data_6WJ2 # _model_server_result.job_id lVfJSwHa2kJL1aAPME7Brg _model_server_result.datetime_utc '2024-11-22 23:35:39' _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 6wj2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":500}' # _entry.id 6WJ2 # _exptl.entry_id 6WJ2 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 540.231 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione _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 90 _cell.entry_id 6WJ2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WJ2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 ? _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 10 _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 metalc ? metalc1 G OG SER 80 G SER 75 1_555 K MG MG . G MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc2 G OG1 THR 101 G THR 96 1_555 K MG MG . G MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc3 J O1G L8S . G L8S 500 1_555 K MG MG . G MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc4 J O2B L8S . G L8S 500 1_555 K MG MG . G MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? # _chem_comp.formula 'C10 H15 N4 O14 P3 S' _chem_comp.formula_weight 540.231 _chem_comp.id L8S _chem_comp.mon_nstd_flag . _chem_comp.name 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione _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 O6 C6 L8S doub 216 n n N7 C5 L8S sing 217 n y N7 C8 L8S doub 218 n y C6 C5 L8S sing 219 n n C6 N1 L8S sing 220 n n C5 C4 L8S doub 221 n y N1 C2 L8S sing 222 n n C8 N9 L8S sing 223 n y C4 N9 L8S sing 224 n y C4 N3 L8S sing 225 n n N9 C1' L8S sing 226 n n C2 N3 L8S sing 227 n n C2 O2 L8S doub 228 n n O2A PA L8S doub 229 n n O4' C1' L8S sing 230 n n O4' C4' L8S sing 231 n n C1' C2' L8S sing 232 n n O2B PB L8S doub 233 n n O1B PB L8S sing 234 n n C2' O2' L8S sing 235 n n C2' C3' L8S sing 236 n n C4' C3' L8S sing 237 n n C4' C5' L8S sing 238 n n PA O5' L8S sing 239 n n PA O3A L8S sing 240 n n PA O1A L8S sing 241 n n PB O3A L8S sing 242 n n PB O3B L8S sing 243 n n O5' C5' L8S sing 244 n n C3' O3' L8S sing 245 n n O1G PG L8S sing 246 n n O2G PG L8S sing 247 n n O3B PG L8S sing 248 n n PG S3G L8S doub 249 n n N1 H1 L8S sing 250 n n N3 H2 L8S sing 251 n n C8 H3 L8S sing 252 n n C1' H4 L8S sing 253 n n C2' H5 L8S sing 254 n n C3' H6 L8S sing 255 n n C4' H7 L8S sing 256 n n C5' H8 L8S sing 257 n n C5' H9 L8S sing 258 n n O1A H10 L8S sing 259 n n O1B H11 L8S sing 260 n n O2' H12 L8S sing 261 n n O2G H13 L8S sing 262 n n O3' H14 L8S sing 263 n n O1G H16 L8S sing 264 n n # _atom_sites.entry_id 6WJ2 _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 9 GDP F 1 500 500 GDP GDP . J 10 L8S G 1 500 500 L8S L8S . K 11 MG G 1 501 501 MG MG . # 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 N N1 L8S . . . J 10 161.467 177.819 193.249 1 57.3 ? N1 L8S 500 G 1 HETATM 2 N N3 L8S . . . J 10 163.268 177.966 195.059 1 57.3 ? N3 L8S 500 G 1 HETATM 3 C C4 L8S . . . J 10 164.174 178.564 194.088 1 57.3 ? C4 L8S 500 G 1 HETATM 4 C C5 L8S . . . J 10 163.761 178.787 192.755 1 57.3 ? C5 L8S 500 G 1 HETATM 5 C C6 L8S . . . J 10 162.386 178.414 192.309 1 57.3 ? C6 L8S 500 G 1 HETATM 6 C C8 L8S . . . J 10 165.89 179.47 193.07 1 57.3 ? C8 L8S 500 G 1 HETATM 7 C C1' L8S . . . J 10 166.105 178.923 195.319 1 57.3 ? C1' L8S 500 G 1 HETATM 8 C C2 L8S . . . J 10 161.899 177.587 194.64 1 57.3 ? C2 L8S 500 G 1 HETATM 9 C C2' L8S . . . J 10 166.948 177.696 195.351 1 57.3 ? C2' L8S 500 G 1 HETATM 10 C C3' L8S . . . J 10 168.265 178.109 195.841 1 57.3 ? C3' L8S 500 G 1 HETATM 11 C C4' L8S . . . J 10 168.384 179.559 195.531 1 57.3 ? C4' L8S 500 G 1 HETATM 12 C C5' L8S . . . J 10 169.096 180.268 196.63 1 57.3 ? C5' L8S 500 G 1 HETATM 13 N N7 L8S . . . J 10 164.974 179.42 192.06 1 57.3 ? N7 L8S 500 G 1 HETATM 14 N N9 L8S . . . J 10 165.362 178.986 194.113 1 57.3 ? N9 L8S 500 G 1 HETATM 15 O O1A L8S . . . J 10 171.694 181.036 195.669 1 57.3 ? O1A L8S 500 G 1 HETATM 16 O O1B L8S . . . J 10 170.28 185.005 193.918 1 57.3 ? O1B L8S 500 G 1 HETATM 17 O O1G L8S . . . J 10 174.489 185.625 195.76 1 57.3 ? O1G L8S 500 G 1 HETATM 18 O O2 L8S . . . J 10 161.017 177.012 195.559 1 57.3 ? O2 L8S 500 G 1 HETATM 19 O O2' L8S . . . J 10 166.367 176.738 196.255 1 57.3 ? O2' L8S 500 G 1 HETATM 20 O O2A L8S . . . J 10 170.441 181.874 193.999 1 57.3 ? O2A L8S 500 G 1 HETATM 21 O O2B L8S . . . J 10 172.427 184.309 193.776 1 57.3 ? O2B L8S 500 G 1 HETATM 22 O O2G L8S . . . J 10 173.707 187.495 196.858 1 57.3 ? O2G L8S 500 G 1 HETATM 23 O O3' L8S . . . J 10 169.296 177.379 195.15 1 57.3 ? O3' L8S 500 G 1 HETATM 24 O O3A L8S . . . J 10 171.12 183.532 195.842 1 57.3 ? O3A L8S 500 G 1 HETATM 25 O O3B L8S . . . J 10 171.938 186.089 195.544 1 57.3 ? O3B L8S 500 G 1 HETATM 26 O O4' L8S . . . J 10 167.012 180.09 195.41 1 57.3 ? O4' L8S 500 G 1 HETATM 27 O O5' L8S . . . J 10 169.269 181.605 196.262 1 57.3 ? O5' L8S 500 G 1 HETATM 28 O O6 L8S . . . J 10 161.993 178.641 190.988 1 57.3 ? O6 L8S 500 G 1 HETATM 29 P PA L8S . . . J 10 170.634 182.011 195.437 1 57.3 ? PA L8S 500 G 1 HETATM 30 P PB L8S . . . J 10 171.438 184.732 194.759 1 57.3 ? PB L8S 500 G 1 HETATM 31 P PG L8S . . . J 10 173.314 186.152 196.445 1 57.3 ? PG L8S 500 G 1 HETATM 32 S S3G L8S . . . J 10 173.224 185.157 198.077 1 57.3 ? S3G L8S 500 G 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 32 #