data_5Y4Q # _model_server_result.job_id FVcJxiEg9RVU21HI7j2yvA _model_server_result.datetime_utc '2024-10-20 03:27:38' _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 5y4q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":301}' # _entry.id 5Y4Q # _exptl.entry_id 5Y4Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 356.444 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.97 _cell.angle_gamma 90 _cell.entry_id 5Y4Q _cell.length_a 43.977 _cell.length_b 99.665 _cell.length_c 134.503 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y4Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 2 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 E N N ? 2 G N N ? 2 I N N ? 2 K N N # _chem_comp.formula 'C14 H24 N6 O3 S' _chem_comp.formula_weight 356.444 _chem_comp.id S4M _chem_comp.mon_nstd_flag . _chem_comp.name "5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE" _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 CA N S4M sing 312 n n CA CB S4M sing 313 n n CA HA1 S4M sing 314 n n CA HA2 S4M sing 315 n n N HN1 S4M sing 316 n n N HN2 S4M sing 317 n n CB CG S4M sing 318 n n CB HB1 S4M sing 319 n n CB HB2 S4M sing 320 n n CG SD S4M sing 321 n n CG HG1 S4M sing 322 n n CG HG2 S4M sing 323 n n SD CE S4M sing 324 n n SD C5' S4M sing 325 n n SD HSD S4M sing 326 n n CE HE1 S4M sing 327 n n CE HE2 S4M sing 328 n n CE HE3 S4M sing 329 n n C5' C4' S4M sing 330 n n C5' "H5'1" S4M sing 331 n n C5' "H5'2" S4M sing 332 n n C4' C3' S4M sing 333 n n C4' O4' S4M sing 334 n n C4' H4' S4M sing 335 n n O4' C1' S4M sing 336 n n C1' C2' S4M sing 337 n n C1' N9 S4M sing 338 n n C1' H1' S4M sing 339 n n C2' O2' S4M sing 340 n n C2' C3' S4M sing 341 n n C2' H2' S4M sing 342 n n O2' HO2' S4M sing 343 n n C3' O3' S4M sing 344 n n C3' H3' S4M sing 345 n n O3' HO3' S4M sing 346 n n N9 C4 S4M sing 347 n y N9 C8 S4M sing 348 n y C8 N7 S4M doub 349 n y C8 H8 S4M sing 350 n n N7 C5 S4M sing 351 n y C5 C4 S4M doub 352 n y C5 C6 S4M sing 353 n y C6 N1 S4M doub 354 n y C6 N6 S4M sing 355 n n N6 HN61 S4M sing 356 n n N6 HN62 S4M sing 357 n n C4 N3 S4M sing 358 n y N3 C2 S4M doub 359 n y C2 N1 S4M sing 360 n y C2 H2 S4M sing 361 n n # _atom_sites.entry_id 5Y4Q _atom_sites.fract_transf_matrix[1][1] 0.022739 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000783 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010034 _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] 0.007439 _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 E 2 S4M A 1 301 1 S4M S4M . F 3 8OF A 1 302 6 8OF UNL . G 2 S4M B 1 301 1 S4M S4M . H 3 8OF B 1 302 10 8OF UNL . I 2 S4M C 1 301 1 S4M S4M . J 3 8OF C 1 302 11 8OF UNL . K 2 S4M D 1 301 1 S4M S4M . L 3 8OF D 1 302 8 8OF UNL . M 4 HOH A 1 401 148 HOH HOH . M 4 HOH A 2 402 163 HOH HOH . M 4 HOH A 3 403 75 HOH HOH . M 4 HOH A 4 404 167 HOH HOH . M 4 HOH A 5 405 99 HOH HOH . M 4 HOH A 6 406 90 HOH HOH . M 4 HOH A 7 407 84 HOH HOH . M 4 HOH A 8 408 41 HOH HOH . M 4 HOH A 9 409 11 HOH HOH . M 4 HOH A 10 410 60 HOH HOH . M 4 HOH A 11 411 68 HOH HOH . M 4 HOH A 12 412 12 HOH HOH . M 4 HOH A 13 413 166 HOH HOH . M 4 HOH A 14 414 80 HOH HOH . M 4 HOH A 15 415 112 HOH HOH . M 4 HOH A 16 416 64 HOH HOH . M 4 HOH A 17 417 63 HOH HOH . M 4 HOH A 18 418 62 HOH HOH . M 4 HOH A 19 419 138 HOH HOH . M 4 HOH A 20 420 174 HOH HOH . M 4 HOH A 21 421 178 HOH HOH . M 4 HOH A 22 422 136 HOH HOH . M 4 HOH A 23 423 89 HOH HOH . M 4 HOH A 24 424 164 HOH HOH . M 4 HOH A 25 425 3 HOH HOH . M 4 HOH A 26 426 81 HOH HOH . M 4 HOH A 27 427 135 HOH HOH . M 4 HOH A 28 428 173 HOH HOH . M 4 HOH A 29 429 72 HOH HOH . M 4 HOH A 30 430 71 HOH HOH . M 4 HOH A 31 431 153 HOH HOH . M 4 HOH A 32 432 93 HOH HOH . N 4 HOH B 1 401 180 HOH HOH . N 4 HOH B 2 402 137 HOH HOH . N 4 HOH B 3 403 169 HOH HOH . N 4 HOH B 4 404 142 HOH HOH . N 4 HOH B 5 405 43 HOH HOH . N 4 HOH B 6 406 17 HOH HOH . N 4 HOH B 7 407 102 HOH HOH . N 4 HOH B 8 408 82 HOH HOH . N 4 HOH B 9 409 129 HOH HOH . N 4 HOH B 10 410 179 HOH HOH . N 4 HOH B 11 411 133 HOH HOH . N 4 HOH B 12 412 77 HOH HOH . N 4 HOH B 13 413 73 HOH HOH . N 4 HOH B 14 414 98 HOH HOH . N 4 HOH B 15 415 97 HOH HOH . N 4 HOH B 16 416 19 HOH HOH . N 4 HOH B 17 417 128 HOH HOH . N 4 HOH B 18 418 59 HOH HOH . N 4 HOH B 19 419 131 HOH HOH . N 4 HOH B 20 420 154 HOH HOH . N 4 HOH B 21 421 144 HOH HOH . N 4 HOH B 22 422 91 HOH HOH . N 4 HOH B 23 423 74 HOH HOH . N 4 HOH B 24 424 40 HOH HOH . N 4 HOH B 25 425 126 HOH HOH . N 4 HOH B 26 426 141 HOH HOH . N 4 HOH B 27 427 47 HOH HOH . N 4 HOH B 28 428 116 HOH HOH . N 4 HOH B 29 429 52 HOH HOH . N 4 HOH B 30 430 152 HOH HOH . N 4 HOH B 31 431 56 HOH HOH . N 4 HOH B 32 432 125 HOH HOH . N 4 HOH B 33 433 171 HOH HOH . N 4 HOH B 34 434 132 HOH HOH . N 4 HOH B 35 435 27 HOH HOH . N 4 HOH B 36 436 57 HOH HOH . N 4 HOH B 37 437 66 HOH HOH . N 4 HOH B 38 438 29 HOH HOH . N 4 HOH B 39 439 96 HOH HOH . O 4 HOH C 1 401 115 HOH HOH . O 4 HOH C 2 402 87 HOH HOH . O 4 HOH C 3 403 65 HOH HOH . O 4 HOH C 4 404 49 HOH HOH . O 4 HOH C 5 405 70 HOH HOH . O 4 HOH C 6 406 121 HOH HOH . O 4 HOH C 7 407 176 HOH HOH . O 4 HOH C 8 408 134 HOH HOH . O 4 HOH C 9 409 5 HOH HOH . O 4 HOH C 10 410 160 HOH HOH . O 4 HOH C 11 411 165 HOH HOH . O 4 HOH C 12 412 107 HOH HOH . O 4 HOH C 13 413 23 HOH HOH . O 4 HOH C 14 414 32 HOH HOH . O 4 HOH C 15 415 61 HOH HOH . O 4 HOH C 16 416 124 HOH HOH . O 4 HOH C 17 417 106 HOH HOH . O 4 HOH C 18 418 94 HOH HOH . O 4 HOH C 19 419 46 HOH HOH . O 4 HOH C 20 420 8 HOH HOH . O 4 HOH C 21 421 53 HOH HOH . O 4 HOH C 22 422 161 HOH HOH . O 4 HOH C 23 423 33 HOH HOH . O 4 HOH C 24 424 54 HOH HOH . O 4 HOH C 25 425 103 HOH HOH . O 4 HOH C 26 426 85 HOH HOH . O 4 HOH C 27 427 4 HOH HOH . O 4 HOH C 28 428 7 HOH HOH . O 4 HOH C 29 429 127 HOH HOH . O 4 HOH C 30 430 79 HOH HOH . O 4 HOH C 31 431 58 HOH HOH . O 4 HOH C 32 432 22 HOH HOH . O 4 HOH C 33 433 175 HOH HOH . O 4 HOH C 34 434 76 HOH HOH . O 4 HOH C 35 435 172 HOH HOH . O 4 HOH C 36 436 100 HOH HOH . O 4 HOH C 37 437 38 HOH HOH . O 4 HOH C 38 438 88 HOH HOH . O 4 HOH C 39 439 48 HOH HOH . O 4 HOH C 40 440 122 HOH HOH . O 4 HOH C 41 441 147 HOH HOH . O 4 HOH C 42 442 105 HOH HOH . O 4 HOH C 43 443 159 HOH HOH . O 4 HOH C 44 444 92 HOH HOH . O 4 HOH C 45 445 95 HOH HOH . O 4 HOH C 46 446 10 HOH HOH . O 4 HOH C 47 447 168 HOH HOH . O 4 HOH C 48 448 39 HOH HOH . O 4 HOH C 49 449 1 HOH HOH . O 4 HOH C 50 450 143 HOH HOH . O 4 HOH C 51 451 6 HOH HOH . O 4 HOH C 52 452 67 HOH HOH . P 4 HOH D 1 401 177 HOH HOH . P 4 HOH D 2 402 111 HOH HOH . P 4 HOH D 3 403 78 HOH HOH . P 4 HOH D 4 404 69 HOH HOH . P 4 HOH D 5 405 83 HOH HOH . P 4 HOH D 6 406 130 HOH HOH . P 4 HOH D 7 407 36 HOH HOH . P 4 HOH D 8 408 21 HOH HOH . P 4 HOH D 9 409 139 HOH HOH . P 4 HOH D 10 410 26 HOH HOH . P 4 HOH D 11 411 50 HOH HOH . P 4 HOH D 12 412 18 HOH HOH . P 4 HOH D 13 413 162 HOH HOH . P 4 HOH D 14 414 86 HOH HOH . P 4 HOH D 15 415 101 HOH HOH . P 4 HOH D 16 416 24 HOH HOH . P 4 HOH D 17 417 13 HOH HOH . P 4 HOH D 18 418 35 HOH HOH . P 4 HOH D 19 419 150 HOH HOH . P 4 HOH D 20 420 109 HOH HOH . P 4 HOH D 21 421 30 HOH HOH . P 4 HOH D 22 422 55 HOH HOH . P 4 HOH D 23 423 14 HOH HOH . P 4 HOH D 24 424 158 HOH HOH . P 4 HOH D 25 425 44 HOH HOH . P 4 HOH D 26 426 51 HOH HOH . P 4 HOH D 27 427 34 HOH HOH . P 4 HOH D 28 428 45 HOH HOH . P 4 HOH D 29 429 155 HOH HOH . P 4 HOH D 30 430 157 HOH HOH . P 4 HOH D 31 431 120 HOH HOH . P 4 HOH D 32 432 146 HOH HOH . P 4 HOH D 33 433 25 HOH HOH . P 4 HOH D 34 434 20 HOH HOH . P 4 HOH D 35 435 15 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 CA S4M . . . K 2 10.48 11.85 39.033 1 48.94 ? CA S4M 301 D 1 HETATM 2 N N S4M . . . K 2 9.89 11.523 37.711 1 43.16 ? N S4M 301 D 1 HETATM 3 C CB S4M . . . K 2 10.906 10.548 39.671 1 50.84 ? CB S4M 301 D 1 HETATM 4 C CG S4M . . . K 2 12.345 10.161 39.353 1 55.85 ? CG S4M 301 D 1 HETATM 5 S SD S4M . . . K 2 12.532 9.155 37.835 1 58.26 ? SD S4M 301 D 1 HETATM 6 C CE S4M . . . K 2 11.492 7.738 38.334 1 56.89 ? CE S4M 301 D 1 HETATM 7 C C5' S4M . . . K 2 14.156 8.45 38.304 1 51.79 ? C5' S4M 301 D 1 HETATM 8 C C4' S4M . . . K 2 14.633 7.499 37.209 1 47.98 ? C4' S4M 301 D 1 HETATM 9 O O4' S4M . . . K 2 16.012 7.639 36.876 1 46.54 ? O4' S4M 301 D 1 HETATM 10 C C1' S4M . . . K 2 16.441 6.342 36.454 1 44.36 ? C1' S4M 301 D 1 HETATM 11 C C2' S4M . . . K 2 15.822 5.433 37.482 1 44.87 ? C2' S4M 301 D 1 HETATM 12 O O2' S4M . . . K 2 15.749 4.095 37.02 1 40.63 ? O2' S4M 301 D 1 HETATM 13 C C3' S4M . . . K 2 14.467 6.074 37.667 1 46.1 ? C3' S4M 301 D 1 HETATM 14 O O3' S4M . . . K 2 13.462 5.535 36.828 1 47.16 ? O3' S4M 301 D 1 HETATM 15 N N9 S4M . . . K 2 17.893 6.257 36.386 1 44.69 ? N9 S4M 301 D 1 HETATM 16 C C8 S4M . . . K 2 18.763 6.169 37.438 1 45.12 ? C8 S4M 301 D 1 HETATM 17 N N7 S4M . . . K 2 20.013 6.108 37.029 1 43.89 ? N7 S4M 301 D 1 HETATM 18 C C5 S4M . . . K 2 19.944 6.161 35.662 1 43.16 ? C5 S4M 301 D 1 HETATM 19 C C6 S4M . . . K 2 20.934 6.135 34.692 1 43.63 ? C6 S4M 301 D 1 HETATM 20 N N6 S4M . . . K 2 22.283 6.042 35.023 1 43.01 ? N6 S4M 301 D 1 HETATM 21 C C4 S4M . . . K 2 18.634 6.255 35.241 1 43.47 ? C4 S4M 301 D 1 HETATM 22 N N3 S4M . . . K 2 18.208 6.319 33.975 1 42.72 ? N3 S4M 301 D 1 HETATM 23 C C2 S4M . . . K 2 19.246 6.29 33.133 1 43.28 ? C2 S4M 301 D 1 HETATM 24 N N1 S4M . . . K 2 20.556 6.205 33.407 1 43.55 ? N1 S4M 301 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #