data_6M83 # _model_server_result.job_id sgmEojS-ANcz-V9jXoltfQ _model_server_result.datetime_utc '2024-11-25 10:49:01' _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 6m83 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 6M83 # _exptl.entry_id 6M83 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 478.284 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6M83 _cell.length_a 64.521 _cell.length_b 91.267 _cell.length_c 93.629 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6M83 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C16 H20 N2 O11 P2' _chem_comp.formula_weight 478.284 _chem_comp.id TLO _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'thymidine diphosphate phenol' # 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 C1' N1 TLO sing 354 n n N1 C6 TLO sing 355 n n N1 C2 TLO sing 356 n n O2 C2 TLO doub 357 n n C2 N3 TLO sing 358 n n N3 C4 TLO sing 359 n n N3 HN3 TLO sing 360 n n C5 C4 TLO sing 361 n n C4 O4 TLO doub 362 n n C6 C5 TLO doub 363 n n C5 C5M TLO sing 364 n n C6 H6 TLO sing 365 n n O3A PA TLO sing 366 n n O2A PA TLO doub 367 n n PA O5' TLO sing 368 n n PA O1A TLO sing 369 n n O3B PB TLO sing 370 n n O2B PB TLO doub 371 n n PB O1B TLO sing 372 n n PB O3A TLO sing 373 n n CD2 CG TLO doub 374 n y CG O3B TLO sing 375 n n CG CD1 TLO sing 376 n y CE2 CZ TLO doub 377 n y CZ CE1 TLO sing 378 n y CZ HZ TLO sing 379 n n C2' C1' TLO sing 380 n n C1' O4' TLO sing 381 n n C1' H1' TLO sing 382 n n O1A HO1A TLO sing 383 n n O1B HO1B TLO sing 384 n n C3' C2' TLO sing 385 n n C2' H2' TLO sing 386 n n C2' "H2'A" TLO sing 387 n n O3' C3' TLO sing 388 n n C3' C4' TLO sing 389 n n C3' H3' TLO sing 390 n n O3' HO3' TLO sing 391 n n C5' C4' TLO sing 392 n n C4' O4' TLO sing 393 n n C4' H4' TLO sing 394 n n O5' C5' TLO sing 395 n n C5' H5' TLO sing 396 n n C5' "H5'A" TLO sing 397 n n C5M H5M TLO sing 398 n n C5M H5MA TLO sing 399 n n C5M H5MB TLO sing 400 n n CE1 CD1 TLO doub 401 n y CD1 HD1 TLO sing 402 n n CE2 CD2 TLO sing 403 n y CD2 HD2 TLO sing 404 n n CE1 HE1 TLO sing 405 n n CE2 HE2 TLO sing 406 n n # _atom_sites.entry_id 6M83 _atom_sites.fract_transf_matrix[1][1] 0.015499 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010957 _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] 0.01068 _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 B 2 SAH A 1 301 1 SAH SAH . C 3 TLO A 1 302 1 TLO TLO . D 4 CL A 1 303 1 CL CL . E 5 HOH A 1 401 201 HOH HOH . E 5 HOH A 2 402 72 HOH HOH . E 5 HOH A 3 403 187 HOH HOH . E 5 HOH A 4 404 141 HOH HOH . E 5 HOH A 5 405 202 HOH HOH . E 5 HOH A 6 406 215 HOH HOH . E 5 HOH A 7 407 189 HOH HOH . E 5 HOH A 8 408 99 HOH HOH . E 5 HOH A 9 409 61 HOH HOH . E 5 HOH A 10 410 168 HOH HOH . E 5 HOH A 11 411 29 HOH HOH . E 5 HOH A 12 412 64 HOH HOH . E 5 HOH A 13 413 48 HOH HOH . E 5 HOH A 14 414 26 HOH HOH . E 5 HOH A 15 415 216 HOH HOH . E 5 HOH A 16 416 50 HOH HOH . E 5 HOH A 17 417 97 HOH HOH . E 5 HOH A 18 418 192 HOH HOH . E 5 HOH A 19 419 111 HOH HOH . E 5 HOH A 20 420 193 HOH HOH . E 5 HOH A 21 421 8 HOH HOH . E 5 HOH A 22 422 167 HOH HOH . E 5 HOH A 23 423 10 HOH HOH . E 5 HOH A 24 424 53 HOH HOH . E 5 HOH A 25 425 103 HOH HOH . E 5 HOH A 26 426 12 HOH HOH . E 5 HOH A 27 427 84 HOH HOH . E 5 HOH A 28 428 133 HOH HOH . E 5 HOH A 29 429 28 HOH HOH . E 5 HOH A 30 430 101 HOH HOH . E 5 HOH A 31 431 183 HOH HOH . E 5 HOH A 32 432 9 HOH HOH . E 5 HOH A 33 433 142 HOH HOH . E 5 HOH A 34 434 47 HOH HOH . E 5 HOH A 35 435 137 HOH HOH . E 5 HOH A 36 436 56 HOH HOH . E 5 HOH A 37 437 18 HOH HOH . E 5 HOH A 38 438 16 HOH HOH . E 5 HOH A 39 439 59 HOH HOH . E 5 HOH A 40 440 65 HOH HOH . E 5 HOH A 41 441 13 HOH HOH . E 5 HOH A 42 442 6 HOH HOH . E 5 HOH A 43 443 130 HOH HOH . E 5 HOH A 44 444 19 HOH HOH . E 5 HOH A 45 445 98 HOH HOH . E 5 HOH A 46 446 163 HOH HOH . E 5 HOH A 47 447 46 HOH HOH . E 5 HOH A 48 448 119 HOH HOH . E 5 HOH A 49 449 158 HOH HOH . E 5 HOH A 50 450 15 HOH HOH . E 5 HOH A 51 451 148 HOH HOH . E 5 HOH A 52 452 40 HOH HOH . E 5 HOH A 53 453 139 HOH HOH . E 5 HOH A 54 454 2 HOH HOH . E 5 HOH A 55 455 14 HOH HOH . E 5 HOH A 56 456 52 HOH HOH . E 5 HOH A 57 457 20 HOH HOH . E 5 HOH A 58 458 4 HOH HOH . E 5 HOH A 59 459 113 HOH HOH . E 5 HOH A 60 460 33 HOH HOH . E 5 HOH A 61 461 45 HOH HOH . E 5 HOH A 62 462 200 HOH HOH . E 5 HOH A 63 463 24 HOH HOH . E 5 HOH A 64 464 54 HOH HOH . E 5 HOH A 65 465 66 HOH HOH . E 5 HOH A 66 466 3 HOH HOH . E 5 HOH A 67 467 76 HOH HOH . E 5 HOH A 68 468 198 HOH HOH . E 5 HOH A 69 469 1 HOH HOH . E 5 HOH A 70 470 67 HOH HOH . E 5 HOH A 71 471 42 HOH HOH . E 5 HOH A 72 472 86 HOH HOH . E 5 HOH A 73 473 35 HOH HOH . E 5 HOH A 74 474 68 HOH HOH . E 5 HOH A 75 475 100 HOH HOH . E 5 HOH A 76 476 44 HOH HOH . E 5 HOH A 77 477 194 HOH HOH . E 5 HOH A 78 478 147 HOH HOH . E 5 HOH A 79 479 184 HOH HOH . E 5 HOH A 80 480 51 HOH HOH . E 5 HOH A 81 481 206 HOH HOH . E 5 HOH A 82 482 7 HOH HOH . E 5 HOH A 83 483 23 HOH HOH . E 5 HOH A 84 484 22 HOH HOH . E 5 HOH A 85 485 69 HOH HOH . E 5 HOH A 86 486 31 HOH HOH . E 5 HOH A 87 487 17 HOH HOH . E 5 HOH A 88 488 89 HOH HOH . E 5 HOH A 89 489 105 HOH HOH . E 5 HOH A 90 490 155 HOH HOH . E 5 HOH A 91 491 49 HOH HOH . E 5 HOH A 92 492 220 HOH HOH . E 5 HOH A 93 493 37 HOH HOH . E 5 HOH A 94 494 117 HOH HOH . E 5 HOH A 95 495 178 HOH HOH . E 5 HOH A 96 496 104 HOH HOH . E 5 HOH A 97 497 136 HOH HOH . E 5 HOH A 98 498 58 HOH HOH . E 5 HOH A 99 499 153 HOH HOH . E 5 HOH A 100 500 134 HOH HOH . E 5 HOH A 101 501 70 HOH HOH . E 5 HOH A 102 502 11 HOH HOH . E 5 HOH A 103 503 209 HOH HOH . E 5 HOH A 104 504 27 HOH HOH . E 5 HOH A 105 505 138 HOH HOH . E 5 HOH A 106 506 71 HOH HOH . E 5 HOH A 107 507 73 HOH HOH . E 5 HOH A 108 508 125 HOH HOH . E 5 HOH A 109 509 170 HOH HOH . E 5 HOH A 110 510 32 HOH HOH . E 5 HOH A 111 511 205 HOH HOH . E 5 HOH A 112 512 171 HOH HOH . E 5 HOH A 113 513 74 HOH HOH . E 5 HOH A 114 514 127 HOH HOH . E 5 HOH A 115 515 166 HOH HOH . E 5 HOH A 116 516 218 HOH HOH . E 5 HOH A 117 517 108 HOH HOH . E 5 HOH A 118 518 157 HOH HOH . E 5 HOH A 119 519 112 HOH HOH . E 5 HOH A 120 520 91 HOH HOH . E 5 HOH A 121 521 174 HOH HOH . E 5 HOH A 122 522 95 HOH HOH . E 5 HOH A 123 523 195 HOH HOH . E 5 HOH A 124 524 21 HOH HOH . E 5 HOH A 125 525 88 HOH HOH . E 5 HOH A 126 526 63 HOH HOH . E 5 HOH A 127 527 173 HOH HOH . E 5 HOH A 128 528 132 HOH HOH . E 5 HOH A 129 529 79 HOH HOH . E 5 HOH A 130 530 60 HOH HOH . E 5 HOH A 131 531 145 HOH HOH . E 5 HOH A 132 532 160 HOH HOH . E 5 HOH A 133 533 172 HOH HOH . E 5 HOH A 134 534 181 HOH HOH . E 5 HOH A 135 535 213 HOH HOH . E 5 HOH A 136 536 165 HOH HOH . E 5 HOH A 137 537 83 HOH HOH . E 5 HOH A 138 538 55 HOH HOH . E 5 HOH A 139 539 38 HOH HOH . E 5 HOH A 140 540 149 HOH HOH . E 5 HOH A 141 541 164 HOH HOH . E 5 HOH A 142 542 78 HOH HOH . E 5 HOH A 143 543 135 HOH HOH . E 5 HOH A 144 544 121 HOH HOH . E 5 HOH A 145 545 204 HOH HOH . E 5 HOH A 146 546 77 HOH HOH . E 5 HOH A 147 547 131 HOH HOH . E 5 HOH A 148 548 102 HOH HOH . E 5 HOH A 149 549 36 HOH HOH . E 5 HOH A 150 550 57 HOH HOH . E 5 HOH A 151 551 199 HOH HOH . E 5 HOH A 152 552 196 HOH HOH . E 5 HOH A 153 553 190 HOH HOH . E 5 HOH A 154 554 5 HOH HOH . E 5 HOH A 155 555 25 HOH HOH . E 5 HOH A 156 556 92 HOH HOH . E 5 HOH A 157 557 109 HOH HOH . E 5 HOH A 158 558 129 HOH HOH . E 5 HOH A 159 559 87 HOH HOH . E 5 HOH A 160 560 93 HOH HOH . E 5 HOH A 161 561 162 HOH HOH . E 5 HOH A 162 562 210 HOH HOH . E 5 HOH A 163 563 81 HOH HOH . E 5 HOH A 164 564 203 HOH HOH . E 5 HOH A 165 565 39 HOH HOH . E 5 HOH A 166 566 106 HOH HOH . E 5 HOH A 167 567 185 HOH HOH . E 5 HOH A 168 568 151 HOH HOH . E 5 HOH A 169 569 62 HOH HOH . E 5 HOH A 170 570 156 HOH HOH . E 5 HOH A 171 571 96 HOH HOH . E 5 HOH A 172 572 126 HOH HOH . E 5 HOH A 173 573 152 HOH HOH . E 5 HOH A 174 574 208 HOH HOH . E 5 HOH A 175 575 114 HOH HOH . E 5 HOH A 176 576 115 HOH HOH . E 5 HOH A 177 577 122 HOH HOH . E 5 HOH A 178 578 159 HOH HOH . E 5 HOH A 179 579 154 HOH HOH . E 5 HOH A 180 580 144 HOH HOH . E 5 HOH A 181 581 118 HOH HOH . E 5 HOH A 182 582 41 HOH HOH . E 5 HOH A 183 583 140 HOH HOH . E 5 HOH A 184 584 179 HOH HOH . E 5 HOH A 185 585 94 HOH HOH . E 5 HOH A 186 586 146 HOH HOH . E 5 HOH A 187 587 217 HOH HOH . E 5 HOH A 188 588 90 HOH HOH . E 5 HOH A 189 589 107 HOH HOH . E 5 HOH A 190 590 123 HOH HOH . E 5 HOH A 191 591 186 HOH HOH . E 5 HOH A 192 592 197 HOH HOH . E 5 HOH A 193 593 110 HOH HOH . E 5 HOH A 194 594 34 HOH HOH . E 5 HOH A 195 595 219 HOH HOH . E 5 HOH A 196 596 124 HOH HOH . E 5 HOH A 197 597 116 HOH HOH . E 5 HOH A 198 598 207 HOH HOH . E 5 HOH A 199 599 150 HOH HOH . E 5 HOH A 200 600 82 HOH HOH . E 5 HOH A 201 601 214 HOH HOH . E 5 HOH A 202 602 175 HOH HOH . E 5 HOH A 203 603 222 HOH HOH . E 5 HOH A 204 604 120 HOH HOH . E 5 HOH A 205 605 188 HOH HOH . E 5 HOH A 206 606 43 HOH HOH . E 5 HOH A 207 607 80 HOH HOH . E 5 HOH A 208 608 143 HOH HOH . E 5 HOH A 209 609 221 HOH HOH . E 5 HOH A 210 610 224 HOH HOH . E 5 HOH A 211 611 75 HOH HOH . E 5 HOH A 212 612 30 HOH HOH . E 5 HOH A 213 613 191 HOH HOH . E 5 HOH A 214 614 212 HOH HOH . E 5 HOH A 215 615 169 HOH HOH . E 5 HOH A 216 616 182 HOH HOH . E 5 HOH A 217 617 128 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 N N1 TLO . . . C 3 -14.591 -19.438 0.186 0.77 16.15 ? N1 TLO 302 A 1 HETATM 2 C C2 TLO . . . C 3 -14.658 -20.753 0.684 0.77 17.41 ? C2 TLO 302 A 1 HETATM 3 O O2 TLO . . . C 3 -15.756 -21.31 0.687 0.77 16.9 ? O2 TLO 302 A 1 HETATM 4 N N3 TLO . . . C 3 -13.535 -21.362 1.139 0.77 17.04 ? N3 TLO 302 A 1 HETATM 5 C C4 TLO . . . C 3 -12.347 -20.681 1.144 0.77 19.06 ? C4 TLO 302 A 1 HETATM 6 O O4 TLO . . . C 3 -11.328 -21.272 1.588 0.77 22.07 ? O4 TLO 302 A 1 HETATM 7 C C5 TLO . . . C 3 -12.283 -19.353 0.695 0.77 18.89 ? C5 TLO 302 A 1 HETATM 8 C C6 TLO . . . C 3 -13.439 -18.741 0.223 0.77 18.37 ? C6 TLO 302 A 1 HETATM 9 P PA TLO . . . C 3 -16.105 -13.674 -3.163 0.77 18.96 ? PA TLO 302 A 1 HETATM 10 P PB TLO . . . C 3 -16.964 -14.862 -5.782 0.77 26.82 ? PB TLO 302 A 1 HETATM 11 C CG TLO . . . C 3 -19.51 -15.584 -5.815 0.77 32.13 ? CG TLO 302 A 1 HETATM 12 C CZ TLO . . . C 3 -21.983 -15.523 -7.07 0.77 33.78 ? CZ TLO 302 A 1 HETATM 13 C C1' TLO . . . C 3 -15.834 -18.867 -0.351 0.77 15.85 ? C1' TLO 302 A 1 HETATM 14 O O1A TLO . . . C 3 -17.189 -12.654 -3.197 0.77 18.3 ? O1A TLO 302 A 1 HETATM 15 O O1B TLO . . . C 3 -16.168 -15.836 -6.624 0.77 27.79 ? O1B TLO 302 A 1 HETATM 16 C C2' TLO . . . C 3 -16.452 -17.791 0.504 0.77 16.56 ? C2' TLO 302 A 1 HETATM 17 O O2A TLO . . . C 3 -14.64 -13.272 -3.262 0.77 22.54 ? O2A TLO 302 A 1 HETATM 18 O O2B TLO . . . C 3 -17.357 -13.515 -6.334 0.77 27.42 ? O2B TLO 302 A 1 HETATM 19 C C3' TLO . . . C 3 -17.195 -17.023 -0.56 0.77 16.2 ? C3' TLO 302 A 1 HETATM 20 O O3' TLO . . . C 3 -18.417 -17.687 -0.9 0.77 17.36 ? O3' TLO 302 A 1 HETATM 21 O O3A TLO . . . C 3 -16.194 -14.726 -4.376 0.77 23.92 ? O3A TLO 302 A 1 HETATM 22 O O3B TLO . . . C 3 -18.286 -15.616 -5.189 0.77 29.86 ? O3B TLO 302 A 1 HETATM 23 C C4' TLO . . . C 3 -16.288 -17.066 -1.772 0.77 16.69 ? C4' TLO 302 A 1 HETATM 24 O O4' TLO . . . C 3 -15.495 -18.243 -1.6 0.77 16.36 ? O4' TLO 302 A 1 HETATM 25 C C5' TLO . . . C 3 -15.38 -15.847 -1.772 0.77 18.62 ? C5' TLO 302 A 1 HETATM 26 O O5' TLO . . . C 3 -16.241 -14.703 -1.949 0.77 18.84 ? O5' TLO 302 A 1 HETATM 27 C C5M TLO . . . C 3 -10.974 -18.597 0.671 0.77 23.38 ? C5M TLO 302 A 1 HETATM 28 C CD1 TLO . . . C 3 -19.956 -16.703 -6.508 0.77 31.75 ? CD1 TLO 302 A 1 HETATM 29 C CD2 TLO . . . C 3 -20.299 -14.442 -5.735 0.77 33.43 ? CD2 TLO 302 A 1 HETATM 30 C CE1 TLO . . . C 3 -21.195 -16.671 -7.142 0.77 33.1 ? CE1 TLO 302 A 1 HETATM 31 C CE2 TLO . . . C 3 -21.541 -14.407 -6.361 0.77 33.28 ? CE2 TLO 302 A 1 # _model_server_stats.io_time_ms 72 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #