data_6TVX # _model_server_result.job_id wNMTCTT5-QMc9ZRPK5BAIw _model_server_result.datetime_utc '2024-11-17 15:34:18' _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 6tvx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":603}' # _entry.id 6TVX # _exptl.entry_id 6TVX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 440.243 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)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 6TVX _cell.length_a 54.519 _cell.length_b 97.453 _cell.length_c 233.697 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6TVX _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 -54.519 0 -116.8485 # _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 328 A CYS 353 1_555 A SG CYS 333 A CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf3 A SG CYS 340 A CYS 365 1_555 A SG CYS 362 A CYS 387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf4 A SG CYS 451 A CYS 476 1_555 A SG CYS 454 A CYS 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc1 A NE2 HIS 13 A HIS 38 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc2 A OD2 ASP 60 A ASP 85 1_555 B ZN ZN . A ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc3 A OD2 ASP 60 A ASP 85 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc4 A OD1 ASN 92 A ASN 117 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc5 A NE2 HIS 195 A HIS 220 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc6 A ND1 HIS 218 A HIS 243 1_555 C ZN ZN . A ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc7 B ZN ZN . A ZN 601 1_555 D O3B NYW . A NYW 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc8 B ZN ZN . A ZN 601 1_555 E O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? metalc ? metalc9 C ZN ZN . A ZN 602 1_555 D O1B NYW . A NYW 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.885 ? # _chem_comp.formula 'C11 H18 N6 O9 P2' _chem_comp.formula_weight 440.243 _chem_comp.id NYW _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)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 N2 C2 NYW sing 237 n n C2 N1 NYW doub 238 n y C2 N3 NYW sing 239 n y N1 C6 NYW sing 240 n y N3 C4 NYW doub 241 n y O2' C2' NYW sing 242 n n C6 N6 NYW sing 243 n n C6 C5 NYW doub 244 n y C4 C5 NYW sing 245 n y C4 N9 NYW sing 246 n y C2' C1' NYW sing 247 n n C2' C3' NYW sing 248 n n C5 N7 NYW sing 249 n y C1' N9 NYW sing 250 n n C1' O4' NYW sing 251 n n N9 C8 NYW sing 252 n y O3' C3' NYW sing 253 n n C3' C4' NYW sing 254 n n N7 C8 NYW doub 255 n y O4' C4' NYW sing 256 n n C4' C5' NYW sing 257 n n C5' O5' NYW sing 258 n n O5' PA NYW sing 259 n n O2A PA NYW doub 260 n n PA O1A NYW sing 261 n n PA C3A NYW sing 262 n n O2B PB NYW doub 263 n n C3A PB NYW sing 264 n n PB O3B NYW sing 265 n n PB O1B NYW sing 266 n n O1B H1 NYW sing 267 n n O3B H2 NYW sing 268 n n O1A H3 NYW sing 269 n n C3A H3A2 NYW sing 270 n n C3A H3A1 NYW sing 271 n n C5' "H5'2" NYW sing 272 n n C5' "H5'1" NYW sing 273 n n C4' H4' NYW sing 274 n n C3' H3' NYW sing 275 n n O3' HO3' NYW sing 276 n n C2' H2' NYW sing 277 n n O2' HO2' NYW sing 278 n n C1' H1' NYW sing 279 n n C8 H8 NYW sing 280 n n N6 HN61 NYW sing 281 n n N6 HN62 NYW sing 282 n n N2 H22 NYW sing 283 n n N2 H21 NYW sing 284 n n # _atom_sites.entry_id 6TVX _atom_sites.fract_transf_matrix[1][1] 0.018342 _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] 0.010261 _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] 0.004279 _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 NYW A 1 603 1 NYW 676 . E 4 HOH A 1 701 73 HOH HOH . E 4 HOH A 2 702 63 HOH HOH . E 4 HOH A 3 703 65 HOH HOH . E 4 HOH A 4 704 75 HOH HOH . E 4 HOH A 5 705 78 HOH HOH . E 4 HOH A 6 706 76 HOH HOH . E 4 HOH A 7 707 35 HOH HOH . E 4 HOH A 8 708 61 HOH HOH . E 4 HOH A 9 709 62 HOH HOH . E 4 HOH A 10 710 79 HOH HOH . E 4 HOH A 11 711 30 HOH HOH . E 4 HOH A 12 712 36 HOH HOH . E 4 HOH A 13 713 74 HOH HOH . E 4 HOH A 14 714 71 HOH HOH . E 4 HOH A 15 715 72 HOH HOH . E 4 HOH A 16 716 77 HOH HOH . E 4 HOH A 17 717 69 HOH HOH . E 4 HOH A 18 718 58 HOH HOH . E 4 HOH A 19 719 53 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 C6 NYW . . . D 3 -13.067 23.967 -35.95 1 95.58 ? C6 NYW 603 A 1 HETATM 2 C C4 NYW . . . D 3 -14.563 22.13 -35.789 1 96.84 ? C4 NYW 603 A 1 HETATM 3 C C2 NYW . . . D 3 -14.382 23.239 -37.737 1 94.97 ? C2 NYW 603 A 1 HETATM 4 P PB NYW . . . D 3 -17.281 20.122 -28.919 1 79.98 ? PB NYW 603 A 1 HETATM 5 O O1B NYW . . . D 3 -16.238 20.209 -27.854 1 79.15 ? O1B NYW 603 A 1 HETATM 6 O O2B NYW . . . D 3 -16.759 20.588 -30.291 1 80.14 ? O2B NYW 603 A 1 HETATM 7 O O3B NYW . . . D 3 -18.495 21.01 -28.578 1 81 ? O3B NYW 603 A 1 HETATM 8 P PA NYW . . . D 3 -19.093 18.187 -30.481 1 83.04 ? PA NYW 603 A 1 HETATM 9 O O1A NYW . . . D 3 -20.496 18.748 -30.382 1 82.41 ? O1A NYW 603 A 1 HETATM 10 O O2A NYW . . . D 3 -19.23 16.639 -30.582 1 85 ? O2A NYW 603 A 1 HETATM 11 C C3A NYW . . . D 3 -17.895 18.451 -29.168 1 82.96 ? C3A NYW 603 A 1 HETATM 12 O O5' NYW . . . D 3 -18.323 18.731 -31.742 1 83.2 ? O5' NYW 603 A 1 HETATM 13 C C5' NYW . . . D 3 -17.139 18.083 -32.256 1 86.58 ? C5' NYW 603 A 1 HETATM 14 C C4' NYW . . . D 3 -16.863 18.484 -33.685 1 89.43 ? C4' NYW 603 A 1 HETATM 15 O O4' NYW . . . D 3 -16.638 19.903 -33.801 1 89.81 ? O4' NYW 603 A 1 HETATM 16 C C3' NYW . . . D 3 -15.596 17.875 -34.261 1 91.59 ? C3' NYW 603 A 1 HETATM 17 O O3' NYW . . . D 3 -15.791 16.51 -34.618 1 90.86 ? O3' NYW 603 A 1 HETATM 18 C C2' NYW . . . D 3 -15.271 18.818 -35.428 1 93.35 ? C2' NYW 603 A 1 HETATM 19 O O2' NYW . . . D 3 -15.799 18.388 -36.676 1 94.37 ? O2' NYW 603 A 1 HETATM 20 C C1' NYW . . . D 3 -15.934 20.14 -35.01 1 93.44 ? C1' NYW 603 A 1 HETATM 21 N N9 NYW . . . D 3 -14.986 21.238 -34.83 1 96.06 ? N9 NYW 603 A 1 HETATM 22 C C8 NYW . . . D 3 -14.289 21.558 -33.694 1 96.73 ? C8 NYW 603 A 1 HETATM 23 N N7 NYW . . . D 3 -13.464 22.567 -33.84 1 97.28 ? N7 NYW 603 A 1 HETATM 24 C C5 NYW . . . D 3 -13.633 22.941 -35.165 1 96.74 ? C5 NYW 603 A 1 HETATM 25 N N6 NYW . . . D 3 -12.14 24.82 -35.497 1 94.41 ? N6 NYW 603 A 1 HETATM 26 N N1 NYW . . . D 3 -13.453 24.111 -37.243 1 95.31 ? N1 NYW 603 A 1 HETATM 27 N N3 NYW . . . D 3 -14.977 22.222 -37.057 1 96.39 ? N3 NYW 603 A 1 HETATM 28 N N2 NYW . . . D 3 -14.758 23.413 -39.007 1 93.53 ? N2 NYW 603 A 1 HETATM 29 H H3A2 NYW . . . D 3 -17.046 17.784 -29.311 1 82.87 ? H3A2 NYW 603 A 1 HETATM 30 H H3A1 NYW . . . D 3 -18.292 18.049 -28.24 1 83.09 ? H3A1 NYW 603 A 1 HETATM 31 H "H5'2" NYW . . . D 3 -16.323 18.363 -31.592 1 86.63 ? "H5'2" NYW 603 A 1 HETATM 32 H "H5'1" NYW . . . D 3 -17.211 16.998 -32.198 1 86.53 ? "H5'1" NYW 603 A 1 HETATM 33 H H4' NYW . . . D 3 -17.735 18.292 -34.308 1 89.45 ? H4' NYW 603 A 1 HETATM 34 H H3' NYW . . . D 3 -14.797 17.906 -33.522 1 91.61 ? H3' NYW 603 A 1 HETATM 35 H HO3' NYW . . . D 3 -15.732 16.434 -35.605 1 90.87 ? HO3' NYW 603 A 1 HETATM 36 H H2' NYW . . . D 3 -14.192 18.92 -35.533 1 93.36 ? H2' NYW 603 A 1 HETATM 37 H HO2' NYW . . . D 3 -15.034 18 -37.175 1 94.37 ? HO2' NYW 603 A 1 HETATM 38 H H1' NYW . . . D 3 -16.667 20.472 -35.742 1 93.45 ? H1' NYW 603 A 1 HETATM 39 H H8 NYW . . . D 3 -14.414 21.011 -32.761 1 96.72 ? H8 NYW 603 A 1 HETATM 40 H HN61 NYW . . . D 3 -11.752 25.553 -36.082 1 94.38 ? HN61 NYW 603 A 1 HETATM 41 H HN62 NYW . . . D 3 -11.796 24.739 -34.545 1 94.44 ? HN62 NYW 603 A 1 HETATM 42 H H22 NYW . . . D 3 -14.371 24.164 -39.57 1 93.59 ? H22 NYW 603 A 1 HETATM 43 H H21 NYW . . . D 3 -15.443 22.808 -39.448 1 93.46 ? H21 NYW 603 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 43 #