data_5TBT # _model_server_result.job_id Tm7jSo_D-s9z3yLBaqtGMg _model_server_result.datetime_utc '2024-11-22 12:33:03' _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 5tbt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5TBT # _exptl.entry_id 5TBT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 243.217 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE _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 5TBT _cell.length_a 100.153 _cell.length_b 100.153 _cell.length_c 100.153 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TBT _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 5_564 z,x+1,y-1 0 0 1 1 0 0 0 1 0 0 100.153 -100.153 3 'crystal symmetry operation' 9_465 y-1,z+1,x 0 1 0 0 0 1 1 0 0 -100.153 100.153 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 'C9 H13 N3 O5' _chem_comp.formula_weight 243.217 _chem_comp.id CTN _chem_comp.mon_nstd_flag . _chem_comp.name 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CYTIDINE # 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 O5' C5' CTN sing 70 n n O5' H5' CTN sing 71 n n C5' C4' CTN sing 72 n n C5' "H5'1" CTN sing 73 n n C5' "H5'2" CTN sing 74 n n C4' O4' CTN sing 75 n n C4' C3' CTN sing 76 n n C4' H4' CTN sing 77 n n O4' C1' CTN sing 78 n n C1' N1 CTN sing 79 n n C1' C2' CTN sing 80 n n C1' H1' CTN sing 81 n n N1 C6 CTN sing 82 n y N1 C2 CTN sing 83 n y C6 C5 CTN doub 84 n y C6 H6 CTN sing 85 n n C5 C4 CTN sing 86 n y C5 H5 CTN sing 87 n n C4 N3 CTN doub 88 n y C4 N4 CTN sing 89 n n N3 C2 CTN sing 90 n y C2 O2 CTN doub 91 n n N4 HN41 CTN sing 92 n n N4 HN42 CTN sing 93 n n C2' O2' CTN sing 94 n n C2' C3' CTN sing 95 n n C2' H2' CTN sing 96 n n O2' H1 CTN sing 97 n n C3' O3' CTN sing 98 n n C3' H3' CTN sing 99 n n O3' H2 CTN sing 100 n n # _atom_sites.entry_id 5TBT _atom_sites.fract_transf_matrix[1][1] 0.009985 _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] 0.009985 _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] 0.009985 _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 CTN A 1 301 2734 CTN CTN . C 3 SO4 A 1 302 1 SO4 SO4 . D 4 HOH A 1 401 137 HOH HOH . D 4 HOH A 2 402 152 HOH HOH . D 4 HOH A 3 403 3 HOH HOH . D 4 HOH A 4 404 40 HOH HOH . D 4 HOH A 5 405 204 HOH HOH . D 4 HOH A 6 406 173 HOH HOH . D 4 HOH A 7 407 209 HOH HOH . D 4 HOH A 8 408 135 HOH HOH . D 4 HOH A 9 409 171 HOH HOH . D 4 HOH A 10 410 162 HOH HOH . D 4 HOH A 11 411 52 HOH HOH . D 4 HOH A 12 412 51 HOH HOH . D 4 HOH A 13 413 176 HOH HOH . D 4 HOH A 14 414 48 HOH HOH . D 4 HOH A 15 415 123 HOH HOH . D 4 HOH A 16 416 14 HOH HOH . D 4 HOH A 17 417 72 HOH HOH . D 4 HOH A 18 418 163 HOH HOH . D 4 HOH A 19 419 18 HOH HOH . D 4 HOH A 20 420 9 HOH HOH . D 4 HOH A 21 421 78 HOH HOH . D 4 HOH A 22 422 144 HOH HOH . D 4 HOH A 23 423 75 HOH HOH . D 4 HOH A 24 424 60 HOH HOH . D 4 HOH A 25 425 183 HOH HOH . D 4 HOH A 26 426 112 HOH HOH . D 4 HOH A 27 427 94 HOH HOH . D 4 HOH A 28 428 77 HOH HOH . D 4 HOH A 29 429 119 HOH HOH . D 4 HOH A 30 430 97 HOH HOH . D 4 HOH A 31 431 76 HOH HOH . D 4 HOH A 32 432 33 HOH HOH . D 4 HOH A 33 433 19 HOH HOH . D 4 HOH A 34 434 45 HOH HOH . D 4 HOH A 35 435 98 HOH HOH . D 4 HOH A 36 436 139 HOH HOH . D 4 HOH A 37 437 58 HOH HOH . D 4 HOH A 38 438 16 HOH HOH . D 4 HOH A 39 439 55 HOH HOH . D 4 HOH A 40 440 73 HOH HOH . D 4 HOH A 41 441 1 HOH HOH . D 4 HOH A 42 442 42 HOH HOH . D 4 HOH A 43 443 110 HOH HOH . D 4 HOH A 44 444 143 HOH HOH . D 4 HOH A 45 445 46 HOH HOH . D 4 HOH A 46 446 218 HOH HOH . D 4 HOH A 47 447 59 HOH HOH . D 4 HOH A 48 448 65 HOH HOH . D 4 HOH A 49 449 90 HOH HOH . D 4 HOH A 50 450 187 HOH HOH . D 4 HOH A 51 451 99 HOH HOH . D 4 HOH A 52 452 149 HOH HOH . D 4 HOH A 53 453 12 HOH HOH . D 4 HOH A 54 454 79 HOH HOH . D 4 HOH A 55 455 22 HOH HOH . D 4 HOH A 56 456 96 HOH HOH . D 4 HOH A 57 457 36 HOH HOH . D 4 HOH A 58 458 189 HOH HOH . D 4 HOH A 59 459 21 HOH HOH . D 4 HOH A 60 460 161 HOH HOH . D 4 HOH A 61 461 74 HOH HOH . D 4 HOH A 62 462 172 HOH HOH . D 4 HOH A 63 463 175 HOH HOH . D 4 HOH A 64 464 121 HOH HOH . D 4 HOH A 65 465 70 HOH HOH . D 4 HOH A 66 466 39 HOH HOH . D 4 HOH A 67 467 43 HOH HOH . D 4 HOH A 68 468 188 HOH HOH . D 4 HOH A 69 469 38 HOH HOH . D 4 HOH A 70 470 4 HOH HOH . D 4 HOH A 71 471 165 HOH HOH . D 4 HOH A 72 472 104 HOH HOH . D 4 HOH A 73 473 7 HOH HOH . D 4 HOH A 74 474 17 HOH HOH . D 4 HOH A 75 475 95 HOH HOH . D 4 HOH A 76 476 128 HOH HOH . D 4 HOH A 77 477 57 HOH HOH . D 4 HOH A 78 478 150 HOH HOH . D 4 HOH A 79 479 29 HOH HOH . D 4 HOH A 80 480 82 HOH HOH . D 4 HOH A 81 481 156 HOH HOH . D 4 HOH A 82 482 118 HOH HOH . D 4 HOH A 83 483 8 HOH HOH . D 4 HOH A 84 484 15 HOH HOH . D 4 HOH A 85 485 5 HOH HOH . D 4 HOH A 86 486 106 HOH HOH . D 4 HOH A 87 487 31 HOH HOH . D 4 HOH A 88 488 130 HOH HOH . D 4 HOH A 89 489 35 HOH HOH . D 4 HOH A 90 490 71 HOH HOH . D 4 HOH A 91 491 63 HOH HOH . D 4 HOH A 92 492 80 HOH HOH . D 4 HOH A 93 493 169 HOH HOH . D 4 HOH A 94 494 10 HOH HOH . D 4 HOH A 95 495 155 HOH HOH . D 4 HOH A 96 496 109 HOH HOH . D 4 HOH A 97 497 164 HOH HOH . D 4 HOH A 98 498 81 HOH HOH . D 4 HOH A 99 499 214 HOH HOH . D 4 HOH A 100 500 20 HOH HOH . D 4 HOH A 101 501 192 HOH HOH . D 4 HOH A 102 502 64 HOH HOH . D 4 HOH A 103 503 167 HOH HOH . D 4 HOH A 104 504 41 HOH HOH . D 4 HOH A 105 505 61 HOH HOH . D 4 HOH A 106 506 2 HOH HOH . D 4 HOH A 107 507 116 HOH HOH . D 4 HOH A 108 508 26 HOH HOH . D 4 HOH A 109 509 127 HOH HOH . D 4 HOH A 110 510 53 HOH HOH . D 4 HOH A 111 511 34 HOH HOH . D 4 HOH A 112 512 37 HOH HOH . D 4 HOH A 113 513 56 HOH HOH . D 4 HOH A 114 514 6 HOH HOH . D 4 HOH A 115 515 120 HOH HOH . D 4 HOH A 116 516 101 HOH HOH . D 4 HOH A 117 517 11 HOH HOH . D 4 HOH A 118 518 62 HOH HOH . D 4 HOH A 119 519 160 HOH HOH . D 4 HOH A 120 520 157 HOH HOH . D 4 HOH A 121 521 25 HOH HOH . D 4 HOH A 122 522 23 HOH HOH . D 4 HOH A 123 523 47 HOH HOH . D 4 HOH A 124 524 32 HOH HOH . D 4 HOH A 125 525 203 HOH HOH . D 4 HOH A 126 526 85 HOH HOH . D 4 HOH A 127 527 103 HOH HOH . D 4 HOH A 128 528 68 HOH HOH . D 4 HOH A 129 529 114 HOH HOH . D 4 HOH A 130 530 13 HOH HOH . D 4 HOH A 131 531 124 HOH HOH . D 4 HOH A 132 532 126 HOH HOH . D 4 HOH A 133 533 30 HOH HOH . D 4 HOH A 134 534 115 HOH HOH . D 4 HOH A 135 535 140 HOH HOH . D 4 HOH A 136 536 87 HOH HOH . D 4 HOH A 137 537 44 HOH HOH . D 4 HOH A 138 538 113 HOH HOH . D 4 HOH A 139 539 141 HOH HOH . D 4 HOH A 140 540 133 HOH HOH . D 4 HOH A 141 541 83 HOH HOH . D 4 HOH A 142 542 91 HOH HOH . D 4 HOH A 143 543 69 HOH HOH . D 4 HOH A 144 544 88 HOH HOH . D 4 HOH A 145 545 134 HOH HOH . D 4 HOH A 146 546 195 HOH HOH . D 4 HOH A 147 547 100 HOH HOH . D 4 HOH A 148 548 148 HOH HOH . D 4 HOH A 149 549 208 HOH HOH . D 4 HOH A 150 550 24 HOH HOH . D 4 HOH A 151 551 147 HOH HOH . D 4 HOH A 152 552 86 HOH HOH . D 4 HOH A 153 553 93 HOH HOH . D 4 HOH A 154 554 89 HOH HOH . D 4 HOH A 155 555 54 HOH HOH . D 4 HOH A 156 556 184 HOH HOH . D 4 HOH A 157 557 205 HOH HOH . D 4 HOH A 158 558 151 HOH HOH . D 4 HOH A 159 559 142 HOH HOH . D 4 HOH A 160 560 122 HOH HOH . D 4 HOH A 161 561 212 HOH HOH . D 4 HOH A 162 562 199 HOH HOH . D 4 HOH A 163 563 196 HOH HOH . D 4 HOH A 164 564 202 HOH HOH . D 4 HOH A 165 565 201 HOH HOH . D 4 HOH A 166 566 108 HOH HOH . D 4 HOH A 167 567 168 HOH HOH . D 4 HOH A 168 568 216 HOH HOH . D 4 HOH A 169 569 219 HOH HOH . D 4 HOH A 170 570 179 HOH HOH . D 4 HOH A 171 571 28 HOH HOH . D 4 HOH A 172 572 206 HOH HOH . D 4 HOH A 173 573 117 HOH HOH . D 4 HOH A 174 574 197 HOH HOH . D 4 HOH A 175 575 185 HOH HOH . D 4 HOH A 176 576 145 HOH HOH . D 4 HOH A 177 577 138 HOH HOH . D 4 HOH A 178 578 177 HOH HOH . D 4 HOH A 179 579 50 HOH HOH . D 4 HOH A 180 580 158 HOH HOH . D 4 HOH A 181 581 200 HOH HOH . D 4 HOH A 182 582 153 HOH HOH . D 4 HOH A 183 583 92 HOH HOH . D 4 HOH A 184 584 207 HOH HOH . D 4 HOH A 185 585 107 HOH HOH . D 4 HOH A 186 586 181 HOH HOH . D 4 HOH A 187 587 193 HOH HOH . D 4 HOH A 188 588 67 HOH HOH . D 4 HOH A 189 589 27 HOH HOH . D 4 HOH A 190 590 215 HOH HOH . D 4 HOH A 191 591 111 HOH HOH . D 4 HOH A 192 592 211 HOH HOH . D 4 HOH A 193 593 154 HOH HOH . D 4 HOH A 194 594 132 HOH HOH . D 4 HOH A 195 595 66 HOH HOH . D 4 HOH A 196 596 178 HOH HOH . D 4 HOH A 197 597 220 HOH HOH . D 4 HOH A 198 598 191 HOH HOH . D 4 HOH A 199 599 210 HOH HOH . D 4 HOH A 200 600 170 HOH HOH . D 4 HOH A 201 601 84 HOH HOH . D 4 HOH A 202 602 146 HOH HOH . D 4 HOH A 203 603 198 HOH HOH . D 4 HOH A 204 604 174 HOH HOH . D 4 HOH A 205 605 136 HOH HOH . D 4 HOH A 206 606 125 HOH HOH . D 4 HOH A 207 607 186 HOH HOH . D 4 HOH A 208 608 213 HOH HOH . D 4 HOH A 209 609 217 HOH HOH . D 4 HOH A 210 610 194 HOH HOH . D 4 HOH A 211 611 182 HOH HOH . D 4 HOH A 212 612 49 HOH HOH . D 4 HOH A 213 613 105 HOH HOH . D 4 HOH A 214 614 166 HOH HOH . D 4 HOH A 215 615 190 HOH HOH . D 4 HOH A 216 616 102 HOH HOH . D 4 HOH A 217 617 159 HOH HOH . D 4 HOH A 218 618 129 HOH HOH . D 4 HOH A 219 619 131 HOH HOH . D 4 HOH A 220 620 180 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 O5' CTN . . . B 2 102.17 172.924 82.251 1 47.96 ? O5' CTN 301 A 1 HETATM 2 C C5' CTN . . . B 2 102.184 174.255 82.665 1 53.76 ? C5' CTN 301 A 1 HETATM 3 C C4' CTN . . . B 2 102.861 175.151 81.641 1 58.28 ? C4' CTN 301 A 1 HETATM 4 O O4' CTN . . . B 2 102.382 174.904 80.341 1 56.19 ? O4' CTN 301 A 1 HETATM 5 C C1' CTN . . . B 2 101.253 175.696 80.054 1 53.51 ? C1' CTN 301 A 1 HETATM 6 N N1 CTN . . . B 2 100.007 174.922 80.075 1 44.02 ? N1 CTN 301 A 1 HETATM 7 C C6 CTN . . . B 2 100.043 173.62 79.989 1 37.23 ? C6 CTN 301 A 1 HETATM 8 C C5 CTN . . . B 2 98.905 172.881 80.003 1 35.82 ? C5 CTN 301 A 1 HETATM 9 C C4 CTN . . . B 2 97.693 173.494 80.116 1 34.32 ? C4 CTN 301 A 1 HETATM 10 N N3 CTN . . . B 2 97.635 174.813 80.184 1 37.24 ? N3 CTN 301 A 1 HETATM 11 C C2 CTN . . . B 2 98.776 175.563 80.147 1 41.84 ? C2 CTN 301 A 1 HETATM 12 O O2 CTN . . . B 2 98.744 176.791 80.218 1 41.19 ? O2 CTN 301 A 1 HETATM 13 N N4 CTN . . . B 2 96.609 172.719 80.116 1 32.6 ? N4 CTN 301 A 1 HETATM 14 C C2' CTN . . . B 2 101.265 176.772 81.117 1 58.87 ? C2' CTN 301 A 1 HETATM 15 O O2' CTN . . . B 2 101.138 178.035 80.505 1 59.13 ? O2' CTN 301 A 1 HETATM 16 C C3' CTN . . . B 2 102.505 176.588 81.922 1 64.84 ? C3' CTN 301 A 1 HETATM 17 O O3' CTN . . . B 2 103.556 177.433 81.509 1 64.63 ? O3' CTN 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 17 #