data_4YUZ # _model_server_result.job_id pG8mnw1D-33a-p06nUgTwA _model_server_result.datetime_utc '2024-11-05 04:39:00' _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 4yuz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":301}' # _entry.id 4YUZ # _exptl.entry_id 4YUZ _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 91.7 _cell.angle_gamma 90 _cell.entry_id 4YUZ _cell.length_a 43.531 _cell.length_b 99.665 _cell.length_c 134.606 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YUZ _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,K,L 1 1 C,D,H,I,J,M,N 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 F N N ? 2 H N N ? 2 I 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 316 n n CA CB S4M sing 317 n n CA HA1 S4M sing 318 n n CA HA2 S4M sing 319 n n N HN1 S4M sing 320 n n N HN2 S4M sing 321 n n CB CG S4M sing 322 n n CB HB1 S4M sing 323 n n CB HB2 S4M sing 324 n n CG SD S4M sing 325 n n CG HG1 S4M sing 326 n n CG HG2 S4M sing 327 n n SD CE S4M sing 328 n n SD C5' S4M sing 329 n n SD HSD S4M sing 330 n n CE HE1 S4M sing 331 n n CE HE2 S4M sing 332 n n CE HE3 S4M sing 333 n n C5' C4' S4M sing 334 n n C5' "H5'1" S4M sing 335 n n C5' "H5'2" S4M sing 336 n n C4' C3' S4M sing 337 n n C4' O4' S4M sing 338 n n C4' H4' S4M sing 339 n n O4' C1' S4M sing 340 n n C1' C2' S4M sing 341 n n C1' N9 S4M sing 342 n n C1' H1' S4M sing 343 n n C2' O2' S4M sing 344 n n C2' C3' S4M sing 345 n n C2' H2' S4M sing 346 n n O2' HO2' S4M sing 347 n n C3' O3' S4M sing 348 n n C3' H3' S4M sing 349 n n O3' HO3' S4M sing 350 n n N9 C4 S4M sing 351 n y N9 C8 S4M sing 352 n y C8 N7 S4M doub 353 n y C8 H8 S4M sing 354 n n N7 C5 S4M sing 355 n y C5 C4 S4M doub 356 n y C5 C6 S4M sing 357 n y C6 N1 S4M doub 358 n y C6 N6 S4M sing 359 n n N6 HN61 S4M sing 360 n n N6 HN62 S4M sing 361 n n C4 N3 S4M sing 362 n y N3 C2 S4M doub 363 n y C2 N1 S4M sing 364 n y C2 H2 S4M sing 365 n n # _atom_sites.entry_id 4YUZ _atom_sites.fract_transf_matrix[1][1] 0.022972 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000683 _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] 0.007432 _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 2 S4M B 1 301 1 S4M S4M . G 3 4JV B 1 302 1 4JV UNL . H 2 S4M C 1 301 1 S4M S4M . I 2 S4M D 1 301 1 S4M S4M . J 3 4JV D 1 302 1 4JV UNL . K 4 HOH A 1 401 49 HOH HOH . K 4 HOH A 2 402 89 HOH HOH . K 4 HOH A 3 403 105 HOH HOH . K 4 HOH A 4 404 123 HOH HOH . K 4 HOH A 5 405 149 HOH HOH . K 4 HOH A 6 406 99 HOH HOH . K 4 HOH A 7 407 94 HOH HOH . K 4 HOH A 8 408 31 HOH HOH . K 4 HOH A 9 409 207 HOH HOH . K 4 HOH A 10 410 208 HOH HOH . K 4 HOH A 11 411 59 HOH HOH . K 4 HOH A 12 412 156 HOH HOH . K 4 HOH A 13 413 163 HOH HOH . K 4 HOH A 14 414 135 HOH HOH . K 4 HOH A 15 415 211 HOH HOH . K 4 HOH A 16 416 29 HOH HOH . K 4 HOH A 17 417 213 HOH HOH . K 4 HOH A 18 418 43 HOH HOH . K 4 HOH A 19 419 78 HOH HOH . K 4 HOH A 20 420 72 HOH HOH . K 4 HOH A 21 421 179 HOH HOH . K 4 HOH A 22 422 197 HOH HOH . K 4 HOH A 23 423 173 HOH HOH . K 4 HOH A 24 424 167 HOH HOH . K 4 HOH A 25 425 210 HOH HOH . K 4 HOH A 26 426 175 HOH HOH . K 4 HOH A 27 427 160 HOH HOH . K 4 HOH A 28 428 34 HOH HOH . K 4 HOH A 29 429 193 HOH HOH . K 4 HOH A 30 430 103 HOH HOH . K 4 HOH A 31 431 174 HOH HOH . K 4 HOH A 32 432 9 HOH HOH . K 4 HOH A 33 433 187 HOH HOH . K 4 HOH A 34 434 128 HOH HOH . K 4 HOH A 35 435 154 HOH HOH . K 4 HOH A 36 436 164 HOH HOH . K 4 HOH A 37 437 125 HOH HOH . K 4 HOH A 38 438 35 HOH HOH . K 4 HOH A 39 439 226 HOH HOH . K 4 HOH A 40 440 137 HOH HOH . K 4 HOH A 41 441 64 HOH HOH . K 4 HOH A 42 442 41 HOH HOH . K 4 HOH A 43 443 152 HOH HOH . K 4 HOH A 44 444 139 HOH HOH . K 4 HOH A 45 445 185 HOH HOH . K 4 HOH A 46 446 203 HOH HOH . K 4 HOH A 47 447 5 HOH HOH . K 4 HOH A 48 448 20 HOH HOH . K 4 HOH A 49 449 228 HOH HOH . K 4 HOH A 50 450 119 HOH HOH . K 4 HOH A 51 451 25 HOH HOH . K 4 HOH A 52 452 81 HOH HOH . K 4 HOH A 53 453 70 HOH HOH . K 4 HOH A 54 454 227 HOH HOH . K 4 HOH A 55 455 95 HOH HOH . K 4 HOH A 56 456 17 HOH HOH . K 4 HOH A 57 457 234 HOH HOH . K 4 HOH A 58 458 233 HOH HOH . K 4 HOH A 59 459 236 HOH HOH . K 4 HOH A 60 460 201 HOH HOH . K 4 HOH A 61 461 237 HOH HOH . L 4 HOH B 1 401 26 HOH HOH . L 4 HOH B 2 402 181 HOH HOH . L 4 HOH B 3 403 84 HOH HOH . L 4 HOH B 4 404 30 HOH HOH . L 4 HOH B 5 405 92 HOH HOH . L 4 HOH B 6 406 62 HOH HOH . L 4 HOH B 7 407 82 HOH HOH . L 4 HOH B 8 408 112 HOH HOH . L 4 HOH B 9 409 60 HOH HOH . L 4 HOH B 10 410 67 HOH HOH . L 4 HOH B 11 411 10 HOH HOH . L 4 HOH B 12 412 65 HOH HOH . L 4 HOH B 13 413 178 HOH HOH . L 4 HOH B 14 414 182 HOH HOH . L 4 HOH B 15 415 238 HOH HOH . L 4 HOH B 16 416 169 HOH HOH . L 4 HOH B 17 417 15 HOH HOH . L 4 HOH B 18 418 75 HOH HOH . L 4 HOH B 19 419 96 HOH HOH . L 4 HOH B 20 420 86 HOH HOH . L 4 HOH B 21 421 28 HOH HOH . L 4 HOH B 22 422 157 HOH HOH . L 4 HOH B 23 423 12 HOH HOH . L 4 HOH B 24 424 23 HOH HOH . L 4 HOH B 25 425 115 HOH HOH . L 4 HOH B 26 426 148 HOH HOH . L 4 HOH B 27 427 22 HOH HOH . L 4 HOH B 28 428 66 HOH HOH . L 4 HOH B 29 429 192 HOH HOH . L 4 HOH B 30 430 6 HOH HOH . L 4 HOH B 31 431 136 HOH HOH . L 4 HOH B 32 432 176 HOH HOH . L 4 HOH B 33 433 61 HOH HOH . L 4 HOH B 34 434 32 HOH HOH . L 4 HOH B 35 435 18 HOH HOH . L 4 HOH B 36 436 19 HOH HOH . L 4 HOH B 37 437 215 HOH HOH . L 4 HOH B 38 438 219 HOH HOH . L 4 HOH B 39 439 126 HOH HOH . L 4 HOH B 40 440 51 HOH HOH . L 4 HOH B 41 441 91 HOH HOH . L 4 HOH B 42 442 186 HOH HOH . L 4 HOH B 43 443 165 HOH HOH . L 4 HOH B 44 444 53 HOH HOH . L 4 HOH B 45 445 13 HOH HOH . L 4 HOH B 46 446 121 HOH HOH . L 4 HOH B 47 447 108 HOH HOH . L 4 HOH B 48 448 33 HOH HOH . L 4 HOH B 49 449 184 HOH HOH . L 4 HOH B 50 450 97 HOH HOH . L 4 HOH B 51 451 7 HOH HOH . L 4 HOH B 52 452 217 HOH HOH . L 4 HOH B 53 453 118 HOH HOH . L 4 HOH B 54 454 117 HOH HOH . L 4 HOH B 55 455 124 HOH HOH . L 4 HOH B 56 456 114 HOH HOH . L 4 HOH B 57 457 170 HOH HOH . L 4 HOH B 58 458 223 HOH HOH . L 4 HOH B 59 459 229 HOH HOH . L 4 HOH B 60 460 80 HOH HOH . L 4 HOH B 61 461 138 HOH HOH . L 4 HOH B 62 462 218 HOH HOH . L 4 HOH B 63 463 224 HOH HOH . L 4 HOH B 64 464 190 HOH HOH . L 4 HOH B 65 465 3 HOH HOH . L 4 HOH B 66 466 231 HOH HOH . L 4 HOH B 67 467 239 HOH HOH . L 4 HOH B 68 468 73 HOH HOH . L 4 HOH B 69 469 235 HOH HOH . L 4 HOH B 70 470 202 HOH HOH . L 4 HOH B 71 471 206 HOH HOH . M 4 HOH C 1 401 225 HOH HOH . M 4 HOH C 2 402 146 HOH HOH . M 4 HOH C 3 403 11 HOH HOH . M 4 HOH C 4 404 55 HOH HOH . M 4 HOH C 5 405 198 HOH HOH . M 4 HOH C 6 406 47 HOH HOH . M 4 HOH C 7 407 109 HOH HOH . M 4 HOH C 8 408 209 HOH HOH . M 4 HOH C 9 409 168 HOH HOH . M 4 HOH C 10 410 158 HOH HOH . M 4 HOH C 11 411 37 HOH HOH . M 4 HOH C 12 412 68 HOH HOH . M 4 HOH C 13 413 63 HOH HOH . M 4 HOH C 14 414 120 HOH HOH . M 4 HOH C 15 415 58 HOH HOH . M 4 HOH C 16 416 83 HOH HOH . M 4 HOH C 17 417 39 HOH HOH . M 4 HOH C 18 418 216 HOH HOH . M 4 HOH C 19 419 111 HOH HOH . M 4 HOH C 20 420 199 HOH HOH . M 4 HOH C 21 421 21 HOH HOH . M 4 HOH C 22 422 133 HOH HOH . M 4 HOH C 23 423 40 HOH HOH . M 4 HOH C 24 424 74 HOH HOH . M 4 HOH C 25 425 71 HOH HOH . M 4 HOH C 26 426 42 HOH HOH . M 4 HOH C 27 427 106 HOH HOH . M 4 HOH C 28 428 102 HOH HOH . M 4 HOH C 29 429 24 HOH HOH . M 4 HOH C 30 430 77 HOH HOH . M 4 HOH C 31 431 180 HOH HOH . M 4 HOH C 32 432 134 HOH HOH . M 4 HOH C 33 433 69 HOH HOH . M 4 HOH C 34 434 110 HOH HOH . M 4 HOH C 35 435 107 HOH HOH . M 4 HOH C 36 436 141 HOH HOH . M 4 HOH C 37 437 116 HOH HOH . M 4 HOH C 38 438 232 HOH HOH . M 4 HOH C 39 439 104 HOH HOH . M 4 HOH C 40 440 205 HOH HOH . M 4 HOH C 41 441 52 HOH HOH . M 4 HOH C 42 442 140 HOH HOH . M 4 HOH C 43 443 113 HOH HOH . M 4 HOH C 44 444 45 HOH HOH . M 4 HOH C 45 445 130 HOH HOH . M 4 HOH C 46 446 122 HOH HOH . M 4 HOH C 47 447 159 HOH HOH . N 4 HOH D 1 401 240 HOH HOH . N 4 HOH D 2 402 177 HOH HOH . N 4 HOH D 3 403 88 HOH HOH . N 4 HOH D 4 404 172 HOH HOH . N 4 HOH D 5 405 166 HOH HOH . N 4 HOH D 6 406 76 HOH HOH . N 4 HOH D 7 407 27 HOH HOH . N 4 HOH D 8 408 101 HOH HOH . N 4 HOH D 9 409 200 HOH HOH . N 4 HOH D 10 410 100 HOH HOH . N 4 HOH D 11 411 222 HOH HOH . N 4 HOH D 12 412 155 HOH HOH . N 4 HOH D 13 413 127 HOH HOH . N 4 HOH D 14 414 98 HOH HOH . N 4 HOH D 15 415 90 HOH HOH . N 4 HOH D 16 416 132 HOH HOH . N 4 HOH D 17 417 14 HOH HOH . N 4 HOH D 18 418 8 HOH HOH . N 4 HOH D 19 419 204 HOH HOH . N 4 HOH D 20 420 220 HOH HOH . N 4 HOH D 21 421 162 HOH HOH . N 4 HOH D 22 422 44 HOH HOH . N 4 HOH D 23 423 241 HOH HOH . N 4 HOH D 24 424 36 HOH HOH . N 4 HOH D 25 425 85 HOH HOH . N 4 HOH D 26 426 142 HOH HOH . N 4 HOH D 27 427 87 HOH HOH . N 4 HOH D 28 428 50 HOH HOH . N 4 HOH D 29 429 144 HOH HOH . N 4 HOH D 30 430 54 HOH HOH . N 4 HOH D 31 431 171 HOH HOH . N 4 HOH D 32 432 129 HOH HOH . N 4 HOH D 33 433 153 HOH HOH . N 4 HOH D 34 434 161 HOH HOH . N 4 HOH D 35 435 150 HOH HOH . N 4 HOH D 36 436 46 HOH HOH . N 4 HOH D 37 437 147 HOH HOH . N 4 HOH D 38 438 151 HOH HOH . N 4 HOH D 39 439 189 HOH HOH . N 4 HOH D 40 440 143 HOH HOH . N 4 HOH D 41 441 16 HOH HOH . N 4 HOH D 42 442 38 HOH HOH . N 4 HOH D 43 443 79 HOH HOH . N 4 HOH D 44 444 212 HOH HOH . N 4 HOH D 45 445 188 HOH HOH . N 4 HOH D 46 446 131 HOH HOH . N 4 HOH D 47 447 183 HOH HOH . N 4 HOH D 48 448 196 HOH HOH . N 4 HOH D 49 449 195 HOH HOH . N 4 HOH D 50 450 191 HOH HOH . N 4 HOH D 51 451 48 HOH HOH . N 4 HOH D 52 452 4 HOH HOH . N 4 HOH D 53 453 57 HOH HOH . N 4 HOH D 54 454 230 HOH HOH . N 4 HOH D 55 455 56 HOH HOH . N 4 HOH D 56 456 93 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 . . . H 2 -13.502 47.832 -2.062 1 42.94 ? CA S4M 301 C 1 HETATM 2 N N S4M . . . H 2 -12.714 48.833 -1.272 1 38.13 ? N S4M 301 C 1 HETATM 3 C CB S4M . . . H 2 -14.261 46.96 -1.086 1 42.13 ? CB S4M 301 C 1 HETATM 4 C CG S4M . . . H 2 -15.684 47.362 -0.76 1 50.49 ? CG S4M 301 C 1 HETATM 5 S SD S4M . . . H 2 -15.765 47.993 0.97 1 61.24 ? SD S4M 301 C 1 HETATM 6 C CE S4M . . . H 2 -14.782 46.73 1.859 1 52.46 ? CE S4M 301 C 1 HETATM 7 C C5' S4M . . . H 2 -17.491 47.574 1.319 1 41.29 ? C5' S4M 301 C 1 HETATM 8 C C4' S4M . . . H 2 -17.804 48.5 2.499 1 37.7 ? C4' S4M 301 C 1 HETATM 9 O O4' S4M . . . H 2 -19.093 49.1 2.465 1 36.38 ? O4' S4M 301 C 1 HETATM 10 C C1' S4M . . . H 2 -19.579 49.206 3.832 1 34.12 ? C1' S4M 301 C 1 HETATM 11 C C2' S4M . . . H 2 -19.052 47.944 4.517 1 34.08 ? C2' S4M 301 C 1 HETATM 12 O O2' S4M . . . H 2 -18.87 48.086 5.948 1 34.19 ? O2' S4M 301 C 1 HETATM 13 C C3' S4M . . . H 2 -17.741 47.71 3.796 1 36.04 ? C3' S4M 301 C 1 HETATM 14 O O3' S4M . . . H 2 -16.591 48.239 4.49 1 41.68 ? O3' S4M 301 C 1 HETATM 15 N N9 S4M . . . H 2 -21.04 49.41 3.909 1 30.16 ? N9 S4M 301 C 1 HETATM 16 C C8 S4M . . . H 2 -22.028 48.498 3.592 1 28.36 ? C8 S4M 301 C 1 HETATM 17 N N7 S4M . . . H 2 -23.218 49.018 3.781 1 31.09 ? N7 S4M 301 C 1 HETATM 18 C C5 S4M . . . H 2 -23.021 50.313 4.233 1 30.5 ? C5 S4M 301 C 1 HETATM 19 C C6 S4M . . . H 2 -23.903 51.333 4.613 1 30.93 ? C6 S4M 301 C 1 HETATM 20 N N6 S4M . . . H 2 -25.322 51.231 4.588 1 29.74 ? N6 S4M 301 C 1 HETATM 21 C C4 S4M . . . H 2 -21.671 50.579 4.301 1 28.65 ? C4 S4M 301 C 1 HETATM 22 N N3 S4M . . . H 2 -21.113 51.722 4.713 1 25.59 ? N3 S4M 301 C 1 HETATM 23 C C2 S4M . . . H 2 -22.04 52.617 5.034 1 25.08 ? C2 S4M 301 C 1 HETATM 24 N N1 S4M . . . H 2 -23.365 52.495 5.004 1 27.89 ? N1 S4M 301 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #