data_7LNG # _model_server_result.job_id I8BcaQjEuChovmn33YY2Mg _model_server_result.datetime_utc '2024-11-08 19:12:07' _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 7lng # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":104}' # _entry.id 7LNG # _exptl.entry_id 7LNG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 269.254 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-AMINO-1-[(1S,3R,4R,7S)-7-HYDROXY-1-(HYDROXYMETHYL)-2,5-DIOXABICYCLO[2.2.1]HEPT-3-YL]-5-METHYLPYRIMIDIN-2(1H)-ONE _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 90 _cell.angle_gamma 120 _cell.entry_id 7LNG _cell.length_a 45.165 _cell.length_b 45.165 _cell.length_c 82.831 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LNG _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 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,F,G,H,I,J,K,L,M,N _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 ? 5 F N N ? 5 J 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 P A 5 A A 5 1_555 D O3' LCG . A LCG 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.646 ? covale ? covale2 A O3' C 13 A C 13 1_555 E P TG . A TG 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.634 ? covale ? covale3 C O3' LCC . A LCC 101 1_555 D P LCG . A LCG 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? covale ? covale4 C P LCC . A LCC 101 1_555 K O3' LCC . B LCC 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.643 ? covale ? covale5 F O3' LKC . A LKC 104 1_555 G P LCC . A LCC 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.612 ? covale ? covale6 G O3' LCC . A LCC 105 1_555 H P LCC . A LCC 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.65 ? covale ? covale7 H O3' LCC . A LCC 106 1_555 M P LCG . B LCG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.684 ? covale ? covale8 B P A 5 B A 5 1_555 M O3' LCG . B LCG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.62 ? covale ? covale9 B O3' C 13 B C 13 1_555 N P TG . B TG 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale10 J O3' LKC . B LKC 101 1_555 K P LCC . B LCC 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.64 ? hydrog WATSON-CRICK hydrog1 A N1 A 5 A A 5 1_555 B N3 U 12 B U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N6 A 5 A A 5 1_555 B O4 U 12 B U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N3 C 6 A C 6 1_555 B N1 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N4 C 6 A C 6 1_555 B O6 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O2 C 6 A C 6 1_555 B N2 G 11 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 U 7 A U 7 1_555 B N1 A 10 B A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O4 U 7 A U 7 1_555 B N6 A 10 B A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 U 8 A U 8 1_555 B N1 A 9 B A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O4 U 8 A U 8 1_555 B N6 A 9 B A 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 A 9 A A 9 1_555 B N3 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N6 A 9 A A 9 1_555 B O4 U 8 B U 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 A 10 A A 10 1_555 B N3 U 7 B U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N6 A 10 A A 10 1_555 B O4 U 7 B U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 G 11 A G 11 1_555 B N3 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N2 G 11 A G 11 1_555 B O2 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O6 G 11 A G 11 1_555 B N4 C 6 B C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N3 U 12 A U 12 1_555 B N1 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O4 U 12 A U 12 1_555 B N6 A 5 B A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C11 H15 N3 O5' _chem_comp.formula_weight 269.254 _chem_comp.id LKC _chem_comp.mon_nstd_flag . _chem_comp.name 4-AMINO-1-[(1S,3R,4R,7S)-7-HYDROXY-1-(HYDROXYMETHYL)-2,5-DIOXABICYCLO[2.2.1]HEPT-3-YL]-5-METHYLPYRIMIDIN-2(1H)-ONE _chem_comp.type 'rna 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 N1 C2 LKC sing 282 n n N1 C6 LKC sing 283 n n N1 C1' LKC sing 284 n n C2 N3 LKC sing 285 n n C2 O2 LKC doub 286 n n N3 C4 LKC doub 287 n n C4 C5 LKC sing 288 n n C4 N4 LKC sing 289 n n C5 C6 LKC doub 290 n n C5 C5A LKC sing 291 n n C6 H6 LKC sing 292 n n N4 H41 LKC sing 293 n n N4 H42 LKC sing 294 n n C1' C2' LKC sing 295 n n C1' O4' LKC sing 296 n n C1' H1' LKC sing 297 n n C2' C3' LKC sing 298 n n C2' O2' LKC sing 299 n n C2' "H2'1" LKC sing 300 n n C3' C4' LKC sing 301 n n C3' O3' LKC sing 302 n n C3' H3' LKC sing 303 n n C4' O4' LKC sing 304 n n C4' C5' LKC sing 305 n n C4' C6' LKC sing 306 n n O3' H3T LKC sing 307 n n C5' O5' LKC sing 308 n n C5' "H5'1" LKC sing 309 n n C5' "H5'2" LKC sing 310 n n O5' H5T LKC sing 311 n n C5A H5M1 LKC sing 312 n n C5A H5M2 LKC sing 313 n n C5A H5M3 LKC sing 314 n n O2' C6' LKC sing 315 n n C6' "H6'1" LKC sing 316 n n C6' "H6'2" LKC sing 317 n n # _atom_sites.entry_id 7LNG _atom_sites.fract_transf_matrix[1][1] 0.022141 _atom_sites.fract_transf_matrix[1][2] 0.012783 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025566 _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] 0.012073 _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 C 2 LCC A 1 101 3 LCC LCC . D 3 LCG A 1 102 4 LCG LCG . E 4 TG A 1 103 14 TG TG . F 5 LKC A 1 104 1 LKC LCC . G 2 LCC A 1 105 2 LCC LCC . H 2 LCC A 1 106 3 LCC LCC . I 6 GP3 A 1 107 101 GP3 GP3 . J 5 LKC B 1 101 1 LKC LCC . K 2 LCC B 1 102 2 LCC LCC . L 6 GP3 B 1 103 101 GP3 GP3 . M 3 LCG B 1 104 4 LCG LCG . N 4 TG B 1 105 14 TG TG . # 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 LKC . . . F 5 19.641 -2.318 1.888 1 103.12 0 N1 LKC 104 A 1 HETATM 2 C C2 LKC . . . F 5 19.773 -0.986 1.711 1 101.15 0 C2 LKC 104 A 1 HETATM 3 N N3 LKC . . . F 5 18.725 -0.155 1.814 1 98.74 0 N3 LKC 104 A 1 HETATM 4 C C4 LKC . . . F 5 17.497 -0.619 2.098 1 106.88 0 C4 LKC 104 A 1 HETATM 5 C C5 LKC . . . F 5 17.286 -1.981 2.291 1 112.26 0 C5 LKC 104 A 1 HETATM 6 C C6 LKC . . . F 5 18.37 -2.84 2.187 1 105.97 0 C6 LKC 104 A 1 HETATM 7 O O2 LKC . . . F 5 20.863 -0.484 1.456 1 103.92 0 O2 LKC 104 A 1 HETATM 8 N N4 LKC . . . F 5 16.434 0.191 2.205 1 100.75 0 N4 LKC 104 A 1 HETATM 9 C C1' LKC . . . F 5 20.795 -3.271 1.762 1 107.83 0 C1' LKC 104 A 1 HETATM 10 C C2' LKC . . . F 5 22.002 -2.97 2.612 1 107.72 0 C2' LKC 104 A 1 HETATM 11 C C3' LKC . . . F 5 21.356 -3.196 3.902 1 110.9 0 C3' LKC 104 A 1 HETATM 12 C C4' LKC . . . F 5 21.081 -4.637 3.578 1 109.68 0 C4' LKC 104 A 1 HETATM 13 O O4' LKC . . . F 5 20.365 -4.547 2.312 1 112.39 0 O4' LKC 104 A 1 HETATM 14 O O3' LKC . . . F 5 22.279 -3.004 4.973 1 113.98 0 O3' LKC 104 A 1 HETATM 15 C C5' LKC . . . F 5 20.267 -5.282 4.684 1 101.31 0 C5' LKC 104 A 1 HETATM 16 O O5' LKC . . . F 5 19.167 -5.869 3.987 1 88.99 0 O5' LKC 104 A 1 HETATM 17 C C5A LKC . . . F 5 16.023 -2.487 2.584 1 119 0 C5A LKC 104 A 1 HETATM 18 O O2' LKC . . . F 5 22.984 -4.072 2.5 1 105.79 0 O2' LKC 104 A 1 HETATM 19 C C6' LKC . . . F 5 22.478 -5.227 3.293 1 108.74 0 C6' LKC 104 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #