data_3HYT # _model_server_result.job_id j56MirlDN7ML10WvpjRZsQ _model_server_result.datetime_utc '2025-06-29 16:50:24' _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 3hyt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":801}' # _entry.id 3HYT # _exptl.entry_id 3HYT _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.95 _cell.angle_gamma 90 _cell.entry_id 3HYT _cell.length_a 76 _cell.length_b 46.41 _cell.length_c 120.07 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HYT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F,G,H,I,J,K,L _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 # 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 F N N ? 2 H N 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 17 1_555 E MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc2 D O1G AGO . A AGO 801 1_555 E MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc3 B OG1 THR 17 B THR 17 1_555 G MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc4 K O HOH . B HOH 307 1_555 G MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc5 F O2B AGO . B AGO 801 1_555 G MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc6 F O1G AGO . B AGO 801 1_555 G MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc7 C OG1 THR 17 C THR 17 1_555 I MG MG . C MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc8 H N3B AGO . C AGO 801 1_555 I MG MG . C MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc9 H O1G AGO . C AGO 801 1_555 I MG MG . C MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? # _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 3HYT _atom_sites.fract_transf_matrix[1][1] 0.013158 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00114 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021547 _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] 0.00836 _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 AGO A 1 801 801 AGO AGO . E 3 MG A 1 802 802 MG MG . F 2 AGO B 1 801 801 AGO AGO . G 3 MG B 1 802 802 MG MG . H 2 AGO C 1 801 801 AGO AGO . I 3 MG C 1 802 802 MG MG . J 4 HOH A 1 271 2 HOH HOH . J 4 HOH A 2 272 3 HOH HOH . J 4 HOH A 3 273 5 HOH HOH . J 4 HOH A 4 274 7 HOH HOH . J 4 HOH A 5 275 9 HOH HOH . J 4 HOH A 6 276 11 HOH HOH . J 4 HOH A 7 277 12 HOH HOH . J 4 HOH A 8 278 13 HOH HOH . J 4 HOH A 9 279 14 HOH HOH . J 4 HOH A 10 280 16 HOH HOH . J 4 HOH A 11 281 18 HOH HOH . J 4 HOH A 12 282 19 HOH HOH . J 4 HOH A 13 283 25 HOH HOH . J 4 HOH A 14 284 26 HOH HOH . J 4 HOH A 15 285 31 HOH HOH . J 4 HOH A 16 286 33 HOH HOH . J 4 HOH A 17 287 37 HOH HOH . J 4 HOH A 18 288 39 HOH HOH . J 4 HOH A 19 289 40 HOH HOH . J 4 HOH A 20 290 43 HOH HOH . J 4 HOH A 21 291 47 HOH HOH . J 4 HOH A 22 292 59 HOH HOH . J 4 HOH A 23 293 60 HOH HOH . J 4 HOH A 24 294 62 HOH HOH . J 4 HOH A 25 295 64 HOH HOH . J 4 HOH A 26 296 67 HOH HOH . J 4 HOH A 27 297 71 HOH HOH . J 4 HOH A 28 298 73 HOH HOH . J 4 HOH A 29 299 76 HOH HOH . J 4 HOH A 30 300 85 HOH HOH . J 4 HOH A 31 301 86 HOH HOH . J 4 HOH A 32 302 91 HOH HOH . J 4 HOH A 33 303 93 HOH HOH . J 4 HOH A 34 304 94 HOH HOH . J 4 HOH A 35 305 95 HOH HOH . J 4 HOH A 36 306 96 HOH HOH . J 4 HOH A 37 307 98 HOH HOH . J 4 HOH A 38 308 100 HOH HOH . J 4 HOH A 39 309 103 HOH HOH . J 4 HOH A 40 310 113 HOH HOH . J 4 HOH A 41 311 120 HOH HOH . J 4 HOH A 42 312 123 HOH HOH . J 4 HOH A 43 313 124 HOH HOH . J 4 HOH A 44 314 129 HOH HOH . J 4 HOH A 45 315 130 HOH HOH . J 4 HOH A 46 316 131 HOH HOH . J 4 HOH A 47 317 132 HOH HOH . J 4 HOH A 48 318 139 HOH HOH . K 4 HOH B 1 271 1 HOH HOH . K 4 HOH B 2 272 6 HOH HOH . K 4 HOH B 3 273 8 HOH HOH . K 4 HOH B 4 274 10 HOH HOH . K 4 HOH B 5 275 17 HOH HOH . K 4 HOH B 6 276 20 HOH HOH . K 4 HOH B 7 277 22 HOH HOH . K 4 HOH B 8 278 28 HOH HOH . K 4 HOH B 9 279 32 HOH HOH . K 4 HOH B 10 280 35 HOH HOH . K 4 HOH B 11 281 36 HOH HOH . K 4 HOH B 12 282 38 HOH HOH . K 4 HOH B 13 283 42 HOH HOH . K 4 HOH B 14 284 44 HOH HOH . K 4 HOH B 15 285 51 HOH HOH . K 4 HOH B 16 286 53 HOH HOH . K 4 HOH B 17 287 63 HOH HOH . K 4 HOH B 18 288 65 HOH HOH . K 4 HOH B 19 289 69 HOH HOH . K 4 HOH B 20 290 70 HOH HOH . K 4 HOH B 21 291 72 HOH HOH . K 4 HOH B 22 292 77 HOH HOH . K 4 HOH B 23 293 80 HOH HOH . K 4 HOH B 24 294 83 HOH HOH . K 4 HOH B 25 295 84 HOH HOH . K 4 HOH B 26 296 89 HOH HOH . K 4 HOH B 27 297 90 HOH HOH . K 4 HOH B 28 298 92 HOH HOH . K 4 HOH B 29 299 97 HOH HOH . K 4 HOH B 30 300 99 HOH HOH . K 4 HOH B 31 301 104 HOH HOH . K 4 HOH B 32 302 111 HOH HOH . K 4 HOH B 33 303 112 HOH HOH . K 4 HOH B 34 304 116 HOH HOH . K 4 HOH B 35 305 118 HOH HOH . K 4 HOH B 36 306 119 HOH HOH . K 4 HOH B 37 307 135 HOH HOH . K 4 HOH B 38 308 140 HOH HOH . L 4 HOH C 1 271 21 HOH HOH . L 4 HOH C 2 272 30 HOH HOH . L 4 HOH C 3 273 41 HOH HOH . L 4 HOH C 4 274 45 HOH HOH . L 4 HOH C 5 275 49 HOH HOH . L 4 HOH C 6 276 54 HOH HOH . L 4 HOH C 7 277 55 HOH HOH . L 4 HOH C 8 278 61 HOH HOH . L 4 HOH C 9 279 66 HOH HOH . L 4 HOH C 10 280 74 HOH HOH . L 4 HOH C 11 281 79 HOH HOH . L 4 HOH C 12 282 81 HOH HOH . L 4 HOH C 13 283 82 HOH HOH . L 4 HOH C 14 284 88 HOH HOH . L 4 HOH C 15 285 114 HOH HOH . L 4 HOH C 16 286 115 HOH HOH . L 4 HOH C 17 287 133 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 . . . F 2 10.853 36.043 -19.177 0.75 49.7 ? CM' AGO 801 B 1 HETATM 2 N N2' AGO . . . F 2 10.872 36.807 -20.438 0.75 49.76 ? N2' AGO 801 B 1 HETATM 3 C C2' AGO . . . F 2 9.732 37.174 -21.028 0.75 49.78 ? C2' AGO 801 B 1 HETATM 4 C C3' AGO . . . F 2 9.024 38.268 -20.516 0.75 50.13 ? C3' AGO 801 B 1 HETATM 5 C C4' AGO . . . F 2 7.826 38.678 -21.106 0.75 50.15 ? C4' AGO 801 B 1 HETATM 6 C C5' AGO . . . F 2 7.333 37.997 -22.219 0.75 50.03 ? C5' AGO 801 B 1 HETATM 7 C C6' AGO . . . F 2 8.038 36.908 -22.735 0.75 49.73 ? C6' AGO 801 B 1 HETATM 8 C C1' AGO . . . F 2 9.237 36.487 -22.148 0.75 49.41 ? C1' AGO 801 B 1 HETATM 9 C C' AGO . . . F 2 9.976 35.276 -22.764 0.75 48.64 ? C' AGO 801 B 1 HETATM 10 O O1' AGO . . . F 2 10.978 34.793 -22.231 0.75 48.98 ? O1' AGO 801 B 1 HETATM 11 O O3' AGO . . . F 2 9.528 34.758 -23.948 0.75 46.93 ? O3' AGO 801 B 1 HETATM 12 C C3B AGO . . . F 2 8.986 33.409 -23.885 0.75 45.11 ? C3B AGO 801 B 1 HETATM 13 C C2B AGO . . . F 2 7.877 33.194 -22.872 0.75 44.34 ? C2B AGO 801 B 1 HETATM 14 O O2' AGO . . . F 2 8.038 32.989 -21.672 0.75 43.85 ? O2' AGO 801 B 1 HETATM 15 C C4B AGO . . . F 2 8.262 33.195 -25.222 0.75 44.54 ? C4B AGO 801 B 1 HETATM 16 C C5B AGO . . . F 2 8.804 31.961 -25.938 0.75 43.88 ? C5B AGO 801 B 1 HETATM 17 O O5' AGO . . . F 2 8.637 30.793 -25.134 0.75 43.11 ? O5' AGO 801 B 1 HETATM 18 P PA AGO . . . F 2 9.458 29.465 -25.476 0.75 43.01 ? PA AGO 801 B 1 HETATM 19 O O1A AGO . . . F 2 9.077 28.41 -24.51 0.75 43.1 ? O1A AGO 801 B 1 HETATM 20 O O2A AGO . . . F 2 10.887 29.8 -25.651 0.75 43.17 ? O2A AGO 801 B 1 HETATM 21 O O3A AGO . . . F 2 8.835 29.105 -26.911 0.75 42.21 ? O3A AGO 801 B 1 HETATM 22 P PB AGO . . . F 2 9.602 28.146 -27.93 0.75 41.71 ? PB AGO 801 B 1 HETATM 23 O O1B AGO . . . F 2 8.588 27.491 -28.781 0.75 41.83 ? O1B AGO 801 B 1 HETATM 24 O O2B AGO . . . F 2 10.579 27.319 -27.191 0.75 41.4 ? O2B AGO 801 B 1 HETATM 25 N N3B AGO . . . F 2 10.391 29.254 -28.82 0.75 41.77 ? N3B AGO 801 B 1 HETATM 26 P PG AGO . . . F 2 11.308 28.592 -29.999 0.75 41.38 ? PG AGO 801 B 1 HETATM 27 O O2G AGO . . . F 2 10.301 27.922 -31.056 0.75 41.8 ? O2G AGO 801 B 1 HETATM 28 O O3G AGO . . . F 2 11.916 29.874 -30.764 0.75 41.46 ? O3G AGO 801 B 1 HETATM 29 O O1G AGO . . . F 2 12.334 27.646 -29.517 0.75 41.47 ? O1G AGO 801 B 1 HETATM 30 O O4' AGO . . . F 2 6.847 32.953 -24.966 0.75 44.04 ? O4' AGO 801 B 1 HETATM 31 C C1B AGO . . . F 2 6.539 33.282 -23.591 0.75 44.04 ? C1B AGO 801 B 1 HETATM 32 N N9 AGO . . . F 2 5.51 32.288 -23.166 0.75 43.67 ? N9 AGO 801 B 1 HETATM 33 C C8 AGO . . . F 2 5.638 30.96 -23.147 0.75 43.32 ? C8 AGO 801 B 1 HETATM 34 N N7 AGO . . . F 2 4.499 30.41 -22.723 0.75 43.06 ? N7 AGO 801 B 1 HETATM 35 C C5 AGO . . . F 2 3.635 31.389 -22.474 0.75 43.11 ? C5 AGO 801 B 1 HETATM 36 C C4 AGO . . . F 2 4.279 32.587 -22.762 0.75 43.45 ? C4 AGO 801 B 1 HETATM 37 N N3 AGO . . . F 2 3.646 33.765 -22.605 0.75 43.24 ? N3 AGO 801 B 1 HETATM 38 C C2 AGO . . . F 2 2.38 33.826 -22.166 0.75 42.86 ? C2 AGO 801 B 1 HETATM 39 N N2 AGO . . . F 2 1.794 35.011 -22.025 0.75 42.69 ? N2 AGO 801 B 1 HETATM 40 N N1 AGO . . . F 2 1.68 32.647 -21.86 0.75 42.82 ? N1 AGO 801 B 1 HETATM 41 C C6 AGO . . . F 2 2.32 31.412 -22.017 0.75 42.84 ? C6 AGO 801 B 1 HETATM 42 O O6 AGO . . . F 2 1.723 30.37 -21.755 0.75 42.72 ? O6 AGO 801 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 957 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 42 #