data_6TWF # _model_server_result.job_id 6_jJSiV6PiGvsD3wspZB8A _model_server_result.datetime_utc '2024-11-22 08:23:59' _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 6twf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":604}' # _entry.id 6TWF # _exptl.entry_id 6TWF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 510.356 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-piperazin-4-ium-1-yl-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 6TWF _cell.length_a 54.453 _cell.length_b 97.217 _cell.length_c 234.369 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TWF _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,F _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 -54.453 0 -117.1845 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 328 A CYS 353 1_555 A SG CYS 333 A CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf3 A SG CYS 340 A CYS 365 1_555 A SG CYS 362 A CYS 387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 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 OD2 ASP 11 A ASP 36 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 A NE2 HIS 13 A HIS 38 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc3 A OD2 ASP 60 A ASP 85 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc4 A OD2 ASP 60 A ASP 85 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc5 A OD1 ASN 92 A ASN 117 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc6 A O ASN 188 A ASN 213 1_555 D CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc7 A NE2 HIS 195 A HIS 220 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc8 A OD1 ASP 212 A ASP 237 1_555 D CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc9 A OD2 ASP 212 A ASP 237 1_555 D CA CA . A CA 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc10 A ND1 HIS 218 A HIS 243 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc11 B ZN ZN . A ZN 601 1_555 E O2B O05 . A O05 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? metalc ? metalc12 C ZN ZN . A ZN 602 1_555 E O3B O05 . A O05 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc13 C ZN ZN . A ZN 602 1_555 F O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? # _chem_comp.formula 'C15 H26 N7 O9 P2 1' _chem_comp.formula_weight 510.356 _chem_comp.id O05 _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-piperazin-4-ium-1-yl-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 N6 C6 O05 sing 237 n n C6 N1 O05 doub 238 n y C6 C5 O05 sing 239 n y N1 C2 O05 sing 240 n y N7 C5 O05 sing 241 n y N7 C8 O05 doub 242 n y C12 C11 O05 sing 243 n n C12 N2 O05 sing 244 n n C5 C4 O05 doub 245 n y C11 N4 O05 sing 246 n n C2 N2 O05 sing 247 n n C2 N3 O05 doub 248 n y C8 N9 O05 sing 249 n y N2 C9 O05 sing 250 n n C4 N3 O05 sing 251 n y C4 N9 O05 sing 252 n y N4 C10 O05 sing 253 n n N9 C1' O05 sing 254 n n C9 C10 O05 sing 255 n n C1' O4' O05 sing 256 n n C1' C2' O05 sing 257 n n O4' C4' O05 sing 258 n n C2' O8 O05 sing 259 n n C2' C3' O05 sing 260 n n C5' C4' O05 sing 261 n n C5' O5' O05 sing 262 n n C4' C3' O05 sing 263 n n O5' PA O05 sing 264 n n C3' O7 O05 sing 265 n n O2A PA O05 doub 266 n n PA O1A O05 sing 267 n n PA C3 O05 sing 268 n n C3 PB O05 sing 269 n n O1B PB O05 doub 270 n n PB O3B O05 sing 271 n n PB O2B O05 sing 272 n n C3 H19 O05 sing 273 n n C3 H18 O05 sing 274 n n C8 H15 O05 sing 275 n n C9 H13 O05 sing 276 n n C9 H14 O05 sing 277 n n C10 H11 O05 sing 278 n n C10 H12 O05 sing 279 n n C11 H9 O05 sing 280 n n C11 H8 O05 sing 281 n n C12 H7 O05 sing 282 n n C12 H6 O05 sing 283 n n O1A H20 O05 sing 284 n n O3B H21 O05 sing 285 n n O2B H22 O05 sing 286 n n C5' H16 O05 sing 287 n n C5' H17 O05 sing 288 n n C4' H1 O05 sing 289 n n C3' H2 O05 sing 290 n n O7 H23 O05 sing 291 n n C2' H3 O05 sing 292 n n O8 H24 O05 sing 293 n n C1' H O05 sing 294 n n N6 H5 O05 sing 295 n n N6 H4 O05 sing 296 n n N4 H10 O05 sing 297 n n N4 H25 O05 sing 298 n n # _atom_sites.entry_id 6TWF _atom_sites.fract_transf_matrix[1][1] 0.018364 _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] 0.010286 _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] 0.004267 _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 CA A 1 603 605 CA CA . E 4 O05 A 1 604 1 O05 604 . F 5 HOH A 1 701 671 HOH HOH . F 5 HOH A 2 702 675 HOH HOH . F 5 HOH A 3 703 673 HOH HOH . F 5 HOH A 4 704 674 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 C2 O05 . . . E 4 -12.693 24.888 -36.628 1 136.47 ? C2 O05 604 A 1 HETATM 2 C C3 O05 . . . E 4 -16.799 18.545 -29.799 1 88.49 ? C3 O05 604 A 1 HETATM 3 C C4 O05 . . . E 4 -13.822 22.995 -36.195 1 131.74 ? C4 O05 604 A 1 HETATM 4 C C5 O05 . . . E 4 -14.494 23.042 -37.405 1 131.96 ? C5 O05 604 A 1 HETATM 5 C C6 O05 . . . E 4 -14.227 24.147 -38.235 1 133.2 ? C6 O05 604 A 1 HETATM 6 C C8 O05 . . . E 4 -15.118 21.252 -36.452 1 130.53 ? C8 O05 604 A 1 HETATM 7 C C9 O05 . . . E 4 -11.06 25.927 -35.066 1 141.08 ? C9 O05 604 A 1 HETATM 8 C C10 O05 . . . E 4 -11.302 27.375 -34.692 1 142.81 ? C10 O05 604 A 1 HETATM 9 C C11 O05 . . . E 4 -11.327 28.005 -37.028 1 142.94 ? C11 O05 604 A 1 HETATM 10 C C12 O05 . . . E 4 -11.04 26.575 -37.41 1 141.99 ? C12 O05 604 A 1 HETATM 11 O O2A O05 . . . E 4 -19.109 18.96 -31.483 1 89.58 ? O2A O05 604 A 1 HETATM 12 P PA O05 . . . E 4 -17.871 18.141 -31.18 1 91.66 ? PA O05 604 A 1 HETATM 13 O O1A O05 . . . E 4 -18.318 16.671 -30.902 1 87.86 ? O1A O05 604 A 1 HETATM 14 P PB O05 . . . E 4 -17.459 19.842 -28.761 1 83.55 ? PB O05 604 A 1 HETATM 15 O O3B O05 . . . E 4 -18.642 19.308 -28.018 1 83.57 ? O3B O05 604 A 1 HETATM 16 O O1B O05 . . . E 4 -17.8 21.034 -29.679 1 79.28 ? O1B O05 604 A 1 HETATM 17 O O2B O05 . . . E 4 -16.306 20.322 -27.863 1 89.7 ? O2B O05 604 A 1 HETATM 18 O O5' O05 . . . E 4 -16.711 18.169 -32.247 1 102.6 ? O5' O05 604 A 1 HETATM 19 C C5' O05 . . . E 4 -16.339 19.287 -33.106 1 110.49 ? C5' O05 604 A 1 HETATM 20 C C4' O05 . . . E 4 -14.934 19.778 -32.83 1 117.56 ? C4' O05 604 A 1 HETATM 21 O O4' O05 . . . E 4 -14.244 20.026 -34.081 1 120.34 ? O4' O05 604 A 1 HETATM 22 C C3' O05 . . . E 4 -14.844 21.088 -32.047 1 120.36 ? C3' O05 604 A 1 HETATM 23 O O7 O05 . . . E 4 -13.686 21.118 -31.216 1 120.73 ? O7 O05 604 A 1 HETATM 24 C C2' O05 . . . E 4 -14.788 22.135 -33.164 1 121.36 ? C2' O05 604 A 1 HETATM 25 O O8 O05 . . . E 4 -14.114 23.339 -32.812 1 120.12 ? O8 O05 604 A 1 HETATM 26 C C1' O05 . . . E 4 -13.948 21.408 -34.212 1 123.58 ? C1' O05 604 A 1 HETATM 27 N N9 O05 . . . E 4 -14.242 21.84 -35.578 1 129.01 ? N9 O05 604 A 1 HETATM 28 N N7 O05 . . . E 4 -15.313 21.935 -37.555 1 131.35 ? N7 O05 604 A 1 HETATM 29 N N6 O05 . . . E 4 -14.794 24.335 -39.433 1 132.61 ? N6 O05 604 A 1 HETATM 30 N N3 O05 . . . E 4 -12.926 23.885 -35.743 1 133.86 ? N3 O05 604 A 1 HETATM 31 N N1 O05 . . . E 4 -13.331 25.065 -37.816 1 134.98 ? N1 O05 604 A 1 HETATM 32 N N2 O05 . . . E 4 -11.594 25.66 -36.405 1 139.86 ? N2 O05 604 A 1 HETATM 33 N N4 O05 . . . E 4 -10.744 28.284 -35.709 1 143.24 ? N4 O05 604 A 1 HETATM 34 H H19 O05 . . . E 4 -15.819 18.858 -30.158 1 88.67 ? H19 O05 604 A 1 HETATM 35 H H18 O05 . . . E 4 -16.537 17.676 -29.197 1 88.28 ? H18 O05 604 A 1 HETATM 36 H H15 O05 . . . E 4 -15.618 20.301 -36.276 1 130.5 ? H15 O05 604 A 1 HETATM 37 H H13 O05 . . . E 4 -10.008 25.644 -35.055 1 141.01 ? H13 O05 604 A 1 HETATM 38 H H14 O05 . . . E 4 -11.512 25.321 -34.283 1 140.95 ? H14 O05 604 A 1 HETATM 39 H H11 O05 . . . E 4 -12.356 27.596 -34.533 1 142.89 ? H11 O05 604 A 1 HETATM 40 H H12 O05 . . . E 4 -10.857 27.64 -33.733 1 142.95 ? H12 O05 604 A 1 HETATM 41 H H9 O05 . . . E 4 -12.405 28.153 -37.06 1 142.91 ? H9 O05 604 A 1 HETATM 42 H H8 O05 . . . E 4 -10.919 28.728 -37.733 1 142.93 ? H8 O05 604 A 1 HETATM 43 H H7 O05 . . . E 4 -9.957 26.476 -37.475 1 142.12 ? H7 O05 604 A 1 HETATM 44 H H6 O05 . . . E 4 -11.374 26.332 -38.417 1 142.02 ? H6 O05 604 A 1 HETATM 45 H H16 O05 . . . E 4 -16.373 18.947 -34.14 1 110.95 ? H16 O05 604 A 1 HETATM 46 H H17 O05 . . . E 4 -17.105 20.053 -33.03 1 110.14 ? H17 O05 604 A 1 HETATM 47 H H1 O05 . . . E 4 -14.358 18.984 -32.356 1 117.57 ? H1 O05 604 A 1 HETATM 48 H H2 O05 . . . E 4 -15.75 21.226 -31.458 1 120.46 ? H2 O05 604 A 1 HETATM 49 H H23 O05 . . . E 4 -13.592 22.054 -30.899 1 120.68 ? H23 O05 604 A 1 HETATM 50 H H3 O05 . . . E 4 -15.788 22.385 -33.513 1 121.1 ? H3 O05 604 A 1 HETATM 51 H H24 O05 . . . E 4 -14.441 24.058 -33.415 1 119.84 ? H24 O05 604 A 1 HETATM 52 H H O05 . . . E 4 -12.883 21.555 -34.044 1 123.62 ? H O05 604 A 1 HETATM 53 H H5 O05 . . . E 4 -14.575 25.15 -39.996 1 132.56 ? H5 O05 604 A 1 HETATM 54 H H4 O05 . . . E 4 -15.457 23.658 -39.797 1 132.42 ? H4 O05 604 A 1 HETATM 55 H H10 O05 . . . E 4 -10.786 29.269 -35.466 1 143.27 ? H10 O05 604 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 432 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 55 #