data_5M83 # _model_server_result.job_id a0sIPHLQjsNlRJaKZ1wMMw _model_server_result.datetime_utc '2024-11-22 10:42:37' _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 5m83 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":300}' # _entry.id 5M83 # _exptl.entry_id 5M83 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 817.533 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate' _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 96.32 _cell.angle_gamma 90 _cell.entry_id 5M83 _cell.length_a 47.06 _cell.length_b 59.74 _cell.length_c 149.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M83 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,F 1 1 B,E,G 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 C N N ? 2 E N N # _chem_comp.formula 'C22 H32 N10 O16 P3 S 1' _chem_comp.formula_weight 817.533 _chem_comp.id YDZ _chem_comp.mon_nstd_flag . _chem_comp.name '[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanyl-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl hydrogen phosphate' _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 O11 P3 YDZ doub 389 n n O12 P3 YDZ sing 390 n n O12 C16 YDZ sing 391 n n P3 O9 YDZ sing 392 n n P3 O10 YDZ sing 393 n n O9 P2 YDZ sing 394 n n C16 C17 YDZ sing 395 n n C22 N7 YDZ sing 396 n n C18 O14 YDZ sing 397 n n C18 C19 YDZ sing 398 n n C18 C17 YDZ sing 399 n n O5 P1 YDZ doub 400 n n O7 P2 YDZ sing 401 n n O7 P1 YDZ sing 402 n n C20 O15 YDZ sing 403 n n C19 O15 YDZ sing 404 n n C19 C21 YDZ sing 405 n n C2 N7 YDZ doub 406 n y C2 N6 YDZ sing 407 n y C17 O13 YDZ sing 408 n n N7 C4 YDZ sing 409 n y P2 S1 YDZ sing 410 n n P2 O8 YDZ doub 411 n n P1 O6 YDZ sing 412 n n P1 O4 YDZ sing 413 n n N3 C7 YDZ doub 414 n y N3 C8 YDZ sing 415 n y O1 C11 YDZ sing 416 n n O1 C14 YDZ sing 417 n n C7 N2 YDZ sing 418 n y C11 N5 YDZ sing 419 n n C11 C12 YDZ sing 420 n n O2 C12 YDZ sing 421 n n N6 C21 YDZ sing 422 n n N6 C3 YDZ sing 423 n y O16 C5 YDZ sing 424 n n C4 C5 YDZ doub 425 n y C4 C3 YDZ sing 426 n y O13 C21 YDZ sing 427 n n C14 C13 YDZ sing 428 n n C14 C15 YDZ sing 429 n n C8 N5 YDZ sing 430 n y C8 C9 YDZ doub 431 n y N5 C10 YDZ sing 432 n y N2 C6 YDZ doub 433 n y O3 C13 YDZ sing 434 n n C5 N10 YDZ sing 435 n y C3 N8 YDZ doub 436 n y C12 C13 YDZ sing 437 n n O4 C15 YDZ sing 438 n n C9 C6 YDZ sing 439 n y C9 N4 YDZ sing 440 n y C6 N1 YDZ sing 441 n n C10 N4 YDZ doub 442 n y N10 C1 YDZ doub 443 n y N8 C1 YDZ sing 444 n y C1 N9 YDZ sing 445 n n C2 H1 YDZ sing 446 n n N1 H2 YDZ sing 447 n n N1 H3 YDZ sing 448 n n C7 H4 YDZ sing 449 n n C10 H5 YDZ sing 450 n n C11 H6 YDZ sing 451 n n C12 H7 YDZ sing 452 n n O2 H8 YDZ sing 453 n n C13 H9 YDZ sing 454 n n O3 H10 YDZ sing 455 n n C14 H11 YDZ sing 456 n n C15 H12 YDZ sing 457 n n C15 H13 YDZ sing 458 n n O6 H14 YDZ sing 459 n n S1 H15 YDZ sing 460 n n O10 H16 YDZ sing 461 n n C16 H17 YDZ sing 462 n n C16 H18 YDZ sing 463 n n C17 H19 YDZ sing 464 n n C18 H20 YDZ sing 465 n n O14 H21 YDZ sing 466 n n C19 H22 YDZ sing 467 n n C20 H23 YDZ sing 468 n n C20 H24 YDZ sing 469 n n C20 H25 YDZ sing 470 n n C21 H26 YDZ sing 471 n n C22 H27 YDZ sing 472 n n C22 H28 YDZ sing 473 n n C22 H29 YDZ sing 474 n n N9 H30 YDZ sing 475 n n N9 H31 YDZ sing 476 n n O16 H32 YDZ sing 477 n n # _atom_sites.entry_id 5M83 _atom_sites.fract_transf_matrix[1][1] 0.021249 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002353 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016739 _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] 0.006744 _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 YDZ A 1 301 300 YDZ RSA . D 3 GOL A 1 302 1 GOL GOL . E 2 YDZ B 1 300 300 YDZ RSA . F 4 HOH A 1 401 130 HOH HOH . F 4 HOH A 2 402 46 HOH HOH . F 4 HOH A 3 403 132 HOH HOH . F 4 HOH A 4 404 31 HOH HOH . F 4 HOH A 5 405 9 HOH HOH . F 4 HOH A 6 406 22 HOH HOH . F 4 HOH A 7 407 12 HOH HOH . F 4 HOH A 8 408 28 HOH HOH . F 4 HOH A 9 409 42 HOH HOH . F 4 HOH A 10 410 36 HOH HOH . F 4 HOH A 11 411 3 HOH HOH . F 4 HOH A 12 412 145 HOH HOH . F 4 HOH A 13 413 38 HOH HOH . F 4 HOH A 14 414 97 HOH HOH . F 4 HOH A 15 415 40 HOH HOH . F 4 HOH A 16 416 14 HOH HOH . F 4 HOH A 17 417 17 HOH HOH . F 4 HOH A 18 418 4 HOH HOH . F 4 HOH A 19 419 25 HOH HOH . F 4 HOH A 20 420 32 HOH HOH . F 4 HOH A 21 421 85 HOH HOH . F 4 HOH A 22 422 26 HOH HOH . F 4 HOH A 23 423 164 HOH HOH . F 4 HOH A 24 424 63 HOH HOH . F 4 HOH A 25 425 124 HOH HOH . F 4 HOH A 26 426 30 HOH HOH . F 4 HOH A 27 427 43 HOH HOH . F 4 HOH A 28 428 11 HOH HOH . F 4 HOH A 29 429 65 HOH HOH . F 4 HOH A 30 430 151 HOH HOH . F 4 HOH A 31 431 62 HOH HOH . F 4 HOH A 32 432 47 HOH HOH . F 4 HOH A 33 433 29 HOH HOH . F 4 HOH A 34 434 153 HOH HOH . F 4 HOH A 35 435 21 HOH HOH . F 4 HOH A 36 436 6 HOH HOH . F 4 HOH A 37 437 24 HOH HOH . F 4 HOH A 38 438 111 HOH HOH . F 4 HOH A 39 439 2 HOH HOH . F 4 HOH A 40 440 1 HOH HOH . F 4 HOH A 41 441 72 HOH HOH . F 4 HOH A 42 442 33 HOH HOH . F 4 HOH A 43 443 39 HOH HOH . F 4 HOH A 44 444 137 HOH HOH . F 4 HOH A 45 445 59 HOH HOH . F 4 HOH A 46 446 135 HOH HOH . F 4 HOH A 47 447 8 HOH HOH . F 4 HOH A 48 448 67 HOH HOH . F 4 HOH A 49 449 61 HOH HOH . F 4 HOH A 50 450 155 HOH HOH . F 4 HOH A 51 451 19 HOH HOH . F 4 HOH A 52 452 48 HOH HOH . F 4 HOH A 53 453 68 HOH HOH . F 4 HOH A 54 454 150 HOH HOH . F 4 HOH A 55 455 96 HOH HOH . F 4 HOH A 56 456 139 HOH HOH . F 4 HOH A 57 457 91 HOH HOH . F 4 HOH A 58 458 123 HOH HOH . F 4 HOH A 59 459 126 HOH HOH . F 4 HOH A 60 460 166 HOH HOH . F 4 HOH A 61 461 121 HOH HOH . F 4 HOH A 62 462 149 HOH HOH . F 4 HOH A 63 463 88 HOH HOH . F 4 HOH A 64 464 51 HOH HOH . F 4 HOH A 65 465 73 HOH HOH . F 4 HOH A 66 466 7 HOH HOH . F 4 HOH A 67 467 95 HOH HOH . F 4 HOH A 68 468 5 HOH HOH . F 4 HOH A 69 469 159 HOH HOH . F 4 HOH A 70 470 54 HOH HOH . F 4 HOH A 71 471 27 HOH HOH . F 4 HOH A 72 472 34 HOH HOH . F 4 HOH A 73 473 114 HOH HOH . F 4 HOH A 74 474 79 HOH HOH . F 4 HOH A 75 475 75 HOH HOH . F 4 HOH A 76 476 80 HOH HOH . F 4 HOH A 77 477 93 HOH HOH . F 4 HOH A 78 478 107 HOH HOH . F 4 HOH A 79 479 16 HOH HOH . F 4 HOH A 80 480 140 HOH HOH . F 4 HOH A 81 481 116 HOH HOH . F 4 HOH A 82 482 165 HOH HOH . F 4 HOH A 83 483 128 HOH HOH . F 4 HOH A 84 484 158 HOH HOH . F 4 HOH A 85 485 141 HOH HOH . F 4 HOH A 86 486 110 HOH HOH . F 4 HOH A 87 487 167 HOH HOH . F 4 HOH A 88 488 103 HOH HOH . F 4 HOH A 89 489 53 HOH HOH . F 4 HOH A 90 490 37 HOH HOH . F 4 HOH A 91 491 157 HOH HOH . F 4 HOH A 92 492 136 HOH HOH . F 4 HOH A 93 493 66 HOH HOH . F 4 HOH A 94 494 143 HOH HOH . F 4 HOH A 95 495 102 HOH HOH . F 4 HOH A 96 496 170 HOH HOH . F 4 HOH A 97 497 20 HOH HOH . F 4 HOH A 98 498 76 HOH HOH . F 4 HOH A 99 499 161 HOH HOH . F 4 HOH A 100 500 154 HOH HOH . F 4 HOH A 101 501 101 HOH HOH . F 4 HOH A 102 502 152 HOH HOH . F 4 HOH A 103 503 142 HOH HOH . F 4 HOH A 104 504 92 HOH HOH . F 4 HOH A 105 505 69 HOH HOH . F 4 HOH A 106 506 77 HOH HOH . F 4 HOH A 107 507 89 HOH HOH . F 4 HOH A 108 508 171 HOH HOH . F 4 HOH A 109 509 70 HOH HOH . F 4 HOH A 110 510 163 HOH HOH . F 4 HOH A 111 511 41 HOH HOH . F 4 HOH A 112 512 156 HOH HOH . F 4 HOH A 113 513 83 HOH HOH . G 4 HOH B 1 401 118 HOH HOH . G 4 HOH B 2 402 23 HOH HOH . G 4 HOH B 3 403 71 HOH HOH . G 4 HOH B 4 404 64 HOH HOH . G 4 HOH B 5 405 50 HOH HOH . G 4 HOH B 6 406 108 HOH HOH . G 4 HOH B 7 407 45 HOH HOH . G 4 HOH B 8 408 81 HOH HOH . G 4 HOH B 9 409 18 HOH HOH . G 4 HOH B 10 410 120 HOH HOH . G 4 HOH B 11 411 15 HOH HOH . G 4 HOH B 12 412 10 HOH HOH . G 4 HOH B 13 413 112 HOH HOH . G 4 HOH B 14 414 57 HOH HOH . G 4 HOH B 15 415 115 HOH HOH . G 4 HOH B 16 416 104 HOH HOH . G 4 HOH B 17 417 35 HOH HOH . G 4 HOH B 18 418 148 HOH HOH . G 4 HOH B 19 419 58 HOH HOH . G 4 HOH B 20 420 49 HOH HOH . G 4 HOH B 21 421 87 HOH HOH . G 4 HOH B 22 422 169 HOH HOH . G 4 HOH B 23 423 134 HOH HOH . G 4 HOH B 24 424 74 HOH HOH . G 4 HOH B 25 425 55 HOH HOH . G 4 HOH B 26 426 44 HOH HOH . G 4 HOH B 27 427 117 HOH HOH . G 4 HOH B 28 428 147 HOH HOH . G 4 HOH B 29 429 56 HOH HOH . G 4 HOH B 30 430 94 HOH HOH . G 4 HOH B 31 431 127 HOH HOH . G 4 HOH B 32 432 131 HOH HOH . G 4 HOH B 33 433 168 HOH HOH . G 4 HOH B 34 434 82 HOH HOH . G 4 HOH B 35 435 99 HOH HOH . G 4 HOH B 36 436 13 HOH HOH . G 4 HOH B 37 437 106 HOH HOH . G 4 HOH B 38 438 162 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 C1 YDZ . . . E 2 -59.67 1.866 17.818 1 95.91 ? C1 YDZ 300 B 1 HETATM 2 C C2 YDZ . . . E 2 -59.041 6.244 18.341 1 90.33 ? C2 YDZ 300 B 1 HETATM 3 C C3 YDZ . . . E 2 -58.952 4.078 18.122 1 93.37 ? C3 YDZ 300 B 1 HETATM 4 C C4 YDZ . . . E 2 -60.262 4.499 18.04 1 91.75 ? C4 YDZ 300 B 1 HETATM 5 C C5 YDZ . . . E 2 -61.291 3.583 17.844 1 93.24 ? C5 YDZ 300 B 1 HETATM 6 O O4 YDZ . . . E 2 -58.122 13.556 15.642 1 110.19 ? O4 YDZ 300 B 1 HETATM 7 P P1 YDZ . . . E 2 -56.559 13.354 15.315 1 110.63 ? P1 YDZ 300 B 1 HETATM 8 O O5 YDZ . . . E 2 -56.091 14.539 14.504 1 110.95 ? O5 YDZ 300 B 1 HETATM 9 O O6 YDZ . . . E 2 -56.377 12.065 14.546 1 108.99 ? O6 YDZ 300 B 1 HETATM 10 O O7 YDZ . . . E 2 -55.72 13.276 16.692 1 107.31 ? O7 YDZ 300 B 1 HETATM 11 P P2 YDZ . . . E 2 -56.323 12.43 17.923 1 101.9 ? P2 YDZ 300 B 1 HETATM 12 O O8 YDZ . . . E 2 -55.236 11.86 18.754 1 98.95 ? O8 YDZ 300 B 1 HETATM 13 S S1 YDZ . . . E 2 -57.566 13.618 19.076 1 95.55 ? S1 YDZ 300 B 1 HETATM 14 O O9 YDZ . . . E 2 -57.236 11.284 17.262 1 99.73 ? O9 YDZ 300 B 1 HETATM 15 P P3 YDZ . . . E 2 -58.108 10.266 18.147 1 92.43 ? P3 YDZ 300 B 1 HETATM 16 O O10 YDZ . . . E 2 -59.548 10.319 17.691 1 89.89 ? O10 YDZ 300 B 1 HETATM 17 O O11 YDZ . . . E 2 -57.969 10.602 19.61 1 90.18 ? O11 YDZ 300 B 1 HETATM 18 O O12 YDZ . . . E 2 -57.462 8.817 17.903 1 96.13 ? O12 YDZ 300 B 1 HETATM 19 C C16 YDZ . . . E 2 -56.053 8.686 18.082 1 95.89 ? C16 YDZ 300 B 1 HETATM 20 C C17 YDZ . . . E 2 -55.628 7.227 17.991 1 96 ? C17 YDZ 300 B 1 HETATM 21 O O13 YDZ . . . E 2 -56.264 6.439 19.005 1 95.81 ? O13 YDZ 300 B 1 HETATM 22 C C18 YDZ . . . E 2 -55.992 6.576 16.666 1 94.25 ? C18 YDZ 300 B 1 HETATM 23 O O14 YDZ . . . E 2 -54.975 6.767 15.68 1 92.79 ? O14 YDZ 300 B 1 HETATM 24 C C19 YDZ . . . E 2 -56.116 5.121 17.052 1 91.77 ? C19 YDZ 300 B 1 HETATM 25 O O15 YDZ . . . E 2 -54.816 4.544 17.103 1 85.37 ? O15 YDZ 300 B 1 HETATM 26 C C20 YDZ . . . E 2 -54.848 3.176 17.499 1 83.41 ? C20 YDZ 300 B 1 HETATM 27 C C21 YDZ . . . E 2 -56.718 5.199 18.446 1 94.48 ? C21 YDZ 300 B 1 HETATM 28 N N6 YDZ . . . E 2 -58.201 5.179 18.315 1 93.3 ? N6 YDZ 300 B 1 HETATM 29 N N7 YDZ . . . E 2 -60.308 5.832 18.175 1 88.22 ? N7 YDZ 300 B 1 HETATM 30 C C22 YDZ . . . E 2 -61.495 6.724 18.157 1 86.94 ? C22 YDZ 300 B 1 HETATM 31 N N8 YDZ . . . E 2 -58.67 2.759 18.01 1 95.16 ? N8 YDZ 300 B 1 HETATM 32 N N9 YDZ . . . E 2 -59.368 0.548 17.71 1 96.55 ? N9 YDZ 300 B 1 HETATM 33 N N10 YDZ . . . E 2 -60.963 2.273 17.74 1 94.49 ? N10 YDZ 300 B 1 HETATM 34 O O16 YDZ . . . E 2 -62.599 3.951 17.757 1 92.83 ? O16 YDZ 300 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 34 #