data_6Y7F # _model_server_result.job_id KKb7jhIklxeAF9o6wGuIcg _model_server_result.datetime_utc '2024-10-19 00:43:37' _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 6y7f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 6Y7F # _exptl.entry_id 6Y7F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 1076.033 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-oxidanylideneicosanethioate' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.03 _cell.angle_gamma 90 _cell.entry_id 6Y7F _cell.length_a 63.229 _cell.length_b 72.459 _cell.length_c 112.043 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y7F _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,G,H,I,J,K,L _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 H N 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 99 A CYS 99 1_555 A SG CYS 231 A CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf2 B SG CYS 99 B CYS 99 1_555 B SG CYS 231 B CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? covale ? covale1 A NE2 HIS 150 A HIS 150 1_555 C C25 OFN . A OFN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.481 ? covale ? covale2 A NE2 HIS 181 A HIS 181 1_555 C C OFN . A OFN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.512 ? covale ? covale3 B NE2 HIS 150 B HIS 150 1_555 H C25 OFN . B OFN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale4 B NE2 HIS 181 B HIS 181 1_555 H C OFN . B OFN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.516 ? # _chem_comp.formula 'C41 H72 N7 O18 P3 S' _chem_comp.formula_weight 1076.033 _chem_comp.id OFN _chem_comp.mon_nstd_flag . _chem_comp.name '~{S}-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-oxidanylideneicosanethioate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6Y7F _atom_sites.fract_transf_matrix[1][1] 0.015816 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002797 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013801 _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] 0.009064 _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 C 2 OFN A 1 301 301 OFN MLS . D 3 37X A 1 302 501 37X 37X . E 3 37X A 1 303 601 37X 37X . F 3 37X A 1 304 701 37X 37X . G 4 CL A 1 305 1 CL CL . H 2 OFN B 1 301 301 OFN MLS . I 3 37X B 1 302 401 37X 37X . J 4 CL B 1 303 2 CL CL . K 5 HOH A 1 401 114 HOH HOH . K 5 HOH A 2 402 27 HOH HOH . K 5 HOH A 3 403 40 HOH HOH . K 5 HOH A 4 404 57 HOH HOH . K 5 HOH A 5 405 76 HOH HOH . K 5 HOH A 6 406 87 HOH HOH . K 5 HOH A 7 407 4 HOH HOH . K 5 HOH A 8 408 5 HOH HOH . K 5 HOH A 9 409 72 HOH HOH . K 5 HOH A 10 410 36 HOH HOH . K 5 HOH A 11 411 74 HOH HOH . K 5 HOH A 12 412 39 HOH HOH . K 5 HOH A 13 413 35 HOH HOH . K 5 HOH A 14 414 1 HOH HOH . K 5 HOH A 15 415 100 HOH HOH . K 5 HOH A 16 416 66 HOH HOH . K 5 HOH A 17 417 49 HOH HOH . K 5 HOH A 18 418 41 HOH HOH . K 5 HOH A 19 419 30 HOH HOH . K 5 HOH A 20 420 37 HOH HOH . K 5 HOH A 21 421 79 HOH HOH . K 5 HOH A 22 422 62 HOH HOH . K 5 HOH A 23 423 15 HOH HOH . K 5 HOH A 24 424 60 HOH HOH . K 5 HOH A 25 425 21 HOH HOH . K 5 HOH A 26 426 102 HOH HOH . K 5 HOH A 27 427 14 HOH HOH . K 5 HOH A 28 428 34 HOH HOH . K 5 HOH A 29 429 3 HOH HOH . K 5 HOH A 30 430 16 HOH HOH . K 5 HOH A 31 431 101 HOH HOH . K 5 HOH A 32 432 69 HOH HOH . K 5 HOH A 33 433 71 HOH HOH . K 5 HOH A 34 434 97 HOH HOH . K 5 HOH A 35 435 17 HOH HOH . K 5 HOH A 36 436 95 HOH HOH . K 5 HOH A 37 437 13 HOH HOH . K 5 HOH A 38 438 70 HOH HOH . K 5 HOH A 39 439 65 HOH HOH . K 5 HOH A 40 440 67 HOH HOH . K 5 HOH A 41 441 106 HOH HOH . K 5 HOH A 42 442 64 HOH HOH . K 5 HOH A 43 443 111 HOH HOH . K 5 HOH A 44 444 38 HOH HOH . K 5 HOH A 45 445 8 HOH HOH . K 5 HOH A 46 446 42 HOH HOH . K 5 HOH A 47 447 9 HOH HOH . K 5 HOH A 48 448 59 HOH HOH . K 5 HOH A 49 449 98 HOH HOH . K 5 HOH A 50 450 115 HOH HOH . K 5 HOH A 51 451 89 HOH HOH . K 5 HOH A 52 452 78 HOH HOH . K 5 HOH A 53 453 85 HOH HOH . K 5 HOH A 54 454 22 HOH HOH . K 5 HOH A 55 455 103 HOH HOH . K 5 HOH A 56 456 94 HOH HOH . K 5 HOH A 57 457 88 HOH HOH . K 5 HOH A 58 458 112 HOH HOH . K 5 HOH A 59 459 80 HOH HOH . K 5 HOH A 60 460 75 HOH HOH . K 5 HOH A 61 461 96 HOH HOH . L 5 HOH B 1 401 48 HOH HOH . L 5 HOH B 2 402 104 HOH HOH . L 5 HOH B 3 403 68 HOH HOH . L 5 HOH B 4 404 53 HOH HOH . L 5 HOH B 5 405 45 HOH HOH . L 5 HOH B 6 406 50 HOH HOH . L 5 HOH B 7 407 28 HOH HOH . L 5 HOH B 8 408 43 HOH HOH . L 5 HOH B 9 409 19 HOH HOH . L 5 HOH B 10 410 51 HOH HOH . L 5 HOH B 11 411 6 HOH HOH . L 5 HOH B 12 412 47 HOH HOH . L 5 HOH B 13 413 44 HOH HOH . L 5 HOH B 14 414 24 HOH HOH . L 5 HOH B 15 415 55 HOH HOH . L 5 HOH B 16 416 23 HOH HOH . L 5 HOH B 17 417 2 HOH HOH . L 5 HOH B 18 418 32 HOH HOH . L 5 HOH B 19 419 90 HOH HOH . L 5 HOH B 20 420 12 HOH HOH . L 5 HOH B 21 421 54 HOH HOH . L 5 HOH B 22 422 84 HOH HOH . L 5 HOH B 23 423 52 HOH HOH . L 5 HOH B 24 424 82 HOH HOH . L 5 HOH B 25 425 91 HOH HOH . L 5 HOH B 26 426 33 HOH HOH . L 5 HOH B 27 427 18 HOH HOH . L 5 HOH B 28 428 25 HOH HOH . L 5 HOH B 29 429 108 HOH HOH . L 5 HOH B 30 430 83 HOH HOH . L 5 HOH B 31 431 31 HOH HOH . L 5 HOH B 32 432 20 HOH HOH . L 5 HOH B 33 433 61 HOH HOH . L 5 HOH B 34 434 7 HOH HOH . L 5 HOH B 35 435 63 HOH HOH . L 5 HOH B 36 436 99 HOH HOH . L 5 HOH B 37 437 113 HOH HOH . L 5 HOH B 38 438 10 HOH HOH . L 5 HOH B 39 439 46 HOH HOH . L 5 HOH B 40 440 109 HOH HOH . L 5 HOH B 41 441 73 HOH HOH . L 5 HOH B 42 442 105 HOH HOH . L 5 HOH B 43 443 58 HOH HOH . L 5 HOH B 44 444 86 HOH HOH . L 5 HOH B 45 445 11 HOH HOH . L 5 HOH B 46 446 93 HOH HOH . L 5 HOH B 47 447 107 HOH HOH . L 5 HOH B 48 448 26 HOH HOH . L 5 HOH B 49 449 110 HOH HOH . L 5 HOH B 50 450 92 HOH HOH . L 5 HOH B 51 451 81 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 C16 OFN . . . C 2 20.36 39.85 -1.546 1 37.87 ? C16 OFN 301 A 1 HETATM 2 C C17 OFN . . . C 2 21.121 39.894 -0.229 1 37.7 ? C17 OFN 301 A 1 HETATM 3 C C18 OFN . . . C 2 21.911 38.342 1.601 1 38.72 ? C18 OFN 301 A 1 HETATM 4 C C19 OFN . . . C 2 23.551 38.404 3.067 1 38.87 ? C19 OFN 301 A 1 HETATM 5 C C20 OFN . . . C 2 22.131 36.588 3.197 1 38.88 ? C20 OFN 301 A 1 HETATM 6 C C21 OFN . . . C 2 21.455 37.125 2.081 1 38.88 ? C21 OFN 301 A 1 HETATM 7 C C22 OFN . . . C 2 20.228 37.603 0.416 1 38.41 ? C22 OFN 301 A 1 HETATM 8 O O10 OFN . . . C 2 18.333 42.632 1.257 1 33.72 ? O10 OFN 301 A 1 HETATM 9 O O14 OFN . . . C 2 20.628 43.359 -4.021 1 41.34 ? O14 OFN 301 A 1 HETATM 10 O O15 OFN . . . C 2 21.107 39.204 -2.568 1 38.02 ? O15 OFN 301 A 1 HETATM 11 C C23 OFN . . . C 2 17.076 38.043 14.562 1 41.91 ? C23 OFN 301 A 1 HETATM 12 C C24 OFN . . . C 2 16.405 39.307 15.039 1 40.58 ? C24 OFN 301 A 1 HETATM 13 C C25 OFN . . . C 2 16.998 40.033 16.248 1 39.31 ? C25 OFN 301 A 1 HETATM 14 O O17 OFN . . . C 2 17.361 37.17 15.358 1 41.85 ? O17 OFN 301 A 1 HETATM 15 C C26 OFN . . . C 2 16.678 39.357 17.581 1 38.72 ? C26 OFN 301 A 1 HETATM 16 C C27 OFN . . . C 2 15.832 40.217 18.519 1 38.11 ? C27 OFN 301 A 1 HETATM 17 C C28 OFN . . . C 2 15.457 39.535 19.837 1 37.3 ? C28 OFN 301 A 1 HETATM 18 C C29 OFN . . . C 2 14.392 40.251 20.675 1 36.2 ? C29 OFN 301 A 1 HETATM 19 C C30 OFN . . . C 2 14.892 41.059 21.882 1 35.34 ? C30 OFN 301 A 1 HETATM 20 C C31 OFN . . . C 2 15.21 40.237 23.128 1 34.64 ? C31 OFN 301 A 1 HETATM 21 C C32 OFN . . . C 2 16.575 39.59 23.076 1 34.22 ? C32 OFN 301 A 1 HETATM 22 C C33 OFN . . . C 2 17.167 39.174 24.4 1 34.4 ? C33 OFN 301 A 1 HETATM 23 C C34 OFN . . . C 2 18.45 38.367 24.215 1 34.81 ? C34 OFN 301 A 1 HETATM 24 C C35 OFN . . . C 2 19.099 37.869 25.504 1 34.52 ? C35 OFN 301 A 1 HETATM 25 C C36 OFN . . . C 2 18.283 36.839 26.234 1 34.43 ? C36 OFN 301 A 1 HETATM 26 C C37 OFN . . . C 2 19.041 36.145 27.341 1 34.83 ? C37 OFN 301 A 1 HETATM 27 C C38 OFN . . . C 2 18.53 34.751 27.627 1 35.45 ? C38 OFN 301 A 1 HETATM 28 C C39 OFN . . . C 2 17.337 34.704 28.54 1 36.01 ? C39 OFN 301 A 1 HETATM 29 C C40 OFN . . . C 2 16.916 33.295 28.86 1 36.64 ? C40 OFN 301 A 1 HETATM 30 C C OFN . . . C 2 17.484 37.871 13.033 1 43.04 ? C OFN 301 A 1 HETATM 31 C C1 OFN . . . C 2 17.666 39.023 12.061 1 45.9 ? C1 OFN 301 A 1 HETATM 32 O O OFN . . . C 2 18.258 38.884 11.023 1 47.68 ? O OFN 301 A 1 HETATM 33 S S OFN . . . C 2 17.19 40.608 12.663 1 46.85 ? S OFN 301 A 1 HETATM 34 C C2 OFN . . . C 2 18.49 41.734 11.957 1 44.53 ? C2 OFN 301 A 1 HETATM 35 C C3 OFN . . . C 2 18.666 41.731 10.444 1 42.67 ? C3 OFN 301 A 1 HETATM 36 N N OFN . . . C 2 18.448 43.021 9.785 1 40.19 ? N OFN 301 A 1 HETATM 37 C C4 OFN . . . C 2 19.403 43.701 9.142 1 37.49 ? C4 OFN 301 A 1 HETATM 38 O O1 OFN . . . C 2 20.537 43.264 8.988 1 36.92 ? O1 OFN 301 A 1 HETATM 39 C C5 OFN . . . C 2 19.056 45.082 8.626 1 36.2 ? C5 OFN 301 A 1 HETATM 40 C C6 OFN . . . C 2 17.726 45.618 9.11 1 34.14 ? C6 OFN 301 A 1 HETATM 41 N N1 OFN . . . C 2 16.698 45.483 8.089 1 31.98 ? N1 OFN 301 A 1 HETATM 42 C C7 OFN . . . C 2 15.76 44.549 8.151 1 29.92 ? C7 OFN 301 A 1 HETATM 43 O O2 OFN . . . C 2 15.751 43.69 9.023 1 29.75 ? O2 OFN 301 A 1 HETATM 44 C C8 OFN . . . C 2 14.65 44.622 7.112 1 29.19 ? C8 OFN 301 A 1 HETATM 45 O O3 OFN . . . C 2 13.394 44.707 7.762 1 29.04 ? O3 OFN 301 A 1 HETATM 46 C C9 OFN . . . C 2 14.728 43.526 6.017 1 28.53 ? C9 OFN 301 A 1 HETATM 47 C C10 OFN . . . C 2 13.603 43.721 4.994 1 27.95 ? C10 OFN 301 A 1 HETATM 48 C C11 OFN . . . C 2 14.597 42.13 6.638 1 28.24 ? C11 OFN 301 A 1 HETATM 49 C C12 OFN . . . C 2 16.068 43.61 5.295 1 28.82 ? C12 OFN 301 A 1 HETATM 50 O O4 OFN . . . C 2 16.214 44.9 4.665 1 29.26 ? O4 OFN 301 A 1 HETATM 51 P P OFN . . . C 2 17.523 45.514 3.991 1 30.22 ? P OFN 301 A 1 HETATM 52 O O5 OFN . . . C 2 17.302 46.786 3.279 1 29.97 ? O5 OFN 301 A 1 HETATM 53 O O6 OFN . . . C 2 18.592 45.588 5.052 1 30.65 ? O6 OFN 301 A 1 HETATM 54 O O7 OFN . . . C 2 18.013 44.409 2.956 1 31.36 ? O7 OFN 301 A 1 HETATM 55 P P1 OFN . . . C 2 17.863 44.185 1.388 1 32 ? P1 OFN 301 A 1 HETATM 56 O O8 OFN . . . C 2 16.459 44.337 0.963 1 32.15 ? O8 OFN 301 A 1 HETATM 57 O O9 OFN . . . C 2 18.909 45.029 0.678 1 31.51 ? O9 OFN 301 A 1 HETATM 58 C C13 OFN . . . C 2 18.464 42.103 -0.07 1 34.98 ? C13 OFN 301 A 1 HETATM 59 C C14 OFN . . . C 2 19.924 41.893 -0.38 1 36.6 ? C14 OFN 301 A 1 HETATM 60 O O16 OFN . . . C 2 20.501 40.92 0.525 1 37.2 ? O16 OFN 301 A 1 HETATM 61 C C15 OFN . . . C 2 20.204 41.351 -1.78 1 37.89 ? C15 OFN 301 A 1 HETATM 62 O O11 OFN . . . C 2 21.454 41.876 -2.267 1 39.47 ? O11 OFN 301 A 1 HETATM 63 P P2 OFN . . . C 2 21.692 42.293 -3.771 1 41.37 ? P2 OFN 301 A 1 HETATM 64 O O13 OFN . . . C 2 23.076 42.905 -3.778 1 42.01 ? O13 OFN 301 A 1 HETATM 65 O O12 OFN . . . C 2 21.574 41.046 -4.641 1 41.63 ? O12 OFN 301 A 1 HETATM 66 N N2 OFN . . . C 2 21.094 38.658 0.543 1 38.26 ? N2 OFN 301 A 1 HETATM 67 N N6 OFN . . . C 2 20.396 36.662 1.314 1 38.67 ? N6 OFN 301 A 1 HETATM 68 N N5 OFN . . . C 2 21.734 35.502 3.865 1 38.56 ? N5 OFN 301 A 1 HETATM 69 N N4 OFN . . . C 2 23.203 37.264 3.663 1 39.01 ? N4 OFN 301 A 1 HETATM 70 N N3 OFN . . . C 2 22.96 39.036 2.051 1 38.84 ? N3 OFN 301 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 70 #