data_7Z43 # _model_server_result.job_id TCM_zFpAu5xA7ttsJ34_Pg _model_server_result.datetime_utc '2024-10-20 01:22:20' _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 7z43 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":101}' # _entry.id 7Z43 # _exptl.entry_id 7Z43 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 458.235 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate' _entity.pdbx_number_of_molecules 1 _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 7Z43 _cell.length_a 200.819 _cell.length_b 200.819 _cell.length_c 257.018 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Z43 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 9 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 F P A 1 MaM A 1 1_555 J O3B IC5 . MaM IC5 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.615 ? covale ? covale2 G C THR 11 XXX THR 25 1_555 G N SEP 12 XXX SEP 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale3 G C SEP 12 XXX SEP 26 1_555 G N PRO 13 XXX PRO 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale4 H C THR 4 YYY THR 34 1_555 H N SEP 5 YYY SEP 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale5 H C SEP 5 YYY SEP 35 1_555 H N PRO 6 YYY PRO 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? covale ? covale6 H C THR 11 YYY THR 41 1_555 H N SEP 12 YYY SEP 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale7 H C SEP 12 YYY SEP 42 1_555 H N PRO 13 YYY PRO 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? hydrog WATSON-CRICK hydrog1 D N3 C 6 RRR C 6 1_555 E N1 G 14 VVV G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D N4 C 6 RRR C 6 1_555 E O6 G 14 VVV G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D O2 C 6 RRR C 6 1_555 E N2 G 14 VVV G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D N3 U 7 RRR U 7 1_555 E N1 A 13 VVV A 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 D O4 U 7 RRR U 7 1_555 E N6 A 13 VVV A 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N3 C 8 RRR C 8 1_555 E N1 G 12 VVV G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D N4 C 8 RRR C 8 1_555 E O6 G 12 VVV G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D O2 C 8 RRR C 8 1_555 E N2 G 12 VVV G 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N3 U 9 RRR U 9 1_555 E N1 A 11 VVV A 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D O4 U 9 RRR U 9 1_555 E N6 A 11 VVV A 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog11 E N6 A 1 VVV A 1 1_555 E N3 A 10 VVV A 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 E N1 G 2 VVV G 2 1_555 E N3 C 9 VVV C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 E N2 G 2 VVV G 2 1_555 E O2 C 9 VVV C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 E O6 G 2 VVV G 2 1_555 E N4 C 9 VVV C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 E N3 U 3 VVV U 3 1_555 E N1 A 8 VVV A 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 E O4 U 3 VVV U 3 1_555 E N6 A 8 VVV A 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-A MISPAIR' hydrog17 E N3 A 4 VVV A 4 1_555 E N6 A 7 VVV A 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C11 H18 N5 O11 P2 1' _chem_comp.formula_weight 458.235 _chem_comp.id IC5 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate' _chem_comp.type non-polymer _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 CM N7 IC5 sing 267 n n O6 C6 IC5 doub 268 n n N7 C8 IC5 sing 269 n y N7 C5 IC5 sing 270 n y C8 N9 IC5 doub 271 n y O4' C4' IC5 sing 272 n n O4' C1' IC5 sing 273 n n C6 C5 IC5 sing 274 n n C6 N1 IC5 sing 275 n n C5 C4 IC5 doub 276 n y C5' C4' IC5 sing 277 n n C5' O5' IC5 sing 278 n n N9 C4 IC5 sing 279 n y N9 C1' IC5 sing 280 n n N1 C2 IC5 sing 281 n n C4 N3 IC5 sing 282 n n C4' C3' IC5 sing 283 n n C1' C2' IC5 sing 284 n n O1A PA IC5 doub 285 n n C2 N3 IC5 doub 286 n n C2 N2 IC5 sing 287 n n O2A PA IC5 sing 288 n n O5' PA IC5 sing 289 n n PA O3A IC5 sing 290 n n C3' C2' IC5 sing 291 n n C3' O3' IC5 sing 292 n n C2' O2' IC5 sing 293 n n O3A PB IC5 sing 294 n n O3B PB IC5 doub 295 n n PB O2B IC5 sing 296 n n PB O1B IC5 sing 297 n n N1 H1 IC5 sing 298 n n N2 H2 IC5 sing 299 n n N2 H3 IC5 sing 300 n n C8 H4 IC5 sing 301 n n C1' H5 IC5 sing 302 n n C2' H6 IC5 sing 303 n n O2' H7 IC5 sing 304 n n C3' H8 IC5 sing 305 n n O3' H9 IC5 sing 306 n n C4' H10 IC5 sing 307 n n C5' H11 IC5 sing 308 n n C5' H12 IC5 sing 309 n n O2A H13 IC5 sing 310 n n O1B H14 IC5 sing 311 n n O2B H15 IC5 sing 312 n n CM H16 IC5 sing 313 n n CM H17 IC5 sing 314 n n CM H18 IC5 sing 315 n n # _atom_sites.entry_id 7Z43 _atom_sites.fract_transf_matrix[1][1] 0.00498 _atom_sites.fract_transf_matrix[1][2] 0.002875 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00575 _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] 0.003891 _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 I 8 PO4 BBB 1 801 1 PO4 PO4 . J 9 IC5 MaM 1 101 0 IC5 GDM . K 10 HOH YYY 1 101 1 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 O6 IC5 . . . J 9 -97.527 3.014 -22.669 1 186.78 0 O6 IC5 101 MaM 1 HETATM 2 N N1 IC5 . . . J 9 -99.31 3.907 -21.592 1 183.28 0 N1 IC5 101 MaM 1 HETATM 3 N N2 IC5 . . . J 9 -101.189 4.652 -20.491 1 183.6 0 N2 IC5 101 MaM 1 HETATM 4 C C2 IC5 . . . J 9 -99.997 4.938 -21.026 1 182.81 0 C2 IC5 101 MaM 1 HETATM 5 C C4 IC5 . . . J 9 -98.323 6.337 -21.553 1 182.51 0 C4 IC5 101 MaM 1 HETATM 6 C C5 IC5 . . . J 9 -97.573 5.335 -22.146 1 183.2 0 C5 IC5 101 MaM 1 HETATM 7 C C6 IC5 . . . J 9 -98.069 4.006 -22.185 1 183.94 0 C6 IC5 101 MaM 1 HETATM 8 C C8 IC5 . . . J 9 -96.41 7.181 -22.22 1 183.65 0 C8 IC5 101 MaM 1 HETATM 9 N N3 IC5 . . . J 9 -99.535 6.184 -20.985 1 181.89 0 N3 IC5 101 MaM 1 HETATM 10 N N7 IC5 . . . J 9 -96.407 5.908 -22.599 1 183.56 0 N7 IC5 101 MaM 1 HETATM 11 N N9 IC5 . . . J 9 -97.585 7.509 -21.679 1 182.85 0 N9 IC5 101 MaM 1 HETATM 12 C C1' IC5 . . . J 9 -98.065 8.849 -21.304 1 181.51 0 C1' IC5 101 MaM 1 HETATM 13 O O4' IC5 . . . J 9 -97.538 9.802 -22.207 1 181 0 O4' IC5 101 MaM 1 HETATM 14 C C2' IC5 . . . J 9 -97.637 9.278 -19.936 1 181.58 0 C2' IC5 101 MaM 1 HETATM 15 O O2' IC5 . . . J 9 -98.554 8.722 -19.002 1 180.29 0 O2' IC5 101 MaM 1 HETATM 16 C C3' IC5 . . . J 9 -97.759 10.78 -20.047 1 183.04 0 C3' IC5 101 MaM 1 HETATM 17 O O3' IC5 . . . J 9 -99.073 11.251 -19.807 1 182.77 0 O3' IC5 101 MaM 1 HETATM 18 C C4' IC5 . . . J 9 -97.329 11.052 -21.498 1 182.19 0 C4' IC5 101 MaM 1 HETATM 19 C C5' IC5 . . . J 9 -95.904 11.501 -21.721 1 181.06 0 C5' IC5 101 MaM 1 HETATM 20 O O5' IC5 . . . J 9 -95.198 11.474 -20.472 1 182.17 0 O5' IC5 101 MaM 1 HETATM 21 P PA IC5 . . . J 9 -93.886 10.566 -20.346 1 181.07 0 PA IC5 101 MaM 1 HETATM 22 O O1A IC5 . . . J 9 -92.793 11.224 -21.097 1 181.04 0 O1A IC5 101 MaM 1 HETATM 23 O O2A IC5 . . . J 9 -94.257 9.166 -20.654 1 179.27 0 O2A IC5 101 MaM 1 HETATM 24 O O3A IC5 . . . J 9 -93.55 10.66 -18.787 1 175.93 0 O3A IC5 101 MaM 1 HETATM 25 P PB IC5 . . . J 9 -94.221 11.489 -17.549 1 168.46 0 PB IC5 101 MaM 1 HETATM 26 O O1B IC5 . . . J 9 -93.193 11.482 -16.44 1 169.15 0 O1B IC5 101 MaM 1 HETATM 27 O O2B IC5 . . . J 9 -95.479 10.734 -17.18 1 164.27 0 O2B IC5 101 MaM 1 HETATM 28 O O3B IC5 . . . J 9 -94.525 12.973 -18.112 1 156.59 0 O3B IC5 101 MaM 1 HETATM 29 C CM IC5 . . . J 9 -95.348 5.241 -23.361 1 183.07 0 CM IC5 101 MaM 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #