data_6TW0 # _model_server_result.job_id q4c0Bp-AvZ87B6-rawJv0w _model_server_result.datetime_utc '2024-11-13 20:48:32' _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 6tw0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":603}' # _entry.id 6TW0 # _exptl.entry_id 6TW0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 441.228 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid' _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 6TW0 _cell.length_a 54.451 _cell.length_b 98.343 _cell.length_c 233.75 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TW0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_454 -x-1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -54.451 0 -116.875 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 26 A CYS 51 1_555 A SG CYS 32 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 328 A CYS 353 1_555 A SG CYS 333 A CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 340 A CYS 365 1_555 A SG CYS 362 A CYS 387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 A SG CYS 451 A CYS 476 1_555 A SG CYS 454 A CYS 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc1 A OD1 ASP 11 A ASP 36 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc2 A NE2 HIS 13 A HIS 38 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc3 A OD2 ASP 60 A ASP 85 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc4 A OD2 ASP 60 A ASP 85 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc5 A OD1 ASN 92 A ASN 117 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc6 A NE2 HIS 195 A HIS 220 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc7 A ND1 HIS 218 A HIS 243 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc8 B ZN ZN . A ZN 601 1_555 D O2B NYZ . A NYZ 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc9 B ZN ZN . A ZN 601 1_555 E O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc10 C ZN ZN . A ZN 602 1_555 D O3B NYZ . A NYZ 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? # _chem_comp.formula 'C11 H17 N5 O10 P2' _chem_comp.formula_weight 441.228 _chem_comp.id NYZ _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid' _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 O C2 NYZ doub 237 n n C2 N1 NYZ sing 238 n n C2 N3 NYZ sing 239 n n N1 C6 NYZ doub 240 n n N3 C4 NYZ sing 241 n n O2' C2' NYZ sing 242 n n C6 N6 NYZ sing 243 n n C6 C5 NYZ sing 244 n n C4 C5 NYZ doub 245 n y C4 N9 NYZ sing 246 n y C2' C1' NYZ sing 247 n n C2' C3' NYZ sing 248 n n C5 N7 NYZ sing 249 n y C1' N9 NYZ sing 250 n n C1' O4' NYZ sing 251 n n N9 C8 NYZ sing 252 n y O3' C3' NYZ sing 253 n n C3' C4' NYZ sing 254 n n O4' C4' NYZ sing 255 n n N7 C8 NYZ doub 256 n y C4' C5' NYZ sing 257 n n C5' O5' NYZ sing 258 n n O5' PA NYZ sing 259 n n O2A PA NYZ doub 260 n n PA O1A NYZ sing 261 n n PA C3A NYZ sing 262 n n C3A PB NYZ sing 263 n n O1B PB NYZ doub 264 n n O2B PB NYZ sing 265 n n PB O3B NYZ sing 266 n n C8 H8 NYZ sing 267 n n O2B H1 NYZ sing 268 n n O3B H2 NYZ sing 269 n n O1A H4 NYZ sing 270 n n C3A H3A2 NYZ sing 271 n n C3A H3A1 NYZ sing 272 n n C5' "H5'1" NYZ sing 273 n n C5' "H5'2" NYZ sing 274 n n C4' H4' NYZ sing 275 n n C3' H3' NYZ sing 276 n n O3' HO3' NYZ sing 277 n n C2' H2' NYZ sing 278 n n O2' HO2' NYZ sing 279 n n C1' H1' NYZ sing 280 n n N6 H61 NYZ sing 281 n n N6 H62 NYZ sing 282 n n N3 H3 NYZ sing 283 n n # _atom_sites.entry_id 6TW0 _atom_sites.fract_transf_matrix[1][1] 0.018365 _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] 0.010168 _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] 0.004278 _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 B 2 ZN A 1 601 601 ZN ZN . C 2 ZN A 1 602 602 ZN ZN . D 3 NYZ A 1 603 1 NYZ 690 . E 4 HOH A 1 701 2 HOH HOH . E 4 HOH A 2 702 1 HOH HOH . E 4 HOH A 3 703 52 HOH HOH . E 4 HOH A 4 704 7 HOH HOH . E 4 HOH A 5 705 4 HOH HOH . E 4 HOH A 6 706 62 HOH HOH . E 4 HOH A 7 707 3 HOH HOH . E 4 HOH A 8 708 8 HOH HOH . E 4 HOH A 9 709 61 HOH HOH . E 4 HOH A 10 710 53 HOH HOH . E 4 HOH A 11 711 63 HOH HOH . E 4 HOH A 12 712 26 HOH HOH . E 4 HOH A 13 713 20 HOH HOH . E 4 HOH A 14 714 15 HOH HOH . E 4 HOH A 15 715 38 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 C C8 NYZ . . . D 3 -14.509 22.053 -33.875 1 101.91 ? C8 NYZ 603 A 1 HETATM 2 C C5 NYZ . . . D 3 -13.884 23.479 -35.347 1 103.8 ? C5 NYZ 603 A 1 HETATM 3 C C6 NYZ . . . D 3 -13.337 24.554 -36.105 1 105.55 ? C6 NYZ 603 A 1 HETATM 4 P PB NYZ . . . D 3 -17.369 20.174 -28.884 1 81.61 1 PB NYZ 603 A 1 HETATM 5 O O1B NYZ . . . D 3 -16.065 20.723 -29.362 1 83.59 ? O1B NYZ 603 A 1 HETATM 6 O O2B NYZ . . . D 3 -18.57 21.058 -29.278 1 79.78 ? O2B NYZ 603 A 1 HETATM 7 O O3B NYZ . . . D 3 -17.44 19.993 -27.36 1 83.1 ? O3B NYZ 603 A 1 HETATM 8 P PA NYZ . . . D 3 -19.002 18.304 -30.623 1 81.08 1 PA NYZ 603 A 1 HETATM 9 O O1A NYZ . . . D 3 -20.39 18.851 -30.354 1 79.13 ? O1A NYZ 603 A 1 HETATM 10 O O2A NYZ . . . D 3 -19.1 16.757 -30.809 1 80.2 ? O2A NYZ 603 A 1 HETATM 11 C C3A NYZ . . . D 3 -17.676 18.498 -29.436 1 81.02 ? C3A NYZ 603 A 1 HETATM 12 O O5' NYZ . . . D 3 -18.365 18.955 -31.907 1 82.73 ? O5' NYZ 603 A 1 HETATM 13 C C5' NYZ . . . D 3 -17.028 18.634 -32.352 1 85.84 ? C5' NYZ 603 A 1 HETATM 14 C C4' NYZ . . . D 3 -16.844 18.892 -33.827 1 87.35 ? C4' NYZ 603 A 1 HETATM 15 O O4' NYZ . . . D 3 -16.792 20.311 -34.075 1 90.35 ? O4' NYZ 603 A 1 HETATM 16 C C3' NYZ . . . D 3 -15.534 18.366 -34.392 1 86.74 ? C3' NYZ 603 A 1 HETATM 17 O O3' NYZ . . . D 3 -15.609 16.972 -34.673 1 82.5 ? O3' NYZ 603 A 1 HETATM 18 C C2' NYZ . . . D 3 -15.339 19.237 -35.638 1 91.27 ? C2' NYZ 603 A 1 HETATM 19 O O2' NYZ . . . D 3 -15.954 18.693 -36.801 1 93.4 ? O2' NYZ 603 A 1 HETATM 20 C C1' NYZ . . . D 3 -16.043 20.549 -35.255 1 94.07 ? C1' NYZ 603 A 1 HETATM 21 N N9 NYZ . . . D 3 -15.127 21.688 -35.034 1 99.9 ? N9 NYZ 603 A 1 HETATM 22 N N7 NYZ . . . D 3 -13.741 23.113 -34.016 1 102.85 ? N7 NYZ 603 A 1 HETATM 23 N N6 NYZ . . . D 3 -12.5 25.45 -35.569 1 105.68 ? N6 NYZ 603 A 1 HETATM 24 N N1 NYZ . . . D 3 -13.627 24.684 -37.411 1 105.46 ? N1 NYZ 603 A 1 HETATM 25 C C2 NYZ . . . D 3 -14.482 23.81 -38.023 1 105.03 ? C2 NYZ 603 A 1 HETATM 26 N N3 NYZ . . . D 3 -15.043 22.787 -37.3 1 103.61 ? N3 NYZ 603 A 1 HETATM 27 C C4 NYZ . . . D 3 -14.737 22.598 -35.979 1 102.75 ? C4 NYZ 603 A 1 HETATM 28 O O NYZ . . . D 3 -14.779 23.918 -39.22 1 107.05 ? O NYZ 603 A 1 HETATM 29 H H8 NYZ . . . D 3 -14.661 21.544 -32.925 1 101.89 ? H8 NYZ 603 A 1 HETATM 30 H H3A2 NYZ . . . D 3 -16.731 18.096 -29.798 1 81.11 ? H3A2 NYZ 603 A 1 HETATM 31 H H3A1 NYZ . . . D 3 -17.854 17.826 -28.601 1 80.72 ? H3A1 NYZ 603 A 1 HETATM 32 H "H5'1" NYZ . . . D 3 -16.382 19.295 -31.776 1 86.32 ? "H5'1" NYZ 603 A 1 HETATM 33 H "H5'2" NYZ . . . D 3 -16.759 17.608 -32.107 1 85.94 ? "H5'2" NYZ 603 A 1 HETATM 34 H H4' NYZ . . . D 3 -17.699 18.55 -34.409 1 87.17 ? H4' NYZ 603 A 1 HETATM 35 H H3' NYZ . . . D 3 -14.724 18.52 -33.681 1 86.85 ? H3' NYZ 603 A 1 HETATM 36 H HO3' NYZ . . . D 3 -15.568 16.494 -33.804 1 82.06 ? HO3' NYZ 603 A 1 HETATM 37 H H2' NYZ . . . D 3 -14.275 19.402 -35.799 1 91.41 ? H2' NYZ 603 A 1 HETATM 38 H HO2' NYZ . . . D 3 -15.768 17.718 -36.799 1 93.67 ? HO2' NYZ 603 A 1 HETATM 39 H H1' NYZ . . . D 3 -16.736 20.869 -36.03 1 94.23 ? H1' NYZ 603 A 1 HETATM 40 H H61 NYZ . . . D 3 -12.118 26.214 -36.118 1 105.49 ? H61 NYZ 603 A 1 HETATM 41 H H62 NYZ . . . D 3 -12.216 25.376 -34.597 1 105.53 ? H62 NYZ 603 A 1 HETATM 42 H H3 NYZ . . . D 3 -15.734 22.185 -37.73 1 103.57 ? H3 NYZ 603 A 1 # _model_server_stats.io_time_ms 140 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 42 #