data_5HBY # _model_server_result.job_id OxIraF1rWqRzZ0YSViEjFQ _model_server_result.datetime_utc '2024-11-08 04:40:16' _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 5hby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":101}' # _entry.id 5HBY # _exptl.entry_id 5HBY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.309 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-(3-methyl-1~{H}-pyrazol-4-yl)phosphinic acid' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 122.03 _cell.angle_gamma 90 _cell.entry_id 5HBY _cell.length_a 45.873 _cell.length_b 31.987 _cell.length_c 33.426 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HBY _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 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 B N N ? 2 C 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 covale ? covale1 A O3' LCC 1 A LCC 1 1_555 A P LCC 2 A LCC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.667 ? covale ? covale2 A O3' LCC 2 A LCC 2 1_555 A P LCC 3 A LCC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.62 ? covale ? covale3 A O3' LCC 3 A LCC 3 1_555 A P LCG 4 A LCG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.66 ? covale ? covale4 A O3' LCG 4 A LCG 4 1_555 A P A 5 A A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.623 ? metalc ? metalc1 D MG MG . A MG 103 1_555 E O HOH . A HOH 211 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc2 D MG MG . A MG 103 1_555 E O HOH . A HOH 219 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc3 D MG MG . A MG 103 1_555 E O HOH . A HOH 220 2_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc4 D MG MG . A MG 103 1_555 E O HOH . A HOH 230 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc5 D MG MG . A MG 103 1_555 E O HOH . A HOH 239 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc6 D MG MG . A MG 103 1_555 E O HOH . A HOH 263 2_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? hydrog WATSON-CRICK hydrog1 A N1 LCG 4 A LCG 4 1_555 A N3 C 13 A C 13 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 LCG 4 A LCG 4 1_555 A O2 C 13 A C 13 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 LCG 4 A LCG 4 1_555 A N4 C 13 A C 13 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 A 5 A A 5 1_555 A N3 U 12 A U 12 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 A 5 A A 5 1_555 A O4 U 12 A U 12 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 C 6 A C 6 1_555 A N1 G 11 A G 11 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N4 C 6 A C 6 1_555 A O6 G 11 A G 11 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O2 C 6 A C 6 1_555 A N2 G 11 A G 11 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 U 7 A U 7 1_555 A N1 A 10 A A 10 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O4 U 7 A U 7 1_555 A N6 A 10 A A 10 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 U 8 A U 8 1_555 A N1 A 9 A A 9 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O4 U 8 A U 8 1_555 A N6 A 9 A A 9 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N1 A 9 A A 9 1_555 A N3 U 8 A U 8 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N6 A 9 A A 9 1_555 A O4 U 8 A U 8 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 A 10 A A 10 1_555 A N3 U 7 A U 7 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N6 A 10 A A 10 1_555 A O4 U 7 A U 7 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 G 11 A G 11 1_555 A N3 C 6 A C 6 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N2 G 11 A G 11 1_555 A O2 C 6 A C 6 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O6 G 11 A G 11 1_555 A N4 C 6 A C 6 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N3 U 12 A U 12 1_555 A N1 A 5 A A 5 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A O4 U 12 A U 12 1_555 A N6 A 5 A A 5 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N3 C 13 A C 13 1_555 A N1 LCG 4 A LCG 4 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N4 C 13 A C 13 1_555 A O6 LCG 4 A LCG 4 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O2 C 13 A C 13 1_555 A N2 LCG 4 A LCG 4 2_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C14 H18 N7 O7 P' _chem_comp.formula_weight 427.309 _chem_comp.id PZG _chem_comp.mon_nstd_flag n _chem_comp.name '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-(3-methyl-1~{H}-pyrazol-4-yl)phosphinic acid' _chem_comp.type 'dna linking' _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 O4 C8 PZG sing 201 n n C8 C9 PZG sing 202 n n C8 C7 PZG sing 203 n n C9 C10 PZG sing 204 n n C9 O2 PZG sing 205 n n C10 O5 PZG sing 206 n n O3 C7 PZG sing 207 n n O6 P1 PZG doub 208 n n C12 N6 PZG sing 209 n y C12 C11 PZG doub 210 n y C7 C6 PZG sing 211 n n N6 N7 PZG sing 212 n y O2 C6 PZG sing 213 n n O5 P1 PZG sing 214 n n C6 N5 PZG sing 215 n n P1 C11 PZG sing 216 n n P1 O7 PZG sing 217 n n C11 C13 PZG sing 218 n y N7 C13 PZG doub 219 n y C13 C14 PZG sing 220 n n N5 C3 PZG sing 221 n y N5 C5 PZG sing 222 n y N3 C3 PZG sing 223 n n N3 C2 PZG doub 224 n n C3 C4 PZG doub 225 n y C5 N4 PZG doub 226 n y N2 C2 PZG sing 227 n n C2 N1 PZG sing 228 n n C4 N4 PZG sing 229 n y C4 C1 PZG sing 230 n n N1 C1 PZG sing 231 n n C1 O1 PZG doub 232 n n N1 H1 PZG sing 233 n n N2 H2 PZG sing 234 n n N2 H3 PZG sing 235 n n C5 H4 PZG sing 236 n n C6 H5 PZG sing 237 n n C7 H6 PZG sing 238 n n O3 H7 PZG sing 239 n n C8 H8 PZG sing 240 n n O4 H9 PZG sing 241 n n C9 H10 PZG sing 242 n n C10 H11 PZG sing 243 n n C10 H12 PZG sing 244 n n O7 H13 PZG sing 245 n n C12 H14 PZG sing 246 n n N6 H15 PZG sing 247 n n C14 H16 PZG sing 248 n n C14 H17 PZG sing 249 n n C14 H18 PZG sing 250 n n # _atom_sites.entry_id 5HBY _atom_sites.fract_transf_matrix[1][1] 0.021799 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.01364 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.031263 _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] 0.03529 _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 PZG A 1 101 1 PZG PZG . C 2 PZG A 1 102 2 PZG PZG . D 3 MG A 1 103 1 MG MG . E 4 HOH A 1 201 63 HOH HOH . E 4 HOH A 2 202 2 HOH HOH . E 4 HOH A 3 203 72 HOH HOH . E 4 HOH A 4 204 48 HOH HOH . E 4 HOH A 5 205 52 HOH HOH . E 4 HOH A 6 206 24 HOH HOH . E 4 HOH A 7 207 17 HOH HOH . E 4 HOH A 8 208 62 HOH HOH . E 4 HOH A 9 209 3 HOH HOH . E 4 HOH A 10 210 23 HOH HOH . E 4 HOH A 11 211 7 HOH HOH . E 4 HOH A 12 212 47 HOH HOH . E 4 HOH A 13 213 60 HOH HOH . E 4 HOH A 14 214 75 HOH HOH . E 4 HOH A 15 215 12 HOH HOH . E 4 HOH A 16 216 57 HOH HOH . E 4 HOH A 17 217 16 HOH HOH . E 4 HOH A 18 218 36 HOH HOH . E 4 HOH A 19 219 9 HOH HOH . E 4 HOH A 20 220 10 HOH HOH . E 4 HOH A 21 221 45 HOH HOH . E 4 HOH A 22 222 66 HOH HOH . E 4 HOH A 23 223 1 HOH HOH . E 4 HOH A 24 224 37 HOH HOH . E 4 HOH A 25 225 29 HOH HOH . E 4 HOH A 26 226 5 HOH HOH . E 4 HOH A 27 227 41 HOH HOH . E 4 HOH A 28 228 22 HOH HOH . E 4 HOH A 29 229 44 HOH HOH . E 4 HOH A 30 230 11 HOH HOH . E 4 HOH A 31 231 67 HOH HOH . E 4 HOH A 32 232 43 HOH HOH . E 4 HOH A 33 233 50 HOH HOH . E 4 HOH A 34 234 25 HOH HOH . E 4 HOH A 35 235 21 HOH HOH . E 4 HOH A 36 236 73 HOH HOH . E 4 HOH A 37 237 15 HOH HOH . E 4 HOH A 38 238 59 HOH HOH . E 4 HOH A 39 239 6 HOH HOH . E 4 HOH A 40 240 38 HOH HOH . E 4 HOH A 41 241 46 HOH HOH . E 4 HOH A 42 242 18 HOH HOH . E 4 HOH A 43 243 68 HOH HOH . E 4 HOH A 44 244 49 HOH HOH . E 4 HOH A 45 245 53 HOH HOH . E 4 HOH A 46 246 35 HOH HOH . E 4 HOH A 47 247 71 HOH HOH . E 4 HOH A 48 248 14 HOH HOH . E 4 HOH A 49 249 27 HOH HOH . E 4 HOH A 50 250 61 HOH HOH . E 4 HOH A 51 251 30 HOH HOH . E 4 HOH A 52 252 13 HOH HOH . E 4 HOH A 53 253 32 HOH HOH . E 4 HOH A 54 254 4 HOH HOH . E 4 HOH A 55 255 56 HOH HOH . E 4 HOH A 56 256 20 HOH HOH . E 4 HOH A 57 257 19 HOH HOH . E 4 HOH A 58 258 54 HOH HOH . E 4 HOH A 59 259 51 HOH HOH . E 4 HOH A 60 260 55 HOH HOH . E 4 HOH A 61 261 58 HOH HOH . E 4 HOH A 62 262 28 HOH HOH . E 4 HOH A 63 263 8 HOH HOH . E 4 HOH A 64 264 31 HOH HOH . E 4 HOH A 65 265 69 HOH HOH . E 4 HOH A 66 266 26 HOH HOH . E 4 HOH A 67 267 70 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 O O1 PZG . . . B 2 -22.521 -17.144 -13.745 1 11.59 ? O1 PZG 101 A 1 HETATM 2 C C1 PZG . . . B 2 -21.484 -16.929 -14.407 1 10.17 ? C1 PZG 101 A 1 HETATM 3 N N1 PZG . . . B 2 -20.916 -18.017 -15.024 1 10.12 ? N1 PZG 101 A 1 HETATM 4 C C2 PZG . . . B 2 -19.8 -17.939 -15.813 1 10.05 ? C2 PZG 101 A 1 HETATM 5 N N2 PZG . . . B 2 -19.363 -19.109 -16.324 1 9.97 ? N2 PZG 101 A 1 HETATM 6 N N3 PZG . . . B 2 -19.175 -16.837 -16.09 1 10.01 ? N3 PZG 101 A 1 HETATM 7 C C3 PZG . . . B 2 -19.764 -15.736 -15.519 1 9.98 ? C3 PZG 101 A 1 HETATM 8 C C4 PZG . . . B 2 -20.851 -15.77 -14.68 1 9.91 ? C4 PZG 101 A 1 HETATM 9 N N4 PZG . . . B 2 -21.114 -14.474 -14.254 1 10.73 ? N4 PZG 101 A 1 HETATM 10 C C5 PZG . . . B 2 -20.198 -13.753 -14.808 1 10.42 ? C5 PZG 101 A 1 HETATM 11 N N5 PZG . . . B 2 -19.337 -14.479 -15.601 1 10.21 ? N5 PZG 101 A 1 HETATM 12 C C6 PZG . . . B 2 -18.136 -14.017 -16.259 1 11.28 ? C6 PZG 101 A 1 HETATM 13 O O2 PZG . . . B 2 -17.757 -12.763 -15.651 1 11.92 ? O2 PZG 101 A 1 HETATM 14 C C7 PZG . . . B 2 -18.326 -13.8 -17.796 1 11.79 ? C7 PZG 101 A 1 HETATM 15 O O3 PZG . . . B 2 -17.033 -13.985 -18.373 1 12.01 ? O3 PZG 101 A 1 HETATM 16 C C8 PZG . . . B 2 -18.716 -12.348 -17.781 1 12.09 ? C8 PZG 101 A 1 HETATM 17 O O4 PZG . . . B 2 -18.456 -11.691 -19.027 1 14.95 ? O4 PZG 101 A 1 HETATM 18 C C9 PZG . . . B 2 -17.811 -11.756 -16.706 1 12.81 ? C9 PZG 101 A 1 HETATM 19 C C10 PZG . . . B 2 -18.359 -10.489 -16.092 1 13.52 ? C10 PZG 101 A 1 HETATM 20 O O5 PZG . . . B 2 -19.741 -10.585 -15.817 1 12.68 ? O5 PZG 101 A 1 HETATM 21 P P1 PZG . . . B 2 -20.527 -9.454 -15.043 1 12.67 ? P1 PZG 101 A 1 HETATM 22 O O6 PZG . . . B 2 -19.976 -8.124 -15.433 1 14.07 ? O6 PZG 101 A 1 HETATM 23 O O7 PZG . . . B 2 -21.938 -9.714 -15.309 1 12.86 ? O7 PZG 101 A 1 HETATM 24 C C11 PZG . . . B 2 -20.193 -9.754 -13.256 1 13.47 ? C11 PZG 101 A 1 HETATM 25 C C12 PZG . . . B 2 -19.225 -9.099 -12.556 1 14.62 ? C12 PZG 101 A 1 HETATM 26 N N6 PZG . . . B 2 -19.329 -9.564 -11.331 1 15.27 ? N6 PZG 101 A 1 HETATM 27 N N7 PZG . . . B 2 -20.27 -10.475 -11.229 1 13.67 ? N7 PZG 101 A 1 HETATM 28 C C13 PZG . . . B 2 -20.841 -10.589 -12.403 1 12.74 ? C13 PZG 101 A 1 HETATM 29 C C14 PZG . . . B 2 -22.032 -11.469 -12.594 1 13.36 ? C14 PZG 101 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 29 #