data_7LNE # _model_server_result.job_id xU8oxbsB-Yq9QWcDsClv1w _model_server_result.datetime_utc '2024-11-22 20:57:52' _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 7lne # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":101}' # _entry.id 7LNE # _exptl.entry_id 7LNE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 269.254 _entity.id 6 _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 7LNE _cell.length_a 43.408 _cell.length_b 43.408 _cell.length_c 86.554 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LNE _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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,O,P,Q,R _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 ? 6 G N N ? 6 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? covale ? covale2 A O3' C 13 A C 13 1_555 E P GAO . A GAO 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? covale ? covale3 C O3' LCC . A LCC 101 1_555 D P LCG . A LCG 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.571 ? covale ? covale4 C P LCC . A LCC 101 1_555 K O3' LCC . B LCC 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.554 ? covale ? covale5 G O3' LKC . A LKC 105 1_555 H P LCC . A LCC 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale6 H O3' LCC . A LCC 106 1_555 L P LCC . B LCC 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.588 ? covale ? covale7 B P A 5 B A 5 1_555 M O3' LCG . B LCG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.582 ? covale ? covale8 B O3' C 13 B C 13 1_555 N P GAO . B GAO 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.62 ? covale ? covale9 J O3' LKC . B LKC 101 1_555 K P LCC . B LCC 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.633 ? covale ? covale10 L O3' LCC . B LCC 103 1_555 M P LCG . B LCG 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? 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 324 n n N1 C6 LKC sing 325 n n N1 C1' LKC sing 326 n n C2 N3 LKC sing 327 n n C2 O2 LKC doub 328 n n N3 C4 LKC doub 329 n n C4 C5 LKC sing 330 n n C4 N4 LKC sing 331 n n C5 C6 LKC doub 332 n n C5 C5A LKC sing 333 n n C6 H6 LKC sing 334 n n N4 H41 LKC sing 335 n n N4 H42 LKC sing 336 n n C1' C2' LKC sing 337 n n C1' O4' LKC sing 338 n n C1' H1' LKC sing 339 n n C2' C3' LKC sing 340 n n C2' O2' LKC sing 341 n n C2' "H2'1" LKC sing 342 n n C3' C4' LKC sing 343 n n C3' O3' LKC sing 344 n n C3' H3' LKC sing 345 n n C4' O4' LKC sing 346 n n C4' C5' LKC sing 347 n n C4' C6' LKC sing 348 n n O3' H3T LKC sing 349 n n C5' O5' LKC sing 350 n n C5' "H5'1" LKC sing 351 n n C5' "H5'2" LKC sing 352 n n O5' H5T LKC sing 353 n n C5A H5M1 LKC sing 354 n n C5A H5M2 LKC sing 355 n n C5A H5M3 LKC sing 356 n n O2' C6' LKC sing 357 n n C6' "H6'1" LKC sing 358 n n C6' "H6'2" LKC sing 359 n n # _atom_sites.entry_id 7LNE _atom_sites.fract_transf_matrix[1][1] 0.023037 _atom_sites.fract_transf_matrix[1][2] 0.013301 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026601 _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] 0.011553 _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 GAO A 1 103 14 GAO ANG . F 5 GP3 A 1 104 101 GP3 GP3 . G 6 LKC A 1 105 1 LKC LCC . H 2 LCC A 1 106 2 LCC LCC . I 7 SO4 A 1 107 1 SO4 SO4 . J 6 LKC B 1 101 1 LKC LCC . K 2 LCC B 1 102 2 LCC LCC . L 2 LCC B 1 103 3 LCC LCC . M 3 LCG B 1 104 4 LCG LCG . N 4 GAO B 1 105 14 GAO ANG . O 5 GP3 B 1 106 101 GP3 GP3 . P 7 SO4 B 1 107 2 SO4 SO4 . Q 8 HOH A 1 201 101 HOH HOH . Q 8 HOH A 2 202 104 HOH HOH . Q 8 HOH A 3 203 64 HOH HOH . Q 8 HOH A 4 204 56 HOH HOH . Q 8 HOH A 5 205 50 HOH HOH . Q 8 HOH A 6 206 38 HOH HOH . Q 8 HOH A 7 207 80 HOH HOH . Q 8 HOH A 8 208 55 HOH HOH . Q 8 HOH A 9 209 84 HOH HOH . Q 8 HOH A 10 210 13 HOH HOH . Q 8 HOH A 11 211 36 HOH HOH . Q 8 HOH A 12 212 53 HOH HOH . Q 8 HOH A 13 213 44 HOH HOH . Q 8 HOH A 14 214 71 HOH HOH . Q 8 HOH A 15 215 76 HOH HOH . Q 8 HOH A 16 216 94 HOH HOH . Q 8 HOH A 17 217 59 HOH HOH . Q 8 HOH A 18 218 60 HOH HOH . Q 8 HOH A 19 219 85 HOH HOH . Q 8 HOH A 20 220 82 HOH HOH . Q 8 HOH A 21 221 29 HOH HOH . Q 8 HOH A 22 222 47 HOH HOH . Q 8 HOH A 23 223 105 HOH HOH . Q 8 HOH A 24 224 15 HOH HOH . Q 8 HOH A 25 225 63 HOH HOH . Q 8 HOH A 26 226 92 HOH HOH . Q 8 HOH A 27 227 14 HOH HOH . Q 8 HOH A 28 228 93 HOH HOH . Q 8 HOH A 29 229 28 HOH HOH . Q 8 HOH A 30 230 91 HOH HOH . Q 8 HOH A 31 231 54 HOH HOH . Q 8 HOH A 32 232 61 HOH HOH . Q 8 HOH A 33 233 41 HOH HOH . Q 8 HOH A 34 234 65 HOH HOH . Q 8 HOH A 35 235 96 HOH HOH . Q 8 HOH A 36 236 107 HOH HOH . Q 8 HOH A 37 237 16 HOH HOH . Q 8 HOH A 38 238 57 HOH HOH . Q 8 HOH A 39 239 97 HOH HOH . Q 8 HOH A 40 240 69 HOH HOH . Q 8 HOH A 41 241 45 HOH HOH . Q 8 HOH A 42 242 30 HOH HOH . Q 8 HOH A 43 243 46 HOH HOH . Q 8 HOH A 44 244 78 HOH HOH . Q 8 HOH A 45 245 52 HOH HOH . Q 8 HOH A 46 246 100 HOH HOH . Q 8 HOH A 47 247 11 HOH HOH . Q 8 HOH A 48 248 48 HOH HOH . Q 8 HOH A 49 249 83 HOH HOH . Q 8 HOH A 50 250 35 HOH HOH . Q 8 HOH A 51 251 40 HOH HOH . Q 8 HOH A 52 252 34 HOH HOH . Q 8 HOH A 53 253 37 HOH HOH . Q 8 HOH A 54 254 43 HOH HOH . Q 8 HOH A 55 255 33 HOH HOH . Q 8 HOH A 56 256 99 HOH HOH . Q 8 HOH A 57 257 77 HOH HOH . Q 8 HOH A 58 258 17 HOH HOH . Q 8 HOH A 59 259 49 HOH HOH . Q 8 HOH A 60 260 87 HOH HOH . Q 8 HOH A 61 261 90 HOH HOH . Q 8 HOH A 62 262 98 HOH HOH . Q 8 HOH A 63 263 51 HOH HOH . Q 8 HOH A 64 264 42 HOH HOH . R 8 HOH B 1 201 20 HOH HOH . R 8 HOH B 2 202 4 HOH HOH . R 8 HOH B 3 203 32 HOH HOH . R 8 HOH B 4 204 106 HOH HOH . R 8 HOH B 5 205 75 HOH HOH . R 8 HOH B 6 206 66 HOH HOH . R 8 HOH B 7 207 67 HOH HOH . R 8 HOH B 8 208 24 HOH HOH . R 8 HOH B 9 209 25 HOH HOH . R 8 HOH B 10 210 81 HOH HOH . R 8 HOH B 11 211 73 HOH HOH . R 8 HOH B 12 212 102 HOH HOH . R 8 HOH B 13 213 31 HOH HOH . R 8 HOH B 14 214 58 HOH HOH . R 8 HOH B 15 215 86 HOH HOH . R 8 HOH B 16 216 7 HOH HOH . R 8 HOH B 17 217 79 HOH HOH . R 8 HOH B 18 218 27 HOH HOH . R 8 HOH B 19 219 5 HOH HOH . R 8 HOH B 20 220 74 HOH HOH . R 8 HOH B 21 221 72 HOH HOH . R 8 HOH B 22 222 26 HOH HOH . R 8 HOH B 23 223 19 HOH HOH . R 8 HOH B 24 224 6 HOH HOH . R 8 HOH B 25 225 21 HOH HOH . R 8 HOH B 26 226 8 HOH HOH . R 8 HOH B 27 227 62 HOH HOH . R 8 HOH B 28 228 10 HOH HOH . R 8 HOH B 29 229 3 HOH HOH . R 8 HOH B 30 230 2 HOH HOH . R 8 HOH B 31 231 39 HOH HOH . R 8 HOH B 32 232 22 HOH HOH . R 8 HOH B 33 233 18 HOH HOH . R 8 HOH B 34 234 95 HOH HOH . R 8 HOH B 35 235 12 HOH HOH . R 8 HOH B 36 236 68 HOH HOH . R 8 HOH B 37 237 103 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 LKC . . . J 6 25.06 1.763 1.74 1 25.79 0 N1 LKC 101 B 1 HETATM 2 C C2 LKC . . . J 6 24.631 0.462 1.723 1 28.05 0 C2 LKC 101 B 1 HETATM 3 N N3 LKC . . . J 6 25.418 -0.578 1.773 1 29.36 0 N3 LKC 101 B 1 HETATM 4 C C4 LKC . . . J 6 26.735 -0.33 1.799 1 35.71 0 C4 LKC 101 B 1 HETATM 5 C C5 LKC . . . J 6 27.276 0.948 1.827 1 31.23 0 C5 LKC 101 B 1 HETATM 6 C C6 LKC . . . J 6 26.437 2.083 1.797 1 33.02 0 C6 LKC 101 B 1 HETATM 7 O O2 LKC . . . J 6 23.471 0.104 1.691 1 27.55 0 O2 LKC 101 B 1 HETATM 8 N N4 LKC . . . J 6 27.601 -1.325 1.834 1 31.39 0 N4 LKC 101 B 1 HETATM 9 C C1' LKC . . . J 6 24.033 2.825 1.702 1 28.75 0 C1' LKC 101 B 1 HETATM 10 C C2' LKC . . . J 6 23.353 3.063 3.038 1 25.51 0 C2' LKC 101 B 1 HETATM 11 C C3' LKC . . . J 6 24.271 4.039 3.593 1 28.83 0 C3' LKC 101 B 1 HETATM 12 C C4' LKC . . . J 6 24.127 4.967 2.476 1 29.88 0 C4' LKC 101 B 1 HETATM 13 O O4' LKC . . . J 6 24.52 4.153 1.387 1 31.02 0 O4' LKC 101 B 1 HETATM 14 O O3' LKC . . . J 6 23.745 4.673 4.835 1 30.67 0 O3' LKC 101 B 1 HETATM 15 C C5' LKC . . . J 6 24.982 6.213 2.707 1 33.02 0 C5' LKC 101 B 1 HETATM 16 O O5' LKC . . . J 6 26.322 5.662 2.821 1 35.28 0 O5' LKC 101 B 1 HETATM 17 C C5A LKC . . . J 6 28.665 1.019 1.884 1 35.77 0 C5A LKC 101 B 1 HETATM 18 O O2' LKC . . . J 6 22.134 3.816 2.734 1 26.96 0 O2' LKC 101 B 1 HETATM 19 C C6' LKC . . . J 6 22.594 5.222 2.335 1 27.81 0 C6' LKC 101 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #