data_3LX5 # _model_server_result.job_id YaasgzsGY94lTjuTiF9VPw _model_server_result.datetime_utc '2024-12-04 05:31:20' _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 3lx5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 3LX5 # _exptl.entry_id 3LX5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 653.327 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-amino-9-(5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-3-O-{[2-(methylamino)phenyl]carbonyl}-beta-D-erythro-pentofuranosyl-2-ulose)-1,9-dihydro-6H-purin-6-one _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 3LX5 _cell.length_a 49.1 _cell.length_b 82.2 _cell.length_c 148.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LX5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # 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 OG1 THR 17 A THR 15 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc2 A OG1 THR 37 A THR 35 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc3 B O2B AGO . A AGO 300 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc4 B O1G AGO . A AGO 300 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc5 C MG MG . A MG 301 1_555 E O HOH . A HOH 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc6 C MG MG . A MG 301 1_555 E O HOH . A HOH 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? # _chem_comp.formula 'C18 H22 N7 O14 P3' _chem_comp.formula_weight 653.327 _chem_comp.id AGO _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-9-(5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]-3-O-{[2-(methylamino)phenyl]carbonyl}-beta-D-erythro-pentofuranosyl-2-ulose)-1,9-dihydro-6H-purin-6-one _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 CM' N2' AGO sing 1 n n N2' C2' AGO sing 2 n n C2' C3' AGO doub 3 n y C2' C1' AGO sing 4 n y C3' C4' AGO sing 5 n y C4' C5' AGO doub 6 n y C5' C6' AGO sing 7 n y C6' C1' AGO doub 8 n y C1' C' AGO sing 9 n n C' O1' AGO doub 10 n n C' O3' AGO sing 11 n n O3' C3B AGO sing 12 n n C3B C2B AGO sing 13 n n C3B C4B AGO sing 14 n n C2B O2' AGO doub 15 n n C2B C1B AGO sing 16 n n C4B C5B AGO sing 17 n n C4B O4' AGO sing 18 n n C5B O5' AGO sing 19 n n O5' PA AGO sing 20 n n PA O1A AGO sing 21 n n PA O2A AGO doub 22 n n PA O3A AGO sing 23 n n O3A PB AGO sing 24 n n PB O1B AGO doub 25 n n PB O2B AGO sing 26 n n PB N3B AGO sing 27 n n N3B PG AGO sing 28 n n PG O2G AGO sing 29 n n PG O3G AGO sing 30 n n PG O1G AGO doub 31 n n O4' C1B AGO sing 32 n n C1B N9 AGO sing 33 n n N9 C8 AGO sing 34 n y N9 C4 AGO sing 35 n y C8 N7 AGO doub 36 n y N7 C5 AGO sing 37 n y C5 C4 AGO doub 38 n y C5 C6 AGO sing 39 n n C4 N3 AGO sing 40 n n N3 C2 AGO doub 41 n n C2 N2 AGO sing 42 n n C2 N1 AGO sing 43 n n N1 C6 AGO sing 44 n n C6 O6 AGO doub 45 n n CM' HM' AGO sing 46 n n CM' "HM'A" AGO sing 47 n n CM' "HM'B" AGO sing 48 n n N2' HN2' AGO sing 49 n n C3' H3' AGO sing 50 n n C4' H4' AGO sing 51 n n C5' H5' AGO sing 52 n n C6' H6' AGO sing 53 n n C3B H3B AGO sing 54 n n C4B H4B AGO sing 55 n n C5B H5B AGO sing 56 n n C5B H5BA AGO sing 57 n n O1A HO1A AGO sing 58 n n O2B HO2B AGO sing 59 n n N3B HN3B AGO sing 60 n n O2G HO2G AGO sing 61 n n O3G HO3G AGO sing 62 n n C1B H1B AGO sing 63 n n C8 H8 AGO sing 64 n n N2 HN2 AGO sing 65 n n N2 HN2A AGO sing 66 n n N1 HN1 AGO sing 67 n n # _atom_sites.entry_id 3LX5 _atom_sites.fract_transf_matrix[1][1] 0.020371 _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] 0.012173 _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] 0.006721 _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 AGO A 1 300 300 AGO AGO . C 3 MG A 1 301 301 MG MG . D 4 GOL A 1 400 400 GOL GOL . E 5 HOH A 1 271 1 HOH HOH . E 5 HOH A 2 272 2 HOH HOH . E 5 HOH A 3 273 3 HOH HOH . E 5 HOH A 4 274 4 HOH HOH . E 5 HOH A 5 275 5 HOH HOH . E 5 HOH A 6 276 6 HOH HOH . E 5 HOH A 7 277 7 HOH HOH . E 5 HOH A 8 278 8 HOH HOH . E 5 HOH A 9 279 9 HOH HOH . E 5 HOH A 10 280 10 HOH HOH . E 5 HOH A 11 281 11 HOH HOH . E 5 HOH A 12 282 12 HOH HOH . E 5 HOH A 13 283 13 HOH HOH . E 5 HOH A 14 284 14 HOH HOH . E 5 HOH A 15 285 15 HOH HOH . E 5 HOH A 16 286 16 HOH HOH . E 5 HOH A 17 287 17 HOH HOH . E 5 HOH A 18 288 18 HOH HOH . E 5 HOH A 19 289 19 HOH HOH . E 5 HOH A 20 290 20 HOH HOH . E 5 HOH A 21 291 21 HOH HOH . E 5 HOH A 22 292 22 HOH HOH . E 5 HOH A 23 293 23 HOH HOH . E 5 HOH A 24 294 24 HOH HOH . E 5 HOH A 25 295 25 HOH HOH . E 5 HOH A 26 296 26 HOH HOH . E 5 HOH A 27 297 27 HOH HOH . E 5 HOH A 28 298 28 HOH HOH . E 5 HOH A 29 299 29 HOH HOH . E 5 HOH A 30 302 30 HOH HOH . E 5 HOH A 31 303 31 HOH HOH . E 5 HOH A 32 304 32 HOH HOH . E 5 HOH A 33 305 33 HOH HOH . E 5 HOH A 34 306 34 HOH HOH . E 5 HOH A 35 307 35 HOH HOH . E 5 HOH A 36 308 36 HOH HOH . E 5 HOH A 37 309 37 HOH HOH . E 5 HOH A 38 310 38 HOH HOH . E 5 HOH A 39 311 39 HOH HOH . E 5 HOH A 40 312 40 HOH HOH . E 5 HOH A 41 313 41 HOH HOH . E 5 HOH A 42 314 42 HOH HOH . E 5 HOH A 43 315 43 HOH HOH . E 5 HOH A 44 316 44 HOH HOH . E 5 HOH A 45 317 45 HOH HOH . E 5 HOH A 46 318 46 HOH HOH . E 5 HOH A 47 319 47 HOH HOH . E 5 HOH A 48 320 48 HOH HOH . E 5 HOH A 49 321 49 HOH HOH . E 5 HOH A 50 322 50 HOH HOH . E 5 HOH A 51 323 51 HOH HOH . E 5 HOH A 52 324 52 HOH HOH . E 5 HOH A 53 325 53 HOH HOH . E 5 HOH A 54 326 54 HOH HOH . E 5 HOH A 55 327 55 HOH HOH . E 5 HOH A 56 328 56 HOH HOH . E 5 HOH A 57 329 57 HOH HOH . E 5 HOH A 58 330 58 HOH HOH . E 5 HOH A 59 331 59 HOH HOH . E 5 HOH A 60 332 60 HOH HOH . E 5 HOH A 61 333 61 HOH HOH . E 5 HOH A 62 334 62 HOH HOH . E 5 HOH A 63 335 63 HOH HOH . E 5 HOH A 64 336 64 HOH HOH . E 5 HOH A 65 337 65 HOH HOH . E 5 HOH A 66 338 66 HOH HOH . E 5 HOH A 67 339 67 HOH HOH . E 5 HOH A 68 340 68 HOH HOH . E 5 HOH A 69 341 69 HOH HOH . E 5 HOH A 70 342 70 HOH HOH . E 5 HOH A 71 343 71 HOH HOH . E 5 HOH A 72 344 72 HOH HOH . E 5 HOH A 73 345 73 HOH HOH . E 5 HOH A 74 346 74 HOH HOH . E 5 HOH A 75 347 75 HOH HOH . E 5 HOH A 76 348 76 HOH HOH . E 5 HOH A 77 349 77 HOH HOH . E 5 HOH A 78 350 78 HOH HOH . E 5 HOH A 79 351 79 HOH HOH . E 5 HOH A 80 352 80 HOH HOH . E 5 HOH A 81 353 81 HOH HOH . E 5 HOH A 82 354 82 HOH HOH . E 5 HOH A 83 355 83 HOH HOH . E 5 HOH A 84 356 84 HOH HOH . E 5 HOH A 85 357 85 HOH HOH . E 5 HOH A 86 358 86 HOH HOH . E 5 HOH A 87 359 87 HOH HOH . E 5 HOH A 88 360 88 HOH HOH . E 5 HOH A 89 361 89 HOH HOH . E 5 HOH A 90 362 90 HOH HOH . E 5 HOH A 91 363 91 HOH HOH . E 5 HOH A 92 364 92 HOH HOH . E 5 HOH A 93 365 93 HOH HOH . E 5 HOH A 94 366 94 HOH HOH . E 5 HOH A 95 367 95 HOH HOH . E 5 HOH A 96 368 96 HOH HOH . E 5 HOH A 97 369 97 HOH HOH . E 5 HOH A 98 370 98 HOH HOH . E 5 HOH A 99 371 99 HOH HOH . E 5 HOH A 100 372 100 HOH HOH . E 5 HOH A 101 373 101 HOH HOH . E 5 HOH A 102 374 102 HOH HOH . E 5 HOH A 103 375 103 HOH HOH . E 5 HOH A 104 376 104 HOH HOH . E 5 HOH A 105 377 105 HOH HOH . E 5 HOH A 106 378 106 HOH HOH . E 5 HOH A 107 379 107 HOH HOH . E 5 HOH A 108 380 108 HOH HOH . E 5 HOH A 109 381 109 HOH HOH . E 5 HOH A 110 382 110 HOH HOH . E 5 HOH A 111 383 111 HOH HOH . E 5 HOH A 112 384 112 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 CM' AGO . . . B 2 3.611 28.38 37.951 0 26.84 ? CM' AGO 300 A 1 HETATM 2 N N2' AGO . . . B 2 3.895 27.164 37.155 0 26.84 ? N2' AGO 300 A 1 HETATM 3 C C2' AGO . . . B 2 5.036 26.464 37.284 0 26.84 ? C2' AGO 300 A 1 HETATM 4 C C3' AGO . . . B 2 6.269 27.149 37.379 0 26.84 ? C3' AGO 300 A 1 HETATM 5 C C4' AGO . . . B 2 7.477 26.45 37.504 0 26.84 ? C4' AGO 300 A 1 HETATM 6 C C5' AGO . . . B 2 7.458 25.053 37.54 0 26.84 ? C5' AGO 300 A 1 HETATM 7 C C6' AGO . . . B 2 6.241 24.364 37.452 0 26.84 ? C6' AGO 300 A 1 HETATM 8 C C1' AGO . . . B 2 5.023 25.046 37.318 0 26.84 ? C1' AGO 300 A 1 HETATM 9 C C' AGO . . . B 2 3.683 24.234 37.214 0 26.84 ? C' AGO 300 A 1 HETATM 10 O O1' AGO . . . B 2 2.598 24.553 38.369 0 26.84 ? O1' AGO 300 A 1 HETATM 11 O O3' AGO . . . B 2 3.508 23.264 36.215 1 27.75 ? O3' AGO 300 A 1 HETATM 12 C C3B AGO . . . B 2 3.54 23.054 34.757 1 24.51 ? C3B AGO 300 A 1 HETATM 13 C C2B AGO . . . B 2 3.293 24.493 34.384 1 24.29 ? C2B AGO 300 A 1 HETATM 14 O O2' AGO . . . B 2 2.3 25.162 34.698 1 27.19 ? O2' AGO 300 A 1 HETATM 15 C C4B AGO . . . B 2 4.993 22.756 34.366 1 22.77 ? C4B AGO 300 A 1 HETATM 16 C C5B AGO . . . B 2 5.115 21.754 33.216 1 18.07 ? C5B AGO 300 A 1 HETATM 17 O O5' AGO . . . B 2 4.113 22.052 32.197 1 18.5 ? O5' AGO 300 A 1 HETATM 18 P PA AGO . . . B 2 3.652 20.914 31.233 1 20.98 ? PA AGO 300 A 1 HETATM 19 O O1A AGO . . . B 2 2.911 21.66 30.213 1 19.71 ? O1A AGO 300 A 1 HETATM 20 O O2A AGO . . . B 2 3.045 19.768 31.942 1 21.27 ? O2A AGO 300 A 1 HETATM 21 O O3A AGO . . . B 2 5.135 20.35 30.656 1 19.87 ? O3A AGO 300 A 1 HETATM 22 P PB AGO . . . B 2 5.397 19.188 29.546 1 18.77 ? PB AGO 300 A 1 HETATM 23 O O1B AGO . . . B 2 6.52 19.723 28.753 1 19.43 ? O1B AGO 300 A 1 HETATM 24 O O2B AGO . . . B 2 4.117 18.902 28.831 1 18.23 ? O2B AGO 300 A 1 HETATM 25 N N3B AGO . . . B 2 5.908 17.963 30.477 1 18.28 ? N3B AGO 300 A 1 HETATM 26 P PG AGO . . . B 2 5.762 16.439 29.867 1 18.42 ? PG AGO 300 A 1 HETATM 27 O O2G AGO . . . B 2 6.825 16.404 28.631 1 18.82 ? O2G AGO 300 A 1 HETATM 28 O O3G AGO . . . B 2 6.245 15.472 31.05 1 21.39 ? O3G AGO 300 A 1 HETATM 29 O O1G AGO . . . B 2 4.334 16.113 29.561 1 18.04 ? O1G AGO 300 A 1 HETATM 30 O O4' AGO . . . B 2 5.579 23.96 33.857 1 22.71 ? O4' AGO 300 A 1 HETATM 31 C C1B AGO . . . B 2 4.65 25.093 34.005 1 24.14 ? C1B AGO 300 A 1 HETATM 32 N N9 AGO . . . B 2 4.817 25.942 32.843 1 24.22 ? N9 AGO 300 A 1 HETATM 33 C C8 AGO . . . B 2 4.685 25.61 31.552 1 23.92 ? C8 AGO 300 A 1 HETATM 34 N N7 AGO . . . B 2 4.981 26.691 30.824 1 25.58 ? N7 AGO 300 A 1 HETATM 35 C C5 AGO . . . B 2 5.32 27.701 31.637 1 24.82 ? C5 AGO 300 A 1 HETATM 36 C C4 AGO . . . B 2 5.223 27.216 32.929 1 26.3 ? C4 AGO 300 A 1 HETATM 37 N N3 AGO . . . B 2 5.507 28.01 33.986 1 23.55 ? N3 AGO 300 A 1 HETATM 38 C C2 AGO . . . B 2 5.884 29.282 33.82 1 26.3 ? C2 AGO 300 A 1 HETATM 39 N N2 AGO . . . B 2 6.138 30.022 34.896 1 26.41 ? N2 AGO 300 A 1 HETATM 40 N N1 AGO . . . B 2 5.999 29.849 32.542 1 25.71 ? N1 AGO 300 A 1 HETATM 41 C C6 AGO . . . B 2 5.718 29.027 31.442 1 26.57 ? C6 AGO 300 A 1 HETATM 42 O O6 AGO . . . B 2 5.82 29.503 30.318 1 25.28 ? O6 AGO 300 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 42 #