data_6Y7F # _model_server_result.job_id SkhdCF_HpeSBlRKI3p7Uqg _model_server_result.datetime_utc '2024-10-19 00:54:05' _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":"H","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 . . . H 2 7.721 62.657 52.316 1 59.93 ? C16 OFN 301 B 1 HETATM 2 C C17 OFN . . . H 2 8.911 62.858 51.387 1 59.12 ? C17 OFN 301 B 1 HETATM 3 C C18 OFN . . . H 2 9.865 64.628 49.843 1 58.16 ? C18 OFN 301 B 1 HETATM 4 C C19 OFN . . . H 2 11.875 65.074 49.066 1 57.65 ? C19 OFN 301 B 1 HETATM 5 C C20 OFN . . . H 2 10.158 66.415 48.3 1 58.77 ? C20 OFN 301 B 1 HETATM 6 C C21 OFN . . . H 2 9.297 65.672 49.133 1 58.5 ? C21 OFN 301 B 1 HETATM 7 C C22 OFN . . . H 2 7.728 64.806 50.27 1 58.53 ? C22 OFN 301 B 1 HETATM 8 O O10 OFN . . . H 2 7.772 59.536 49.164 1 53.58 ? O10 OFN 301 B 1 HETATM 9 O O14 OFN . . . H 2 7.754 59.376 55.034 1 65.81 ? O14 OFN 301 B 1 HETATM 10 O O15 OFN . . . H 2 7.789 63.452 53.499 1 60.3 ? O15 OFN 301 B 1 HETATM 11 C C23 OFN . . . H 2 9.716 64.052 35.983 1 50.41 ? C23 OFN 301 B 1 HETATM 12 C C24 OFN . . . H 2 9.711 62.651 35.423 1 48.14 ? C24 OFN 301 B 1 HETATM 13 C C25 OFN . . . H 2 10.86 62.29 34.481 1 45.69 ? C25 OFN 301 B 1 HETATM 14 O O17 OFN . . . H 2 9.917 64.987 35.236 1 51.19 ? O17 OFN 301 B 1 HETATM 15 C C26 OFN . . . H 2 10.78 63.008 33.13 1 44.61 ? C26 OFN 301 B 1 HETATM 16 C C27 OFN . . . H 2 10.163 62.179 31.986 1 43.12 ? C27 OFN 301 B 1 HETATM 17 C C28 OFN . . . H 2 10.217 62.873 30.62 1 41.47 ? C28 OFN 301 B 1 HETATM 18 C C29 OFN . . . H 2 9.747 62.069 29.399 1 39.68 ? C29 OFN 301 B 1 HETATM 19 C C30 OFN . . . H 2 10.793 61.201 28.683 1 37.98 ? C30 OFN 301 B 1 HETATM 20 C C31 OFN . . . H 2 11.516 61.842 27.487 1 35.85 ? C31 OFN 301 B 1 HETATM 21 C C32 OFN . . . H 2 12.412 62.999 27.898 1 34.21 ? C32 OFN 301 B 1 HETATM 22 C C33 OFN . . . H 2 13.406 63.493 26.871 1 33.26 ? C33 OFN 301 B 1 HETATM 23 C C34 OFN . . . H 2 14.31 64.575 27.445 1 33.27 ? C34 OFN 301 B 1 HETATM 24 C C35 OFN . . . H 2 15.248 65.238 26.441 1 33.52 ? C35 OFN 301 B 1 HETATM 25 C C36 OFN . . . H 2 14.555 66.152 25.443 1 33.55 ? C36 OFN 301 B 1 HETATM 26 C C37 OFN . . . H 2 15.518 66.971 24.606 1 33.77 ? C37 OFN 301 B 1 HETATM 27 C C38 OFN . . . H 2 14.939 68.282 24.07 1 33.56 ? C38 OFN 301 B 1 HETATM 28 C C39 OFN . . . H 2 13.722 68.108 23.196 1 33.7 ? C39 OFN 301 B 1 HETATM 29 C C40 OFN . . . H 2 13.307 69.363 22.465 1 33.86 ? C40 OFN 301 B 1 HETATM 30 C C OFN . . . H 2 9.579 64.325 37.548 1 51.51 ? C OFN 301 B 1 HETATM 31 C C1 OFN . . . H 2 9.588 63.243 38.61 1 53.89 ? C1 OFN 301 B 1 HETATM 32 O O OFN . . . H 2 9.719 63.515 39.775 1 54.7 ? O OFN 301 B 1 HETATM 33 S S OFN . . . H 2 9.693 61.588 38.011 1 55.74 ? S OFN 301 B 1 HETATM 34 C C2 OFN . . . H 2 10.903 60.812 39.181 1 53.48 ? C2 OFN 301 B 1 HETATM 35 C C3 OFN . . . H 2 10.668 60.846 40.686 1 50.93 ? C3 OFN 301 B 1 HETATM 36 N N OFN . . . H 2 10.607 59.508 41.271 1 48.64 ? N OFN 301 B 1 HETATM 37 C C4 OFN . . . H 2 11.486 59.026 42.159 1 46.1 ? C4 OFN 301 B 1 HETATM 38 O O1 OFN . . . H 2 12.383 59.709 42.642 1 45.23 ? O1 OFN 301 B 1 HETATM 39 C C5 OFN . . . H 2 11.357 57.56 42.537 1 44.65 ? C5 OFN 301 B 1 HETATM 40 C C6 OFN . . . H 2 10.378 56.774 41.677 1 42.93 ? C6 OFN 301 B 1 HETATM 41 N N1 OFN . . . H 2 9.082 56.619 42.322 1 42.1 ? N1 OFN 301 B 1 HETATM 42 C C7 OFN . . . H 2 7.995 57.278 41.921 1 42.39 ? C7 OFN 301 B 1 HETATM 43 O O2 OFN . . . H 2 8.015 58.08 40.991 1 42.02 ? O2 OFN 301 B 1 HETATM 44 C C8 OFN . . . H 2 6.69 56.965 42.649 1 43.04 ? C8 OFN 301 B 1 HETATM 45 O O3 OFN . . . H 2 5.707 56.645 41.678 1 43.03 ? O3 OFN 301 B 1 HETATM 46 C C9 OFN . . . H 2 6.198 58.021 43.676 1 43.52 ? C9 OFN 301 B 1 HETATM 47 C C10 OFN . . . H 2 4.884 57.551 44.315 1 43.31 ? C10 OFN 301 B 1 HETATM 48 C C11 OFN . . . H 2 5.971 59.379 43.008 1 43.08 ? C11 OFN 301 B 1 HETATM 49 C C12 OFN . . . H 2 7.229 58.207 44.782 1 44.45 ? C12 OFN 301 B 1 HETATM 50 O O4 OFN . . . H 2 7.6 56.93 45.324 1 45.81 ? O4 OFN 301 B 1 HETATM 51 P P OFN . . . H 2 8.671 56.658 46.425 1 46.93 ? P OFN 301 B 1 HETATM 52 O O5 OFN . . . H 2 8.496 55.362 47.126 1 46.87 ? O5 OFN 301 B 1 HETATM 53 O O6 OFN . . . H 2 10.017 56.959 45.786 1 46.47 ? O6 OFN 301 B 1 HETATM 54 O O7 OFN . . . H 2 8.36 57.86 47.418 1 48.72 ? O7 OFN 301 B 1 HETATM 55 P P1 OFN . . . H 2 7.668 57.967 48.847 1 50.96 ? P1 OFN 301 B 1 HETATM 56 O O8 OFN . . . H 2 6.26 57.551 48.837 1 50.79 ? O8 OFN 301 B 1 HETATM 57 O O9 OFN . . . H 2 8.58 57.295 49.855 1 51.36 ? O9 OFN 301 B 1 HETATM 58 C C13 OFN . . . H 2 7.184 60.032 50.374 1 55.87 ? C13 OFN 301 B 1 HETATM 59 C C14 OFN . . . H 2 8.292 60.612 51.213 1 58.4 ? C14 OFN 301 B 1 HETATM 60 O O16 OFN . . . H 2 8.915 61.728 50.532 1 58.93 ? O16 OFN 301 B 1 HETATM 61 C C15 OFN . . . H 2 7.845 61.156 52.565 1 60.36 ? C15 OFN 301 B 1 HETATM 62 O O11 OFN . . . H 2 8.91 60.907 53.501 1 62.94 ? O11 OFN 301 B 1 HETATM 63 P P2 OFN . . . H 2 8.704 60.58 55.024 1 65.63 ? P2 OFN 301 B 1 HETATM 64 O O13 OFN . . . H 2 10.079 60.172 55.566 1 66.27 ? O13 OFN 301 B 1 HETATM 65 O O12 OFN . . . H 2 8.152 61.82 55.683 1 65.97 ? O12 OFN 301 B 1 HETATM 66 N N2 OFN . . . H 2 8.839 64.059 50.558 1 58.63 ? N2 OFN 301 B 1 HETATM 67 N N6 OFN . . . H 2 7.945 65.783 49.421 1 58.54 ? N6 OFN 301 B 1 HETATM 68 N N5 OFN . . . H 2 9.745 67.368 47.456 1 58.91 ? N5 OFN 301 B 1 HETATM 69 N N4 OFN . . . H 2 11.468 66.088 48.303 1 58.37 ? N4 OFN 301 B 1 HETATM 70 N N3 OFN . . . H 2 11.153 64.278 49.853 1 57.69 ? N3 OFN 301 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 70 #