data_5NV8 # _model_server_result.job_id lJqxBr9QEbULkA4vH6MbnQ _model_server_result.datetime_utc '2024-10-28 02:27:56' _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 5nv8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5NV8 # _exptl.entry_id 5NV8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 548.33 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" _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 5NV8 _cell.length_a 131.68 _cell.length_b 131.68 _cell.length_c 46.24 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NV8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C16 H26 N2 O15 P2' _chem_comp.formula_weight 548.33 _chem_comp.id TRH _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" _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 O4P P2 TRH sing 306 n n O4P H4PO TRH sing 307 n n P2 O3P TRH doub 308 n n P2 O1 TRH sing 309 n n P2 OPP TRH sing 310 n n O1 C1 TRH sing 311 n n C1 C2 TRH sing 312 n n C1 O5 TRH sing 313 n n C1 HC1 TRH sing 314 n n C2 O2 TRH sing 315 n n C2 C3 TRH sing 316 n n C2 HC2 TRH sing 317 n n O2 HO2 TRH sing 318 n n C3 O3 TRH sing 319 n n C3 C4 TRH sing 320 n n C3 HC3 TRH sing 321 n n O3 HO3 TRH sing 322 n n C4 O4 TRH sing 323 n n C4 C5 TRH sing 324 n n C4 HC4 TRH sing 325 n n O4 HO4 TRH sing 326 n n C5 O5 TRH sing 327 n n C5 C6 TRH sing 328 n n C5 HC5 TRH sing 329 n n C6 HC61 TRH sing 330 n n C6 HC62 TRH sing 331 n n C6 HC63 TRH sing 332 n n OPP P TRH sing 333 n n P O1P TRH sing 334 n n P O2P TRH doub 335 n n P O5' TRH sing 336 n n O1P H1PO TRH sing 337 n n O5' C5' TRH sing 338 n n C5' C4' TRH sing 339 n n C5' "H5'1" TRH sing 340 n n C5' "H5'2" TRH sing 341 n n C4' O4' TRH sing 342 n n C4' C3' TRH sing 343 n n C4' "H4'C" TRH sing 344 n n O4' C1' TRH sing 345 n n C3' O3' TRH sing 346 n n C3' C2' TRH sing 347 n n C3' "H3'C" TRH sing 348 n n O3' "H3'O" TRH sing 349 n n C2' C1' TRH sing 350 n n C2' "H2'1" TRH sing 351 n n C2' "H2'2" TRH sing 352 n n C1' N11 TRH sing 353 n n C1' "H1'C" TRH sing 354 n n N11 C21 TRH sing 355 n n N11 C61 TRH sing 356 n n C21 O21 TRH doub 357 n n C21 N31 TRH sing 358 n n N31 C41 TRH sing 359 n n N31 H31N TRH sing 360 n n C41 O41 TRH doub 361 n n C41 C51 TRH sing 362 n n C51 C5A TRH sing 363 n n C51 C61 TRH doub 364 n n C5A HCA1 TRH sing 365 n n C5A HCA2 TRH sing 366 n n C5A HCA3 TRH sing 367 n n C61 H61C TRH sing 368 n n # _atom_sites.entry_id 5NV8 _atom_sites.fract_transf_matrix[1][1] 0.007594 _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] 0.007594 _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] 0.021626 _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 TRH A 1 401 1 TRH DRG . C 3 HOH A 1 501 191 HOH HOH . C 3 HOH A 2 502 208 HOH HOH . C 3 HOH A 3 503 121 HOH HOH . C 3 HOH A 4 504 144 HOH HOH . C 3 HOH A 5 505 54 HOH HOH . C 3 HOH A 6 506 159 HOH HOH . C 3 HOH A 7 507 177 HOH HOH . C 3 HOH A 8 508 150 HOH HOH . C 3 HOH A 9 509 203 HOH HOH . C 3 HOH A 10 510 92 HOH HOH . C 3 HOH A 11 511 146 HOH HOH . C 3 HOH A 12 512 52 HOH HOH . C 3 HOH A 13 513 172 HOH HOH . C 3 HOH A 14 514 148 HOH HOH . C 3 HOH A 15 515 157 HOH HOH . C 3 HOH A 16 516 196 HOH HOH . C 3 HOH A 17 517 127 HOH HOH . C 3 HOH A 18 518 169 HOH HOH . C 3 HOH A 19 519 202 HOH HOH . C 3 HOH A 20 520 23 HOH HOH . C 3 HOH A 21 521 40 HOH HOH . C 3 HOH A 22 522 51 HOH HOH . C 3 HOH A 23 523 119 HOH HOH . C 3 HOH A 24 524 103 HOH HOH . C 3 HOH A 25 525 38 HOH HOH . C 3 HOH A 26 526 34 HOH HOH . C 3 HOH A 27 527 158 HOH HOH . C 3 HOH A 28 528 125 HOH HOH . C 3 HOH A 29 529 53 HOH HOH . C 3 HOH A 30 530 118 HOH HOH . C 3 HOH A 31 531 6 HOH HOH . C 3 HOH A 32 532 14 HOH HOH . C 3 HOH A 33 533 180 HOH HOH . C 3 HOH A 34 534 147 HOH HOH . C 3 HOH A 35 535 20 HOH HOH . C 3 HOH A 36 536 152 HOH HOH . C 3 HOH A 37 537 19 HOH HOH . C 3 HOH A 38 538 44 HOH HOH . C 3 HOH A 39 539 114 HOH HOH . C 3 HOH A 40 540 178 HOH HOH . C 3 HOH A 41 541 113 HOH HOH . C 3 HOH A 42 542 75 HOH HOH . C 3 HOH A 43 543 12 HOH HOH . C 3 HOH A 44 544 60 HOH HOH . C 3 HOH A 45 545 96 HOH HOH . C 3 HOH A 46 546 22 HOH HOH . C 3 HOH A 47 547 161 HOH HOH . C 3 HOH A 48 548 185 HOH HOH . C 3 HOH A 49 549 79 HOH HOH . C 3 HOH A 50 550 15 HOH HOH . C 3 HOH A 51 551 46 HOH HOH . C 3 HOH A 52 552 210 HOH HOH . C 3 HOH A 53 553 80 HOH HOH . C 3 HOH A 54 554 94 HOH HOH . C 3 HOH A 55 555 128 HOH HOH . C 3 HOH A 56 556 21 HOH HOH . C 3 HOH A 57 557 58 HOH HOH . C 3 HOH A 58 558 37 HOH HOH . C 3 HOH A 59 559 30 HOH HOH . C 3 HOH A 60 560 13 HOH HOH . C 3 HOH A 61 561 10 HOH HOH . C 3 HOH A 62 562 88 HOH HOH . C 3 HOH A 63 563 17 HOH HOH . C 3 HOH A 64 564 155 HOH HOH . C 3 HOH A 65 565 16 HOH HOH . C 3 HOH A 66 566 61 HOH HOH . C 3 HOH A 67 567 5 HOH HOH . C 3 HOH A 68 568 4 HOH HOH . C 3 HOH A 69 569 26 HOH HOH . C 3 HOH A 70 570 108 HOH HOH . C 3 HOH A 71 571 28 HOH HOH . C 3 HOH A 72 572 7 HOH HOH . C 3 HOH A 73 573 59 HOH HOH . C 3 HOH A 74 574 93 HOH HOH . C 3 HOH A 75 575 209 HOH HOH . C 3 HOH A 76 576 101 HOH HOH . C 3 HOH A 77 577 141 HOH HOH . C 3 HOH A 78 578 3 HOH HOH . C 3 HOH A 79 579 57 HOH HOH . C 3 HOH A 80 580 1 HOH HOH . C 3 HOH A 81 581 175 HOH HOH . C 3 HOH A 82 582 189 HOH HOH . C 3 HOH A 83 583 8 HOH HOH . C 3 HOH A 84 584 36 HOH HOH . C 3 HOH A 85 585 116 HOH HOH . C 3 HOH A 86 586 170 HOH HOH . C 3 HOH A 87 587 42 HOH HOH . C 3 HOH A 88 588 18 HOH HOH . C 3 HOH A 89 589 182 HOH HOH . C 3 HOH A 90 590 186 HOH HOH . C 3 HOH A 91 591 164 HOH HOH . C 3 HOH A 92 592 130 HOH HOH . C 3 HOH A 93 593 149 HOH HOH . C 3 HOH A 94 594 11 HOH HOH . C 3 HOH A 95 595 142 HOH HOH . C 3 HOH A 96 596 123 HOH HOH . C 3 HOH A 97 597 41 HOH HOH . C 3 HOH A 98 598 105 HOH HOH . C 3 HOH A 99 599 190 HOH HOH . C 3 HOH A 100 600 131 HOH HOH . C 3 HOH A 101 601 100 HOH HOH . C 3 HOH A 102 602 168 HOH HOH . C 3 HOH A 103 603 66 HOH HOH . C 3 HOH A 104 604 136 HOH HOH . C 3 HOH A 105 605 195 HOH HOH . C 3 HOH A 106 606 102 HOH HOH . C 3 HOH A 107 607 183 HOH HOH . C 3 HOH A 108 608 72 HOH HOH . C 3 HOH A 109 609 39 HOH HOH . C 3 HOH A 110 610 154 HOH HOH . C 3 HOH A 111 611 97 HOH HOH . C 3 HOH A 112 612 43 HOH HOH . C 3 HOH A 113 613 163 HOH HOH . C 3 HOH A 114 614 187 HOH HOH . C 3 HOH A 115 615 85 HOH HOH . C 3 HOH A 116 616 35 HOH HOH . C 3 HOH A 117 617 201 HOH HOH . C 3 HOH A 118 618 55 HOH HOH . C 3 HOH A 119 619 192 HOH HOH . C 3 HOH A 120 620 64 HOH HOH . C 3 HOH A 121 621 129 HOH HOH . C 3 HOH A 122 622 199 HOH HOH . C 3 HOH A 123 623 32 HOH HOH . C 3 HOH A 124 624 31 HOH HOH . C 3 HOH A 125 625 206 HOH HOH . C 3 HOH A 126 626 74 HOH HOH . C 3 HOH A 127 627 107 HOH HOH . C 3 HOH A 128 628 126 HOH HOH . C 3 HOH A 129 629 29 HOH HOH . C 3 HOH A 130 630 67 HOH HOH . C 3 HOH A 131 631 111 HOH HOH . C 3 HOH A 132 632 63 HOH HOH . C 3 HOH A 133 633 84 HOH HOH . C 3 HOH A 134 634 56 HOH HOH . C 3 HOH A 135 635 9 HOH HOH . C 3 HOH A 136 636 117 HOH HOH . C 3 HOH A 137 637 207 HOH HOH . C 3 HOH A 138 638 73 HOH HOH . C 3 HOH A 139 639 162 HOH HOH . C 3 HOH A 140 640 115 HOH HOH . C 3 HOH A 141 641 204 HOH HOH . C 3 HOH A 142 642 50 HOH HOH . C 3 HOH A 143 643 132 HOH HOH . C 3 HOH A 144 644 140 HOH HOH . C 3 HOH A 145 645 95 HOH HOH . C 3 HOH A 146 646 33 HOH HOH . C 3 HOH A 147 647 153 HOH HOH . C 3 HOH A 148 648 200 HOH HOH . C 3 HOH A 149 649 193 HOH HOH . C 3 HOH A 150 650 49 HOH HOH . C 3 HOH A 151 651 48 HOH HOH . C 3 HOH A 152 652 45 HOH HOH . C 3 HOH A 153 653 69 HOH HOH . C 3 HOH A 154 654 90 HOH HOH . C 3 HOH A 155 655 197 HOH HOH . C 3 HOH A 156 656 137 HOH HOH . C 3 HOH A 157 657 68 HOH HOH . C 3 HOH A 158 658 112 HOH HOH . C 3 HOH A 159 659 82 HOH HOH . C 3 HOH A 160 660 104 HOH HOH . C 3 HOH A 161 661 87 HOH HOH . C 3 HOH A 162 662 166 HOH HOH . C 3 HOH A 163 663 24 HOH HOH . C 3 HOH A 164 664 181 HOH HOH . C 3 HOH A 165 665 62 HOH HOH . C 3 HOH A 166 666 77 HOH HOH . C 3 HOH A 167 667 184 HOH HOH . C 3 HOH A 168 668 98 HOH HOH . C 3 HOH A 169 669 167 HOH HOH . C 3 HOH A 170 670 173 HOH HOH . C 3 HOH A 171 671 133 HOH HOH . C 3 HOH A 172 672 47 HOH HOH . C 3 HOH A 173 673 65 HOH HOH . C 3 HOH A 174 674 171 HOH HOH . C 3 HOH A 175 675 139 HOH HOH . C 3 HOH A 176 676 145 HOH HOH . C 3 HOH A 177 677 89 HOH HOH . C 3 HOH A 178 678 160 HOH HOH . C 3 HOH A 179 679 194 HOH HOH . C 3 HOH A 180 680 81 HOH HOH . C 3 HOH A 181 681 76 HOH HOH . C 3 HOH A 182 682 27 HOH HOH . C 3 HOH A 183 683 109 HOH HOH . C 3 HOH A 184 684 70 HOH HOH . C 3 HOH A 185 685 174 HOH HOH . C 3 HOH A 186 686 156 HOH HOH . C 3 HOH A 187 687 134 HOH HOH . C 3 HOH A 188 688 83 HOH HOH . C 3 HOH A 189 689 71 HOH HOH . C 3 HOH A 190 690 120 HOH HOH . C 3 HOH A 191 691 2 HOH HOH . C 3 HOH A 192 692 124 HOH HOH . C 3 HOH A 193 693 179 HOH HOH . C 3 HOH A 194 694 78 HOH HOH . C 3 HOH A 195 695 91 HOH HOH . C 3 HOH A 196 696 86 HOH HOH . C 3 HOH A 197 697 122 HOH HOH . C 3 HOH A 198 698 138 HOH HOH . C 3 HOH A 199 699 188 HOH HOH . C 3 HOH A 200 700 135 HOH HOH . C 3 HOH A 201 701 106 HOH HOH . C 3 HOH A 202 702 205 HOH HOH . C 3 HOH A 203 703 25 HOH HOH . C 3 HOH A 204 704 110 HOH HOH . C 3 HOH A 205 705 143 HOH HOH . C 3 HOH A 206 706 176 HOH HOH . C 3 HOH A 207 707 151 HOH HOH . C 3 HOH A 208 708 198 HOH HOH . C 3 HOH A 209 709 165 HOH HOH . C 3 HOH A 210 710 99 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 O O4P TRH . . . B 2 47.558 32.48 11.887 1 49.66 ? O4P TRH 401 A 1 HETATM 2 P P2 TRH . . . B 2 49.032 32.332 11.785 1 49.48 ? P2 TRH 401 A 1 HETATM 3 O O3P TRH . . . B 2 49.609 32.94 10.401 1 30.25 ? O3P TRH 401 A 1 HETATM 4 O O1 TRH . . . B 2 49.509 30.797 11.892 1 55.6 ? O1 TRH 401 A 1 HETATM 5 C C1 TRH . . . B 2 48.498 29.78 12.048 1 62.45 ? C1 TRH 401 A 1 HETATM 6 C C2 TRH . . . B 2 49.139 28.403 12.273 1 63.66 ? C2 TRH 401 A 1 HETATM 7 O O2 TRH . . . B 2 50.341 28.261 11.515 1 71.02 ? O2 TRH 401 A 1 HETATM 8 C C3 TRH . . . B 2 48.184 27.294 11.816 1 63.07 ? C3 TRH 401 A 1 HETATM 9 O O3 TRH . . . B 2 48.279 27.137 10.394 1 61.61 ? O3 TRH 401 A 1 HETATM 10 C C4 TRH . . . B 2 46.763 27.677 12.174 1 63.69 ? C4 TRH 401 A 1 HETATM 11 O O4 TRH . . . B 2 46.681 27.905 13.593 1 69.59 ? O4 TRH 401 A 1 HETATM 12 C C5 TRH . . . B 2 46.392 28.948 11.383 0 60.7 ? C5 TRH 401 A 1 HETATM 13 O O5 TRH . . . B 2 47.579 29.689 10.958 0 60.41 ? O5 TRH 401 A 1 HETATM 14 C C6 TRH . . . B 2 45.566 28.6 10.144 0 59.44 ? C6 TRH 401 A 1 HETATM 15 O OPP TRH . . . B 2 49.771 33.159 12.961 1 51.61 ? OPP TRH 401 A 1 HETATM 16 P P TRH . . . B 2 51.306 32.858 13.297 1 44.85 ? P TRH 401 A 1 HETATM 17 O O1P TRH . . . B 2 51.553 31.473 13.77 1 42.09 ? O1P TRH 401 A 1 HETATM 18 O O2P TRH . . . B 2 51.78 33.949 14.388 1 55.46 ? O2P TRH 401 A 1 HETATM 19 O O5' TRH . . . B 2 52.161 33.218 11.982 1 36.83 ? O5' TRH 401 A 1 HETATM 20 C C5' TRH . . . B 2 52.425 34.581 11.657 1 30.53 ? C5' TRH 401 A 1 HETATM 21 C C4' TRH . . . B 2 53.878 34.696 11.228 1 25.71 ? C4' TRH 401 A 1 HETATM 22 O O4' TRH . . . B 2 53.972 35.897 10.414 1 25.46 ? O4' TRH 401 A 1 HETATM 23 C C3' TRH . . . B 2 54.727 34.99 12.449 1 37.48 ? C3' TRH 401 A 1 HETATM 24 O O3' TRH . . . B 2 56.112 34.851 12.109 1 38.8 ? O3' TRH 401 A 1 HETATM 25 C C2' TRH . . . B 2 54.404 36.458 12.608 1 35.03 ? C2' TRH 401 A 1 HETATM 26 C C1' TRH . . . B 2 54.783 36.812 11.191 1 32.79 ? C1' TRH 401 A 1 HETATM 27 N N11 TRH . . . B 2 54.502 38.213 10.809 1 45.27 ? N11 TRH 401 A 1 HETATM 28 C C21 TRH . . . B 2 55.482 38.928 10.243 1 43.68 ? C21 TRH 401 A 1 HETATM 29 O O21 TRH . . . B 2 56.59 38.427 10.06 1 45.28 ? O21 TRH 401 A 1 HETATM 30 N N31 TRH . . . B 2 55.258 40.246 9.857 1 37.3 ? N31 TRH 401 A 1 HETATM 31 C C41 TRH . . . B 2 54.016 40.84 10.05 1 31.96 ? C41 TRH 401 A 1 HETATM 32 O O41 TRH . . . B 2 53.845 42.007 9.702 1 34.08 ? O41 TRH 401 A 1 HETATM 33 C C51 TRH . . . B 2 52.995 40.102 10.633 1 41.6 ? C51 TRH 401 A 1 HETATM 34 C C5A TRH . . . B 2 51.75 40.686 10.829 1 37.39 ? C5A TRH 401 A 1 HETATM 35 C C61 TRH . . . B 2 53.231 38.783 11.013 1 47.36 ? C61 TRH 401 A 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 217 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 35 #