data_7LNG # _model_server_result.job_id 85lUGIBYKqPpQisypM2IrQ _model_server_result.datetime_utc '2024-11-24 14:00:55' _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":"D","auth_seq_id":102}' # _entry.id 7LNG # _exptl.entry_id 7LNG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 375.231 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' _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 ? 3 D N N ? 3 M 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 H14 N5 O8 P' _chem_comp.formula_weight 375.231 _chem_comp.id LCG _chem_comp.mon_nstd_flag n _chem_comp.name '[(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' _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 P OP1 LCG doub 240 n n P O5' LCG sing 241 n n P OP2 LCG sing 242 n n P OP3 LCG sing 243 n n O5' C5' LCG sing 244 n n C5' C4' LCG sing 245 n n C5' H5' LCG sing 246 n n C5' "H5''" LCG sing 247 n n C3' C2' LCG sing 248 n n C3' C4' LCG sing 249 n n C3' O3' LCG sing 250 n n C3' H3' LCG sing 251 n n C6' C4' LCG sing 252 n n C6' O2' LCG sing 253 n n C6' "H6'1" LCG sing 254 n n C6' "H6'2" LCG sing 255 n n N9 C8 LCG sing 256 n y N9 C4 LCG sing 257 n y N9 C1' LCG sing 258 n n C8 N7 LCG doub 259 n y C8 H8 LCG sing 260 n n C4 C5 LCG doub 261 n y C4 N3 LCG sing 262 n n N7 C5 LCG sing 263 n y C5 C6 LCG sing 264 n n C6 O6 LCG doub 265 n n C6 N1 LCG sing 266 n n C2' C1' LCG sing 267 n n C2' O2' LCG sing 268 n n C2' H2' LCG sing 269 n n C4' O4' LCG sing 270 n n C1' O4' LCG sing 271 n n C1' H1' LCG sing 272 n n C2 N1 LCG sing 273 n n C2 N2 LCG sing 274 n n C2 N3 LCG doub 275 n n N1 H1 LCG sing 276 n n OP2 HOP2 LCG sing 277 n n N2 H21 LCG sing 278 n n N2 H22 LCG sing 279 n n O3' HO3' LCG sing 280 n n OP3 HOP3 LCG sing 281 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 P P LCG . . . D 3 15.16 15.276 28.516 1 41.58 0 P LCG 102 A 1 HETATM 2 O OP1 LCG . . . D 3 15.413 16.373 27.529 1 39.06 0 OP1 LCG 102 A 1 HETATM 3 O O5' LCG . . . D 3 16.389 14.251 28.555 1 42.28 0 O5' LCG 102 A 1 HETATM 4 C C5' LCG . . . D 3 17.751 14.711 28.733 1 41.95 0 C5' LCG 102 A 1 HETATM 5 C C3' LCG . . . D 3 18.257 12.348 28.144 1 38.42 0 C3' LCG 102 A 1 HETATM 6 C C6' LCG . . . D 3 20.061 13.738 28.737 1 44.9 0 C6' LCG 102 A 1 HETATM 7 N N9 LCG . . . D 3 17.531 10.89 30.66 1 37.89 0 N9 LCG 102 A 1 HETATM 8 C C8 LCG . . . D 3 16.244 11.261 30.632 1 36.11 0 C8 LCG 102 A 1 HETATM 9 C C4 LCG . . . D 3 17.552 9.642 31.14 1 36.09 0 C4 LCG 102 A 1 HETATM 10 N N7 LCG . . . D 3 15.489 10.256 31.118 1 34.44 0 N7 LCG 102 A 1 HETATM 11 C C5 LCG . . . D 3 16.297 9.249 31.414 1 34 0 C5 LCG 102 A 1 HETATM 12 C C6 LCG . . . D 3 16.058 8.047 31.924 1 44.36 0 C6 LCG 102 A 1 HETATM 13 C C2' LCG . . . D 3 19.255 11.499 28.832 1 37.98 0 C2' LCG 102 A 1 HETATM 14 O O6 LCG . . . D 3 14.915 7.689 32.196 1 46.43 0 O6 LCG 102 A 1 HETATM 15 C C4' LCG . . . D 3 18.61 13.498 28.99 1 40.31 0 C4' LCG 102 A 1 HETATM 16 C C1' LCG . . . D 3 18.782 11.603 30.267 1 39.53 0 C1' LCG 102 A 1 HETATM 17 C C2 LCG . . . D 3 18.439 7.629 31.825 1 38.52 0 C2 LCG 102 A 1 HETATM 18 N N1 LCG . . . D 3 17.136 7.18 32.155 1 41.04 0 N1 LCG 102 A 1 HETATM 19 O O4' LCG . . . D 3 18.397 13.001 30.35 1 39.13 0 O4' LCG 102 A 1 HETATM 20 O OP2 LCG . . . D 3 13.876 14.44 28.539 1 35.44 0 OP2 LCG 102 A 1 HETATM 21 N N2 LCG . . . D 3 19.511 6.879 32.008 1 40.55 0 N2 LCG 102 A 1 HETATM 22 N N3 LCG . . . D 3 18.607 8.844 31.322 1 31.92 0 N3 LCG 102 A 1 HETATM 23 O O2' LCG . . . D 3 20.49 12.29 28.656 1 44.88 0 O2' LCG 102 A 1 HETATM 24 O O3' LCG . . . D 3 18.528 12.6 26.717 1 36.89 0 O3' LCG 102 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #