOH HOH . H 3 HOH B 10 229 32 HOH HOH . H 3 HOH B 11 230 33 HOH HOH . H 3 HOH B 12 231 35 HOH HOH . H 3 HOH B 13 232 37 HOH HOH . H 3 HOH B 14 233 43 HOH HOH . H 3 HOH B 15 234 44 HOH HOH . H 3 HOH B 16 235 45 HOH HOH . H 3 HOH B 17 236 47 HOH HOH . H 3 HOH B 18 237 48 HOH HOH . H 3 HOH B 19 238 57 HOH HOH . H 3 HOH B 20 239 59 HOH HOH . H 3 HOH B 21 240 73 HOH HOH . H 3 HOH B 22 241 76 HOH HOH . H 3 HOH B 23 242 79 HOH HOH . H 3 HOH B 24 243 83 HOH HOH . H 3 HOH B 25 244 85 HOH HOH . H 3 HOH B 26 245 88 HOH HOH . H 3 HOH B 27 246 98 HOH HOH . H 3 HOH B 28 247 102 HOH HOH . H 3 HOH B 29 248 108 HOH HOH . H 3 HOH B 30 249 114 HOH HOH . H 3 HOH B 31 250 115 HOH HOH . H 3 HOH B 32 251 118 HOH HOH . H 3 HOH B 33 252 120 HOH HOH . H 3 HOH B 34 253 123 HOH HOH . H 3 HOH B 35 254 124 HOH HOH . H 3 HOH B 36 255 125 HOH HOH . H 3 HOH B 37 256 132 HOH HOH . H 3 HOH B 38 257 142 HOH HOH . H 3 HOH B 39 258 143 HOH HOH . H 3 HOH B 40 259 144 HOH HOH . H 3 HOH B 41 260 145 HOH HOH . H 3 HOH B 42 261 146 HOH HOH . H 3 HOH B 43 262 147 HOH HOH . H 3 HOH B 44 263 148 HOH HOH . H 3 HOH B 45 264 151 HOH HOH . H 3 HOH B 46 265 152 HOH HOH . H 3 HOH B 47 266 153 HOH HOH . H 3 HOH B 48 267 158 HOH HOH . I 3 HOH C 1 221 9 HOH HOH . I 3 HOH C 2 222 12 HOH HOH . I 3 HOH C 3 223 19 HOH HOH . I 3 HOH C 4 224 20 HOH HOH . I 3 HOH C 5 225 21 HOH HOH . I 3 HOH C 6 226 22 HOH HOH . I 3 HOH C 7 227 25 HOH HOH . I 3 HOH C 8 228 26 HOH HOH . I 3 HOH C 9 229 27 HOH HOH . I 3 HOH C 10 230 28 HOH HOH . I 3 HOH C 11 231 34 HOH HOH . I 3 HOH C 12 232 38 HOH HOH . I 3 HOH C 13 233 39 HOH HOH . I 3 HOH C 14 234 40 HOH HOH . I 3 HOH C 15 235 42 HOH HOH . I 3 HOH C 16 236 49 HOH HOH . I 3 HOH C 17 237 51 HOH HOH . I 3 HOH C 18 238 52 HOH HOH . I 3 HOH C 19 239 53 HOH HOH . I 3 HOH C 20 240 55 HOH HOH . I 3 HOH C 21 241 60 HOH HOH . I 3 HOH C 22 242 61 HOH HOH . I 3 HOH C 23 243 62 HOH HOH . I 3 HOH C 24 244 63 HOH HOH . I 3 HOH C 25 245 64 HOH HOH . I 3 HOH C 26 246 67 HOH HOH . I 3 HOH C 27 247 69 HOH HOH . I 3 HOH C 28 248 70 HOH HOH . I 3 HOH C 29 249 72 HOH HOH . I 3 HOH C 30 250 75 HOH HOH . I 3 HOH C 31 251 78 HOH HOH . I 3 HOH C 32 252 81 HOH HOH . I 3 HOH C 33 253 82 HOH HOH . I 3 HOH C 34 254 84 HOH HOH . I 3 HOH C 35 255 93 HOH HOH . I 3 HOH C 36 256 94 HOH HOH . I 3 HOH C 37 257 99 HOH HOH . I 3 HOH C 38 258 101 HOH HOH . I 3 HOH C 39 259 104 HOH HOH . I 3 HOH C 40 260 105 HOH HOH . I 3 HOH C 41 261 107 HOH HOH . I 3 HOH C 42 262 112 HOH HOH . I 3 HOH C 43 263 117 HOH HOH . I 3 HOH C 44 264 119 HOH HOH . I 3 HOH C 45 265 126 HOH HOH . I 3 HOH C 46 266 127 HOH HOH . I 3 HOH C 47 267 128 HOH HOH . I 3 HOH C 48 268 129 HOH HOH . I 3 HOH C 49 269 133 HOH HOH . I 3 HOH C 50 270 134 HOH HOH . I 3 HOH C 51 271 149 HOH HOH . I 3 HOH C 52 272 154 HOH HOH . I 3 HOH C 53 273 156 HOH HOH . I 3 HOH C 54 274 157 HOH HOH . I 3 HOH C 55 275 159 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 N N1 GDN . . . E 2 82.206 -25.724 -0.233 1 16.01 ? N1 GDN 219 B 1 HETATM 2 C CA1 GDN . . . E 2 80.789 -25.803 0.125 1 25.67 ? CA1 GDN 219 B 1 HETATM 3 C C1 GDN . . . E 2 80.509 -24.805 1.221 1 20.16 ? C1 GDN 219 B 1 HETATM 4 O O11 GDN . . . E 2 81.392 -24.624 2.053 1 35.39 ? O11 GDN 219 B 1 HETATM 5 O O12 GDN . . . E 2 79.426 -24.193 1.235 1 26.88 ? O12 GDN 219 B 1 HETATM 6 C CB1 GDN . . . E 2 80.459 -27.235 0.477 1 3.01 ? CB1 GDN 219 B 1 HETATM 7 C CG1 GDN . . . E 2 78.984 -27.446 0.66 1 7.92 ? CG1 GDN 219 B 1 HETATM 8 C CD1 GDN . . . E 2 78.666 -28.888 0.948 1 28.65 ? CD1 GDN 219 B 1 HETATM 9 O OE1 GDN . . . E 2 79.487 -29.782 0.725 1 22.3 ? OE1 GDN 219 B 1 HETATM 10 N N2 GDN . . . E 2 77.452 -29.122 1.424 1 28.77 ? N2 GDN 219 B 1 HETATM 11 C CA2 GDN . . . E 2 76.998 -30.469 1.72 1 42.63 ? CA2 GDN 219 B 1 HETATM 12 C C2 GDN . . . E 2 75.623 -30.706 1.099 1 44.22 ? C2 GDN 219 B 1 HETATM 13 O O2 GDN . . . E 2 74.946 -31.659 1.446 1 48.16 ? O2 GDN 219 B 1 HETATM 14 C CB2 GDN . . . E 2 77.009 -30.724 3.217 1 65.54 ? CB2 GDN 219 B 1 HETATM 15 S SG2 GDN . . . E 2 78.562 -30.544 4.115 1 55.86 ? SG2 GDN 219 B 1 HETATM 16 N N3 GDN . . . E 2 75.225 -29.826 0.176 1 43.44 ? N3 GDN 219 B 1 HETATM 17 C CA3 GDN . . . E 2 73.946 -29.894 -0.527 1 47.35 ? CA3 GDN 219 B 1 HETATM 18 C C3 GDN . . . E 2 74.058 -30.686 -1.82 1 44.44 ? C3 GDN 219 B 1 HETATM 19 O O31 GDN . . . E 2 73.065 -30.787 -2.554 1 49.94 ? O31 GDN 219 B 1 HETATM 20 O O32 GDN . . . E 2 75.139 -31.215 -2.096 1 37.13 ? O32 GDN 219 B 1 HETATM 21 C C1' GDN . . . E 2 79.579 -32.079 3.962 1 71.42 ? C1' GDN 219 B 1 HETATM 22 C C2' GDN . . . E 2 80.831 -32.162 4.638 1 77.47 ? C2' GDN 219 B 1 HETATM 23 C C3' GDN . . . E 2 81.611 -33.333 4.522 1 79.27 ? C3' GDN 219 B 1 HETATM 24 C C4' GDN . . . E 2 81.166 -34.417 3.747 1 80.3 ? C4' GDN 219 B 1 HETATM 25 C C5' GDN . . . E 2 79.921 -34.336 3.08 1 77.17 ? C5' GDN 219 B 1 HETATM 26 C C6' GDN . . . E 2 79.132 -33.17 3.187 1 72.23 ? C6' GDN 219 B 1 HETATM 27 N N2' GDN . . . E 2 81.331 -31.036 5.46 1 79.8 ? N2' GDN 219 B 1 HETATM 28 O O2A GDN . . . E 2 82.502 -31.013 5.805 1 81.22 ? O2A GDN 219 B 1 HETATM 29 O O2B GDN . . . E 2 80.589 -30.144 5.799 1 78.86 ? O2B GDN 219 B 1 HETATM 30 N N4' GDN . . . E 2 81.99 -35.61 3.637 1 80.63 ? N4' GDN 219 B 1 HETATM 31 O O4A GDN . . . E 2 81.691 -36.545 2.92 1 78.24 ? O4A GDN 219 B 1 HETATM 32 O O4B GDN . . . E 2 83.016 -35.658 4.282 1 81.06 ? O4B GDN 219 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #