data_7LNG # _model_server_result.job_id SxjqId7MQM9EQlcVzgIcRg _model_server_result.datetime_utc '2024-11-08 18:54:08' _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":"C","auth_seq_id":101}' # _entry.id 7LNG # _exptl.entry_id 7LNG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 349.234 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' _entity.pdbx_number_of_molecules 4 _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 ? 2 C N N ? 2 G N N ? 2 H N N ? 2 K 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 H16 N3 O8 P' _chem_comp.formula_weight 349.234 _chem_comp.id LCC _chem_comp.mon_nstd_flag . _chem_comp.name '[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-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 O5' C5' LCC sing 199 n n O5' P LCC sing 200 n n C5' C4' LCC sing 201 n n C5' "H5'1" LCC sing 202 n n C5' "H5'2" LCC sing 203 n n C4' O4' LCC sing 204 n n C4' C3' LCC sing 205 n n C4' C6' LCC sing 206 n n O4' C1' LCC sing 207 n n C1' N1 LCC sing 208 n n C1' C2' LCC sing 209 n n C1' H1' LCC sing 210 n n N1 C6 LCC sing 211 n n N1 C2 LCC sing 212 n n C6 C5 LCC doub 213 n n C6 H6 LCC sing 214 n n C5 C5M LCC sing 215 n n C5 C4 LCC sing 216 n n C5M H5M1 LCC sing 217 n n C5M H5M2 LCC sing 218 n n C5M H5M3 LCC sing 219 n n C4 N4 LCC sing 220 n n C4 N3 LCC doub 221 n n N4 H41 LCC sing 222 n n N4 H42 LCC sing 223 n n N3 C2 LCC sing 224 n n C2 O2 LCC doub 225 n n C3' C2' LCC sing 226 n n C3' O3' LCC sing 227 n n C3' H3' LCC sing 228 n n C2' O2' LCC sing 229 n n C2' "H2'1" LCC sing 230 n n O2' C6' LCC sing 231 n n O3' H3T LCC sing 232 n n C6' "H6'1" LCC sing 233 n n C6' "H6'2" LCC sing 234 n n P O1P LCC sing 235 n n P O2P LCC doub 236 n n P OXT LCC sing 237 n n O1P H1P LCC sing 238 n n OXT HXT LCC sing 239 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 O O5' LCC . . . C 2 12.463 16.627 31.215 1 51.65 0 O5' LCC 101 A 1 HETATM 2 C C5' LCC . . . C 2 13.343 17.491 31.962 1 46.61 0 C5' LCC 101 A 1 HETATM 3 C C4' LCC . . . C 2 14.64 16.723 32.172 1 39.72 0 C4' LCC 101 A 1 HETATM 4 O O4' LCC . . . C 2 14.614 15.931 33.4 1 41.22 0 O4' LCC 101 A 1 HETATM 5 C C1' LCC . . . C 2 15.716 15.07 33.277 1 36.44 0 C1' LCC 101 A 1 HETATM 6 N N1 LCC . . . C 2 15.11 13.74 33.491 1 44.35 0 N1 LCC 101 A 1 HETATM 7 C C6 LCC . . . C 2 13.709 13.546 33.371 1 42.16 0 C6 LCC 101 A 1 HETATM 8 C C5 LCC . . . C 2 13.21 12.273 33.641 1 38.33 0 C5 LCC 101 A 1 HETATM 9 C C5M LCC . . . C 2 11.846 12.12 33.46 1 44.43 0 C5M LCC 101 A 1 HETATM 10 C C4 LCC . . . C 2 14.101 11.24 34.033 1 44.05 0 C4 LCC 101 A 1 HETATM 11 N N4 LCC . . . C 2 13.674 9.989 34.315 1 47.18 0 N4 LCC 101 A 1 HETATM 12 N N3 LCC . . . C 2 15.414 11.493 34.162 1 45.52 0 N3 LCC 101 A 1 HETATM 13 C C2 LCC . . . C 2 15.912 12.717 33.886 1 40.65 0 C2 LCC 101 A 1 HETATM 14 O O2 LCC . . . C 2 17.128 12.904 34.014 1 41.36 0 O2 LCC 101 A 1 HETATM 15 C C3' LCC . . . C 2 14.987 15.693 31.184 1 35.07 0 C3' LCC 101 A 1 HETATM 16 C C2' LCC . . . C 2 16.245 15.346 31.897 1 37.28 0 C2' LCC 101 A 1 HETATM 17 O O2' LCC . . . C 2 16.947 16.634 31.809 1 33.97 0 O2' LCC 101 A 1 HETATM 18 O O3' LCC . . . C 2 15.346 16.128 29.863 1 33.07 0 O3' LCC 101 A 1 HETATM 19 C C6' LCC . . . C 2 15.865 17.664 32.101 1 43.22 0 C6' LCC 101 A 1 HETATM 20 P P LCC . . . C 2 10.911 16.565 31.655 1 55.83 0 P LCC 101 A 1 HETATM 21 O O1P LCC . . . C 2 10.509 15.124 31.853 1 42.63 0 O1P LCC 101 A 1 HETATM 22 O O2P LCC . . . C 2 10.272 17.434 30.693 1 40.26 0 O2P LCC 101 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #