data_5TIV # _model_server_result.job_id tDicDdG39CPNhJ2UyCbDyw _model_server_result.datetime_utc '2024-11-13 04:46:23' _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 5tiv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5TIV # _exptl.entry_id 5TIV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3'-5'-DIPHOSPHATE" _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 5TIV _cell.length_a 52.595 _cell.length_b 73.561 _cell.length_c 139.624 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TIV _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 5TIV _atom_sites.fract_transf_matrix[1][1] 0.019013 _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] 0.013594 _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] 0.007162 _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 A3P A 1 301 301 A3P A3P . C 3 TRS A 1 302 401 TRS TRS . D 4 HOH A 1 401 225 HOH HOH . D 4 HOH A 2 402 229 HOH HOH . D 4 HOH A 3 403 211 HOH HOH . D 4 HOH A 4 404 99 HOH HOH . D 4 HOH A 5 405 120 HOH HOH . D 4 HOH A 6 406 202 HOH HOH . D 4 HOH A 7 407 199 HOH HOH . D 4 HOH A 8 408 133 HOH HOH . D 4 HOH A 9 409 42 HOH HOH . D 4 HOH A 10 410 237 HOH HOH . D 4 HOH A 11 411 84 HOH HOH . D 4 HOH A 12 412 102 HOH HOH . D 4 HOH A 13 413 165 HOH HOH . D 4 HOH A 14 414 198 HOH HOH . D 4 HOH A 15 415 194 HOH HOH . D 4 HOH A 16 416 231 HOH HOH . D 4 HOH A 17 417 130 HOH HOH . D 4 HOH A 18 418 129 HOH HOH . D 4 HOH A 19 419 216 HOH HOH . D 4 HOH A 20 420 185 HOH HOH . D 4 HOH A 21 421 134 HOH HOH . D 4 HOH A 22 422 207 HOH HOH . D 4 HOH A 23 423 142 HOH HOH . D 4 HOH A 24 424 34 HOH HOH . D 4 HOH A 25 425 117 HOH HOH . D 4 HOH A 26 426 159 HOH HOH . D 4 HOH A 27 427 68 HOH HOH . D 4 HOH A 28 428 75 HOH HOH . D 4 HOH A 29 429 1 HOH HOH . D 4 HOH A 30 430 213 HOH HOH . D 4 HOH A 31 431 58 HOH HOH . D 4 HOH A 32 432 9 HOH HOH . D 4 HOH A 33 433 77 HOH HOH . D 4 HOH A 34 434 110 HOH HOH . D 4 HOH A 35 435 21 HOH HOH . D 4 HOH A 36 436 136 HOH HOH . D 4 HOH A 37 437 190 HOH HOH . D 4 HOH A 38 438 26 HOH HOH . D 4 HOH A 39 439 22 HOH HOH . D 4 HOH A 40 440 141 HOH HOH . D 4 HOH A 41 441 80 HOH HOH . D 4 HOH A 42 442 60 HOH HOH . D 4 HOH A 43 443 24 HOH HOH . D 4 HOH A 44 444 2 HOH HOH . D 4 HOH A 45 445 144 HOH HOH . D 4 HOH A 46 446 27 HOH HOH . D 4 HOH A 47 447 111 HOH HOH . D 4 HOH A 48 448 59 HOH HOH . D 4 HOH A 49 449 33 HOH HOH . D 4 HOH A 50 450 161 HOH HOH . D 4 HOH A 51 451 157 HOH HOH . D 4 HOH A 52 452 7 HOH HOH . D 4 HOH A 53 453 14 HOH HOH . D 4 HOH A 54 454 126 HOH HOH . D 4 HOH A 55 455 28 HOH HOH . D 4 HOH A 56 456 114 HOH HOH . D 4 HOH A 57 457 70 HOH HOH . D 4 HOH A 58 458 239 HOH HOH . D 4 HOH A 59 459 55 HOH HOH . D 4 HOH A 60 460 204 HOH HOH . D 4 HOH A 61 461 107 HOH HOH . D 4 HOH A 62 462 193 HOH HOH . D 4 HOH A 63 463 79 HOH HOH . D 4 HOH A 64 464 238 HOH HOH . D 4 HOH A 65 465 17 HOH HOH . D 4 HOH A 66 466 154 HOH HOH . D 4 HOH A 67 467 104 HOH HOH . D 4 HOH A 68 468 37 HOH HOH . D 4 HOH A 69 469 48 HOH HOH . D 4 HOH A 70 470 191 HOH HOH . D 4 HOH A 71 471 135 HOH HOH . D 4 HOH A 72 472 176 HOH HOH . D 4 HOH A 73 473 30 HOH HOH . D 4 HOH A 74 474 127 HOH HOH . D 4 HOH A 75 475 232 HOH HOH . D 4 HOH A 76 476 73 HOH HOH . D 4 HOH A 77 477 155 HOH HOH . D 4 HOH A 78 478 148 HOH HOH . D 4 HOH A 79 479 112 HOH HOH . D 4 HOH A 80 480 151 HOH HOH . D 4 HOH A 81 481 94 HOH HOH . D 4 HOH A 82 482 189 HOH HOH . D 4 HOH A 83 483 115 HOH HOH . D 4 HOH A 84 484 146 HOH HOH . D 4 HOH A 85 485 132 HOH HOH . D 4 HOH A 86 486 19 HOH HOH . D 4 HOH A 87 487 41 HOH HOH . D 4 HOH A 88 488 15 HOH HOH . D 4 HOH A 89 489 50 HOH HOH . D 4 HOH A 90 490 64 HOH HOH . D 4 HOH A 91 491 5 HOH HOH . D 4 HOH A 92 492 87 HOH HOH . D 4 HOH A 93 493 81 HOH HOH . D 4 HOH A 94 494 218 HOH HOH . D 4 HOH A 95 495 4 HOH HOH . D 4 HOH A 96 496 25 HOH HOH . D 4 HOH A 97 497 197 HOH HOH . D 4 HOH A 98 498 49 HOH HOH . D 4 HOH A 99 499 11 HOH HOH . D 4 HOH A 100 500 113 HOH HOH . D 4 HOH A 101 501 89 HOH HOH . D 4 HOH A 102 502 20 HOH HOH . D 4 HOH A 103 503 105 HOH HOH . D 4 HOH A 104 504 240 HOH HOH . D 4 HOH A 105 505 90 HOH HOH . D 4 HOH A 106 506 12 HOH HOH . D 4 HOH A 107 507 215 HOH HOH . D 4 HOH A 108 508 13 HOH HOH . D 4 HOH A 109 509 97 HOH HOH . D 4 HOH A 110 510 78 HOH HOH . D 4 HOH A 111 511 95 HOH HOH . D 4 HOH A 112 512 221 HOH HOH . D 4 HOH A 113 513 3 HOH HOH . D 4 HOH A 114 514 160 HOH HOH . D 4 HOH A 115 515 39 HOH HOH . D 4 HOH A 116 516 46 HOH HOH . D 4 HOH A 117 517 164 HOH HOH . D 4 HOH A 118 518 93 HOH HOH . D 4 HOH A 119 519 192 HOH HOH . D 4 HOH A 120 520 226 HOH HOH . D 4 HOH A 121 521 32 HOH HOH . D 4 HOH A 122 522 128 HOH HOH . D 4 HOH A 123 523 184 HOH HOH . D 4 HOH A 124 524 8 HOH HOH . D 4 HOH A 125 525 36 HOH HOH . D 4 HOH A 126 526 69 HOH HOH . D 4 HOH A 127 527 56 HOH HOH . D 4 HOH A 128 528 66 HOH HOH . D 4 HOH A 129 529 182 HOH HOH . D 4 HOH A 130 530 54 HOH HOH . D 4 HOH A 131 531 10 HOH HOH . D 4 HOH A 132 532 131 HOH HOH . D 4 HOH A 133 533 71 HOH HOH . D 4 HOH A 134 534 72 HOH HOH . D 4 HOH A 135 535 147 HOH HOH . D 4 HOH A 136 536 31 HOH HOH . D 4 HOH A 137 537 233 HOH HOH . D 4 HOH A 138 538 45 HOH HOH . D 4 HOH A 139 539 103 HOH HOH . D 4 HOH A 140 540 67 HOH HOH . D 4 HOH A 141 541 140 HOH HOH . D 4 HOH A 142 542 63 HOH HOH . D 4 HOH A 143 543 123 HOH HOH . D 4 HOH A 144 544 16 HOH HOH . D 4 HOH A 145 545 101 HOH HOH . D 4 HOH A 146 546 86 HOH HOH . D 4 HOH A 147 547 57 HOH HOH . D 4 HOH A 148 548 82 HOH HOH . D 4 HOH A 149 549 178 HOH HOH . D 4 HOH A 150 550 175 HOH HOH . D 4 HOH A 151 551 203 HOH HOH . D 4 HOH A 152 552 61 HOH HOH . D 4 HOH A 153 553 6 HOH HOH . D 4 HOH A 154 554 18 HOH HOH . D 4 HOH A 155 555 195 HOH HOH . D 4 HOH A 156 556 35 HOH HOH . D 4 HOH A 157 557 23 HOH HOH . D 4 HOH A 158 558 208 HOH HOH . D 4 HOH A 159 559 43 HOH HOH . D 4 HOH A 160 560 124 HOH HOH . D 4 HOH A 161 561 150 HOH HOH . D 4 HOH A 162 562 145 HOH HOH . D 4 HOH A 163 563 38 HOH HOH . D 4 HOH A 164 564 91 HOH HOH . D 4 HOH A 165 565 65 HOH HOH . D 4 HOH A 166 566 187 HOH HOH . D 4 HOH A 167 567 47 HOH HOH . D 4 HOH A 168 568 83 HOH HOH . D 4 HOH A 169 569 139 HOH HOH . D 4 HOH A 170 570 109 HOH HOH . D 4 HOH A 171 571 153 HOH HOH . D 4 HOH A 172 572 121 HOH HOH . D 4 HOH A 173 573 100 HOH HOH . D 4 HOH A 174 574 223 HOH HOH . D 4 HOH A 175 575 62 HOH HOH . D 4 HOH A 176 576 51 HOH HOH . D 4 HOH A 177 577 40 HOH HOH . D 4 HOH A 178 578 143 HOH HOH . D 4 HOH A 179 579 29 HOH HOH . D 4 HOH A 180 580 149 HOH HOH . D 4 HOH A 181 581 106 HOH HOH . D 4 HOH A 182 582 88 HOH HOH . D 4 HOH A 183 583 172 HOH HOH . D 4 HOH A 184 584 53 HOH HOH . D 4 HOH A 185 585 219 HOH HOH . D 4 HOH A 186 586 177 HOH HOH . D 4 HOH A 187 587 44 HOH HOH . D 4 HOH A 188 588 180 HOH HOH . D 4 HOH A 189 589 183 HOH HOH . D 4 HOH A 190 590 230 HOH HOH . D 4 HOH A 191 591 179 HOH HOH . D 4 HOH A 192 592 170 HOH HOH . D 4 HOH A 193 593 212 HOH HOH . D 4 HOH A 194 594 168 HOH HOH . D 4 HOH A 195 595 162 HOH HOH . D 4 HOH A 196 596 92 HOH HOH . D 4 HOH A 197 597 222 HOH HOH . D 4 HOH A 198 598 85 HOH HOH . D 4 HOH A 199 599 186 HOH HOH . D 4 HOH A 200 600 235 HOH HOH . D 4 HOH A 201 601 188 HOH HOH . D 4 HOH A 202 602 169 HOH HOH . D 4 HOH A 203 603 76 HOH HOH . D 4 HOH A 204 604 171 HOH HOH . D 4 HOH A 205 605 224 HOH HOH . D 4 HOH A 206 606 227 HOH HOH . D 4 HOH A 207 607 74 HOH HOH . D 4 HOH A 208 608 166 HOH HOH . D 4 HOH A 209 609 220 HOH HOH . D 4 HOH A 210 610 181 HOH HOH . D 4 HOH A 211 611 201 HOH HOH . D 4 HOH A 212 612 206 HOH HOH . D 4 HOH A 213 613 108 HOH HOH . D 4 HOH A 214 614 98 HOH HOH . D 4 HOH A 215 615 214 HOH HOH . D 4 HOH A 216 616 156 HOH HOH . D 4 HOH A 217 617 138 HOH HOH . D 4 HOH A 218 618 125 HOH HOH . D 4 HOH A 219 619 174 HOH HOH . D 4 HOH A 220 620 158 HOH HOH . D 4 HOH A 221 621 228 HOH HOH . D 4 HOH A 222 622 205 HOH HOH . D 4 HOH A 223 623 167 HOH HOH . D 4 HOH A 224 624 137 HOH HOH . D 4 HOH A 225 625 173 HOH HOH . D 4 HOH A 226 626 152 HOH HOH . D 4 HOH A 227 627 209 HOH HOH . D 4 HOH A 228 628 116 HOH HOH . D 4 HOH A 229 629 52 HOH HOH . D 4 HOH A 230 630 122 HOH HOH . D 4 HOH A 231 631 234 HOH HOH . D 4 HOH A 232 632 196 HOH HOH . D 4 HOH A 233 633 118 HOH HOH . D 4 HOH A 234 634 210 HOH HOH . D 4 HOH A 235 635 96 HOH HOH . D 4 HOH A 236 636 119 HOH HOH . D 4 HOH A 237 637 236 HOH HOH . D 4 HOH A 238 638 217 HOH HOH . D 4 HOH A 239 639 200 HOH HOH . D 4 HOH A 240 640 163 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 P P1 A3P . . . B 2 -6.687 3.197 16.987 1 14.95 ? P1 A3P 301 A 1 HETATM 2 O O1P A3P . . . B 2 -6.464 2.195 15.888 1 16.22 ? O1P A3P 301 A 1 HETATM 3 O O2P A3P . . . B 2 -7.422 4.434 16.573 1 15.49 ? O2P A3P 301 A 1 HETATM 4 O O3P A3P . . . B 2 -7.244 2.602 18.242 1 16.5 ? O3P A3P 301 A 1 HETATM 5 P P2 A3P . . . B 2 -2.711 9.215 18.434 1 13.28 ? P2 A3P 301 A 1 HETATM 6 O O4P A3P . . . B 2 -1.469 9.6 17.684 1 14.13 ? O4P A3P 301 A 1 HETATM 7 O O5P A3P . . . B 2 -2.612 9.354 19.936 1 12.75 ? O5P A3P 301 A 1 HETATM 8 O O6P A3P . . . B 2 -3.925 9.88 17.873 1 14.58 ? O6P A3P 301 A 1 HETATM 9 O O5' A3P . . . B 2 -2.824 7.634 18.156 1 13.88 ? O5' A3P 301 A 1 HETATM 10 C C5' A3P . . . B 2 -3.899 6.863 18.672 1 14.51 ? C5' A3P 301 A 1 HETATM 11 C C4' A3P . . . B 2 -3.796 5.437 18.138 1 15.26 ? C4' A3P 301 A 1 HETATM 12 O O4' A3P . . . B 2 -2.71 4.752 18.763 1 16.55 ? O4' A3P 301 A 1 HETATM 13 C C3' A3P . . . B 2 -5.032 4.626 18.463 1 15.3 ? C3' A3P 301 A 1 HETATM 14 O O3' A3P . . . B 2 -5.212 3.69 17.398 1 14.58 ? O3' A3P 301 A 1 HETATM 15 C C2' A3P . . . B 2 -4.629 3.924 19.744 1 15.05 ? C2' A3P 301 A 1 HETATM 16 O O2' A3P . . . B 2 -5.395 2.756 20.02 1 17.27 ? O2' A3P 301 A 1 HETATM 17 C C1' A3P . . . B 2 -3.19 3.59 19.433 1 15.55 ? C1' A3P 301 A 1 HETATM 18 N N9 A3P . . . B 2 -2.377 3.349 20.639 1 15.25 ? N9 A3P 301 A 1 HETATM 19 C C8 A3P . . . B 2 -2.006 4.279 21.526 1 17.1 ? C8 A3P 301 A 1 HETATM 20 N N7 A3P . . . B 2 -1.254 3.733 22.5 1 17.63 ? N7 A3P 301 A 1 HETATM 21 C C5 A3P . . . B 2 -1.129 2.428 22.242 1 16.49 ? C5 A3P 301 A 1 HETATM 22 C C6 A3P . . . B 2 -0.461 1.279 22.878 1 20.27 ? C6 A3P 301 A 1 HETATM 23 N N6 A3P . . . B 2 0.246 1.422 24.017 1 22.37 ? N6 A3P 301 A 1 HETATM 24 N N1 A3P . . . B 2 -0.58 0.085 22.274 1 20.7 ? N1 A3P 301 A 1 HETATM 25 C C2 A3P . . . B 2 -1.28 -0.061 21.139 1 19.18 ? C2 A3P 301 A 1 HETATM 26 N N3 A3P . . . B 2 -1.911 0.934 20.508 1 15.84 ? N3 A3P 301 A 1 HETATM 27 C C4 A3P . . . B 2 -1.87 2.182 21.005 1 14.71 ? C4 A3P 301 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 230 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #