data_7LNE # _model_server_result.job_id 0NBdzqxZhQSWgLvqf3IS-Q _model_server_result.datetime_utc '2024-11-22 20:24:28' _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":"M","auth_seq_id":104}' # _entry.id 7LNE # _exptl.entry_id 7LNE _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 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 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.513 ? 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 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 282 n n P O5' LCG sing 283 n n P OP2 LCG sing 284 n n P OP3 LCG sing 285 n n O5' C5' LCG sing 286 n n C5' C4' LCG sing 287 n n C5' H5' LCG sing 288 n n C5' "H5''" LCG sing 289 n n C3' C2' LCG sing 290 n n C3' C4' LCG sing 291 n n C3' O3' LCG sing 292 n n C3' H3' LCG sing 293 n n C6' C4' LCG sing 294 n n C6' O2' LCG sing 295 n n C6' "H6'1" LCG sing 296 n n C6' "H6'2" LCG sing 297 n n N9 C8 LCG sing 298 n y N9 C4 LCG sing 299 n y N9 C1' LCG sing 300 n n C8 N7 LCG doub 301 n y C8 H8 LCG sing 302 n n C4 C5 LCG doub 303 n y C4 N3 LCG sing 304 n n N7 C5 LCG sing 305 n y C5 C6 LCG sing 306 n n C6 O6 LCG doub 307 n n C6 N1 LCG sing 308 n n C2' C1' LCG sing 309 n n C2' O2' LCG sing 310 n n C2' H2' LCG sing 311 n n C4' O4' LCG sing 312 n n C1' O4' LCG sing 313 n n C1' H1' LCG sing 314 n n C2 N1 LCG sing 315 n n C2 N2 LCG sing 316 n n C2 N3 LCG doub 317 n n N1 H1 LCG sing 318 n n OP2 HOP2 LCG sing 319 n n N2 H21 LCG sing 320 n n N2 H22 LCG sing 321 n n O3' HO3' LCG sing 322 n n OP3 HOP3 LCG sing 323 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 P P LCG . . . M 3 29.324 -14.245 30.631 1 11.44 0 P LCG 104 B 1 HETATM 2 O OP1 LCG . . . M 3 30.419 -13.315 30.584 1 12.37 0 OP1 LCG 104 B 1 HETATM 3 O O5' LCG . . . M 3 28.069 -13.382 30.857 1 11.77 0 O5' LCG 104 B 1 HETATM 4 C C5' LCG . . . M 3 26.781 -14.003 30.914 1 11.47 0 C5' LCG 104 B 1 HETATM 5 C C3' LCG . . . M 3 25.842 -11.659 30.327 1 10.91 0 C3' LCG 104 B 1 HETATM 6 C C6' LCG . . . M 3 24.283 -13.216 31.227 1 11.43 0 C6' LCG 104 B 1 HETATM 7 N N9 LCG . . . M 3 26.503 -9.997 32.626 1 9.98 0 N9 LCG 104 B 1 HETATM 8 C C8 LCG . . . M 3 27.853 -10.288 32.71 1 9.68 0 C8 LCG 104 B 1 HETATM 9 C C4 LCG . . . M 3 26.357 -8.678 32.95 1 9.28 0 C4 LCG 104 B 1 HETATM 10 N N7 LCG . . . M 3 28.519 -9.152 32.962 1 10.65 0 N7 LCG 104 B 1 HETATM 11 C C5 LCG . . . M 3 27.623 -8.182 33.194 1 9.11 0 C5 LCG 104 B 1 HETATM 12 C C6 LCG . . . M 3 27.804 -6.848 33.56 1 9.25 0 C6 LCG 104 B 1 HETATM 13 C C2' LCG . . . M 3 24.801 -10.932 31.049 1 10.87 0 C2' LCG 104 B 1 HETATM 14 O O6 LCG . . . M 3 28.893 -6.237 33.785 1 10.92 0 O6 LCG 104 B 1 HETATM 15 C C4' LCG . . . M 3 25.781 -12.861 31.219 1 11.36 0 C4' LCG 104 B 1 HETATM 16 C C1' LCG . . . M 3 25.402 -10.89 32.419 1 10.17 0 C1' LCG 104 B 1 HETATM 17 C C2 LCG . . . M 3 25.367 -6.655 33.386 1 10.03 0 C2 LCG 104 B 1 HETATM 18 N N1 LCG . . . M 3 26.654 -6.124 33.595 1 9.02 0 N1 LCG 104 B 1 HETATM 19 O O4' LCG . . . M 3 26.023 -12.227 32.525 1 11.39 0 O4' LCG 104 B 1 HETATM 20 O OP2 LCG . . . M 3 29.141 -15.331 29.648 1 13.47 0 OP2 LCG 104 B 1 HETATM 21 N N2 LCG . . . M 3 24.314 -5.89 33.523 1 10.27 0 N2 LCG 104 B 1 HETATM 22 N N3 LCG . . . M 3 25.216 -7.97 33.053 1 9.97 0 N3 LCG 104 B 1 HETATM 23 O O2' LCG . . . M 3 23.715 -11.825 31.148 1 12.3 0 O2' LCG 104 B 1 HETATM 24 O O3' LCG . . . M 3 25.493 -12.057 28.967 1 11.73 0 O3' LCG 104 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #