data_3LX3 # _model_server_result.job_id 2kPdQGWSquG8fULALNl4Lg _model_server_result.datetime_utc '2024-11-22 09:33:20' _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 3lx3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":211}' # _entry.id 3LX3 # _exptl.entry_id 3LX3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 179.136 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-amino-1,5-dihydropteridine-4,6-dione _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 120 _cell.entry_id 3LX3 _cell.length_a 131.358 _cell.length_b 131.358 _cell.length_c 73.577 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LX3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 73.577 5 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 73.577 6 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 73.577 # _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 # 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 36 A HIS 28 1_555 B ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc2 A NE2 HIS 48 A HIS 40 1_555 B ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc3 A NE2 HIS 50 A HIS 42 1_555 B ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc4 A OE2 GLU 168 A GLU 160 1_555 B ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc5 B ZN ZN . A ZN 201 1_555 D O HOH . A HOH 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc6 B ZN ZN . A ZN 201 1_555 D O HOH . A HOH 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? # _chem_comp.formula 'C6 H5 N5 O2' _chem_comp.formula_weight 179.136 _chem_comp.id XTN _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-1,5-dihydropteridine-4,6-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Xanthopterin # 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 C2 XTN sing 348 n n N1 C8A XTN sing 349 n n N1 HN1 XTN sing 350 n n C2 N2 XTN sing 351 n n C2 N3 XTN doub 352 n n N2 HN2 XTN sing 353 n n N2 HN2A XTN sing 354 n n N3 C4 XTN sing 355 n n C4 O4 XTN doub 356 n n C4 C4A XTN sing 357 n n N5 C6 XTN sing 358 n n N5 C4A XTN sing 359 n n C6 O6 XTN doub 360 n n C6 C7 XTN sing 361 n n C7 N8 XTN doub 362 n n C7 H7 XTN sing 363 n n N8 C8A XTN sing 364 n n C4A C8A XTN doub 365 n n N5 H5 XTN sing 366 n n # _atom_sites.entry_id 3LX3 _atom_sites.fract_transf_matrix[1][1] 0.007613 _atom_sites.fract_transf_matrix[1][2] 0.004395 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00879 _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] 0.013591 _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 1 201 201 ZN ZN . C 3 XTN A 1 211 211 XTN XTN . D 4 HOH A 1 221 221 HOH HOH . D 4 HOH A 2 222 222 HOH HOH . D 4 HOH A 3 223 223 HOH HOH . D 4 HOH A 4 224 224 HOH HOH . D 4 HOH A 5 225 225 HOH HOH . D 4 HOH A 6 226 226 HOH HOH . D 4 HOH A 7 227 227 HOH HOH . D 4 HOH A 8 228 228 HOH HOH . D 4 HOH A 9 229 229 HOH HOH . D 4 HOH A 10 230 230 HOH HOH . D 4 HOH A 11 231 231 HOH HOH . D 4 HOH A 12 232 232 HOH HOH . D 4 HOH A 13 233 233 HOH HOH . D 4 HOH A 14 234 234 HOH HOH . D 4 HOH A 15 235 235 HOH HOH . D 4 HOH A 16 236 236 HOH HOH . D 4 HOH A 17 237 237 HOH HOH . D 4 HOH A 18 238 238 HOH HOH . D 4 HOH A 19 239 239 HOH HOH . D 4 HOH A 20 240 240 HOH HOH . D 4 HOH A 21 241 241 HOH HOH . D 4 HOH A 22 242 242 HOH HOH . D 4 HOH A 23 243 243 HOH HOH . D 4 HOH A 24 244 244 HOH HOH . D 4 HOH A 25 245 245 HOH HOH . D 4 HOH A 26 246 246 HOH HOH . D 4 HOH A 27 247 247 HOH HOH . D 4 HOH A 28 248 248 HOH HOH . D 4 HOH A 29 249 249 HOH HOH . D 4 HOH A 30 250 250 HOH HOH . D 4 HOH A 31 251 251 HOH HOH . D 4 HOH A 32 252 252 HOH HOH . D 4 HOH A 33 253 253 HOH HOH . D 4 HOH A 34 254 254 HOH HOH . D 4 HOH A 35 255 255 HOH HOH . D 4 HOH A 36 256 256 HOH HOH . D 4 HOH A 37 257 257 HOH HOH . D 4 HOH A 38 258 258 HOH HOH . D 4 HOH A 39 259 259 HOH HOH . D 4 HOH A 40 260 260 HOH HOH . D 4 HOH A 41 261 261 HOH HOH . D 4 HOH A 42 262 262 HOH HOH . D 4 HOH A 43 263 263 HOH HOH . D 4 HOH A 44 264 264 HOH HOH . D 4 HOH A 45 265 265 HOH HOH . D 4 HOH A 46 266 266 HOH HOH . D 4 HOH A 47 267 267 HOH HOH . D 4 HOH A 48 268 268 HOH HOH . D 4 HOH A 49 269 269 HOH HOH . D 4 HOH A 50 270 270 HOH HOH . D 4 HOH A 51 271 271 HOH HOH . D 4 HOH A 52 272 272 HOH HOH . D 4 HOH A 53 273 273 HOH HOH . D 4 HOH A 54 274 274 HOH HOH . D 4 HOH A 55 275 275 HOH HOH . D 4 HOH A 56 276 276 HOH HOH . D 4 HOH A 57 277 277 HOH HOH . D 4 HOH A 58 278 278 HOH HOH . D 4 HOH A 59 279 279 HOH HOH . D 4 HOH A 60 280 280 HOH HOH . D 4 HOH A 61 281 281 HOH HOH . D 4 HOH A 62 282 282 HOH HOH . D 4 HOH A 63 283 283 HOH HOH . D 4 HOH A 64 284 284 HOH HOH . D 4 HOH A 65 285 285 HOH HOH . D 4 HOH A 66 286 286 HOH HOH . D 4 HOH A 67 287 287 HOH HOH . D 4 HOH A 68 288 288 HOH HOH . D 4 HOH A 69 289 289 HOH HOH . D 4 HOH A 70 290 290 HOH HOH . D 4 HOH A 71 291 291 HOH HOH . D 4 HOH A 72 292 292 HOH HOH . D 4 HOH A 73 293 293 HOH HOH . D 4 HOH A 74 294 294 HOH HOH . D 4 HOH A 75 295 295 HOH HOH . D 4 HOH A 76 296 296 HOH HOH . D 4 HOH A 77 297 297 HOH HOH . D 4 HOH A 78 298 298 HOH HOH . D 4 HOH A 79 299 299 HOH HOH . D 4 HOH A 80 300 300 HOH HOH . D 4 HOH A 81 301 301 HOH HOH . D 4 HOH A 82 302 302 HOH HOH . D 4 HOH A 83 303 303 HOH HOH . D 4 HOH A 84 304 304 HOH HOH . D 4 HOH A 85 305 305 HOH HOH . D 4 HOH A 86 306 306 HOH HOH . D 4 HOH A 87 307 307 HOH HOH . D 4 HOH A 88 308 308 HOH HOH . D 4 HOH A 89 309 309 HOH HOH . D 4 HOH A 90 310 310 HOH HOH . D 4 HOH A 91 311 311 HOH HOH . D 4 HOH A 92 312 312 HOH HOH . D 4 HOH A 93 313 313 HOH HOH . D 4 HOH A 94 314 314 HOH HOH . D 4 HOH A 95 315 315 HOH HOH . D 4 HOH A 96 316 316 HOH HOH . D 4 HOH A 97 317 317 HOH HOH . D 4 HOH A 98 318 318 HOH HOH . D 4 HOH A 99 319 319 HOH HOH . D 4 HOH A 100 320 320 HOH HOH . D 4 HOH A 101 321 321 HOH HOH . D 4 HOH A 102 322 322 HOH HOH . D 4 HOH A 103 323 323 HOH HOH . D 4 HOH A 104 324 324 HOH HOH . D 4 HOH A 105 325 325 HOH HOH . D 4 HOH A 106 326 326 HOH HOH . D 4 HOH A 107 327 327 HOH HOH . D 4 HOH A 108 328 328 HOH HOH . D 4 HOH A 109 329 329 HOH HOH . D 4 HOH A 110 330 330 HOH HOH . D 4 HOH A 111 331 331 HOH HOH . D 4 HOH A 112 332 332 HOH HOH . D 4 HOH A 113 333 333 HOH HOH . D 4 HOH A 114 334 334 HOH HOH . D 4 HOH A 115 335 335 HOH HOH . D 4 HOH A 116 336 336 HOH HOH . D 4 HOH A 117 337 337 HOH HOH . D 4 HOH A 118 338 338 HOH HOH . D 4 HOH A 119 339 339 HOH HOH . D 4 HOH A 120 340 340 HOH HOH . D 4 HOH A 121 341 341 HOH HOH . D 4 HOH A 122 342 342 HOH HOH . D 4 HOH A 123 343 343 HOH HOH . D 4 HOH A 124 344 344 HOH HOH . D 4 HOH A 125 345 345 HOH HOH . D 4 HOH A 126 346 346 HOH HOH . D 4 HOH A 127 347 347 HOH HOH . D 4 HOH A 128 348 348 HOH HOH . D 4 HOH A 129 349 349 HOH HOH . D 4 HOH A 130 350 350 HOH HOH . D 4 HOH A 131 351 351 HOH HOH . D 4 HOH A 132 352 352 HOH HOH . D 4 HOH A 133 353 353 HOH HOH . D 4 HOH A 134 354 354 HOH HOH . D 4 HOH A 135 355 355 HOH HOH . D 4 HOH A 136 356 356 HOH HOH . D 4 HOH A 137 357 357 HOH HOH . D 4 HOH A 138 358 358 HOH HOH . D 4 HOH A 139 359 359 HOH HOH . D 4 HOH A 140 360 360 HOH HOH . D 4 HOH A 141 361 361 HOH HOH . D 4 HOH A 142 362 362 HOH HOH . D 4 HOH A 143 363 363 HOH HOH . D 4 HOH A 144 364 364 HOH HOH . D 4 HOH A 145 365 365 HOH HOH . D 4 HOH A 146 366 366 HOH HOH . D 4 HOH A 147 367 367 HOH HOH . D 4 HOH A 148 368 368 HOH HOH . D 4 HOH A 149 369 369 HOH HOH . D 4 HOH A 150 370 370 HOH HOH . D 4 HOH A 151 371 371 HOH HOH . D 4 HOH A 152 372 372 HOH HOH . D 4 HOH A 153 373 373 HOH HOH . D 4 HOH A 154 374 374 HOH HOH . D 4 HOH A 155 375 375 HOH HOH . D 4 HOH A 156 376 376 HOH HOH . D 4 HOH A 157 377 377 HOH HOH . D 4 HOH A 158 378 378 HOH HOH . D 4 HOH A 159 379 379 HOH HOH . D 4 HOH A 160 380 380 HOH HOH . D 4 HOH A 161 381 381 HOH HOH . D 4 HOH A 162 382 382 HOH HOH . D 4 HOH A 163 383 383 HOH HOH . D 4 HOH A 164 384 384 HOH HOH . D 4 HOH A 165 385 385 HOH HOH . D 4 HOH A 166 386 386 HOH HOH . D 4 HOH A 167 387 387 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 XTN . . . C 3 -16.387 10.704 23.859 1 18.61 ? N1 XTN 211 A 1 HETATM 2 C C2 XTN . . . C 3 -15.341 11.009 23.065 1 16.14 ? C2 XTN 211 A 1 HETATM 3 N N2 XTN . . . C 3 -15.171 10.39 21.882 1 17.81 ? N2 XTN 211 A 1 HETATM 4 N N3 XTN . . . C 3 -14.433 12.034 23.435 1 17.5 ? N3 XTN 211 A 1 HETATM 5 C C4 XTN . . . C 3 -14.53 12.676 24.61 1 19.02 ? C4 XTN 211 A 1 HETATM 6 O O4 XTN . . . C 3 -13.671 13.544 24.898 1 19.89 ? O4 XTN 211 A 1 HETATM 7 N N5 XTN . . . C 3 -15.789 12.915 26.64 1 20.14 ? N5 XTN 211 A 1 HETATM 8 C C6 XTN . . . C 3 -16.86 12.574 27.417 1 22.62 ? C6 XTN 211 A 1 HETATM 9 O O6 XTN . . . C 3 -17.024 13.134 28.504 1 25.61 ? O6 XTN 211 A 1 HETATM 10 C C7 XTN . . . C 3 -17.788 11.59 26.959 1 25.28 ? C7 XTN 211 A 1 HETATM 11 N N8 XTN . . . C 3 -17.571 11.011 25.776 1 21.39 ? N8 XTN 211 A 1 HETATM 12 C C4A XTN . . . C 3 -15.599 12.309 25.431 1 18.6 ? C4A XTN 211 A 1 HETATM 13 C C8A XTN . . . C 3 -16.511 11.333 25.03 1 20.6 ? C8A XTN 211 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 13 #