data_7LNE # _model_server_result.job_id Yb7Gw3sjq7JoxiXXbSpQLQ _model_server_result.datetime_utc '2024-11-22 20:45:12' _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":"C","auth_seq_id":101}' # _entry.id 7LNE # _exptl.entry_id 7LNE _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 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 ? 2 C N N ? 2 H N N ? 2 K N N ? 2 L 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 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 241 n n O5' P LCC sing 242 n n C5' C4' LCC sing 243 n n C5' "H5'1" LCC sing 244 n n C5' "H5'2" LCC sing 245 n n C4' O4' LCC sing 246 n n C4' C3' LCC sing 247 n n C4' C6' LCC sing 248 n n O4' C1' LCC sing 249 n n C1' N1 LCC sing 250 n n C1' C2' LCC sing 251 n n C1' H1' LCC sing 252 n n N1 C6 LCC sing 253 n n N1 C2 LCC sing 254 n n C6 C5 LCC doub 255 n n C6 H6 LCC sing 256 n n C5 C5M LCC sing 257 n n C5 C4 LCC sing 258 n n C5M H5M1 LCC sing 259 n n C5M H5M2 LCC sing 260 n n C5M H5M3 LCC sing 261 n n C4 N4 LCC sing 262 n n C4 N3 LCC doub 263 n n N4 H41 LCC sing 264 n n N4 H42 LCC sing 265 n n N3 C2 LCC sing 266 n n C2 O2 LCC doub 267 n n C3' C2' LCC sing 268 n n C3' O3' LCC sing 269 n n C3' H3' LCC sing 270 n n C2' O2' LCC sing 271 n n C2' "H2'1" LCC sing 272 n n O2' C6' LCC sing 273 n n O3' H3T LCC sing 274 n n C6' "H6'1" LCC sing 275 n n C6' "H6'2" LCC sing 276 n n P O1P LCC sing 277 n n P O2P LCC doub 278 n n P OXT LCC sing 279 n n O1P H1P LCC sing 280 n n OXT HXT LCC sing 281 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 O O5' LCC . . . C 2 21.783 -1.536 10.076 1 17.07 0 O5' LCC 101 A 1 HETATM 2 C C5' LCC . . . C 2 20.472 -2.106 9.976 1 14.65 0 C5' LCC 101 A 1 HETATM 3 C C4' LCC . . . C 2 20.764 -3.556 9.636 1 13.05 0 C4' LCC 101 A 1 HETATM 4 O O4' LCC . . . C 2 21.505 -3.714 8.405 1 13.69 0 O4' LCC 101 A 1 HETATM 5 C C1' LCC . . . C 2 22.098 -5.049 8.5 1 12.36 0 C1' LCC 101 A 1 HETATM 6 N N1 LCC . . . C 2 23.561 -4.857 8.386 1 12.69 0 N1 LCC 101 A 1 HETATM 7 C C6 LCC . . . C 2 24.11 -3.581 8.549 1 14.31 0 C6 LCC 101 A 1 HETATM 8 C C5 LCC . . . C 2 25.464 -3.461 8.391 1 13.95 0 C5 LCC 101 A 1 HETATM 9 C C5M LCC . . . C 2 26.011 -2.173 8.591 1 14.93 0 C5M LCC 101 A 1 HETATM 10 C C4 LCC . . . C 2 26.215 -4.591 8.077 1 13.86 0 C4 LCC 101 A 1 HETATM 11 N N4 LCC . . . C 2 27.517 -4.385 7.901 1 15.22 0 N4 LCC 101 A 1 HETATM 12 N N3 LCC . . . C 2 25.664 -5.816 7.951 1 12.99 0 N3 LCC 101 A 1 HETATM 13 C C2 LCC . . . C 2 24.309 -5.948 8.126 1 12.71 0 C2 LCC 101 A 1 HETATM 14 O O2 LCC . . . C 2 23.781 -7.04 8.002 1 13.52 0 O2 LCC 101 A 1 HETATM 15 C C3' LCC . . . C 2 21.59 -4.338 10.629 1 13.27 0 C3' LCC 101 A 1 HETATM 16 C C2' LCC . . . C 2 21.588 -5.588 9.787 1 12.64 0 C2' LCC 101 A 1 HETATM 17 O O2' LCC . . . C 2 20.13 -5.834 9.54 1 13.41 0 O2' LCC 101 A 1 HETATM 18 O O3' LCC . . . C 2 20.925 -4.503 11.898 1 13.16 0 O3' LCC 101 A 1 HETATM 19 C C6' LCC . . . C 2 19.506 -4.412 9.509 1 13.22 0 C6' LCC 101 A 1 HETATM 20 P P LCC . . . C 2 22.041 0.054 10.088 1 20.2 0 P LCC 101 A 1 HETATM 21 O O1P LCC . . . C 2 21.215 0.556 11.257 1 21.88 0 O1P LCC 101 A 1 HETATM 22 O O2P LCC . . . C 2 23.481 0.278 10.087 1 24.06 0 O2P LCC 101 A 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 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #