data_8E5Q # _model_server_result.job_id kRwVEI9NTJXtlFTT6WJ4tQ _model_server_result.datetime_utc '2024-11-14 17:53:11' _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 8e5q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 8E5Q # _exptl.entry_id 8E5Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 8E5Q _cell.length_a 46.769 _cell.length_b 58.486 _cell.length_c 90.528 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8E5Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 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 3 _struct_asym.id C _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 8E5Q _atom_sites.fract_transf_matrix[1][1] 0.021382 _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] 0.017098 _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] 0.011046 _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 UMI A 1 401 401 UMI 68 . C 3 A3P A 1 402 402 A3P A3P . D 4 HOH A 1 501 501 HOH HOH . D 4 HOH A 2 502 502 HOH HOH . D 4 HOH A 3 503 503 HOH HOH . D 4 HOH A 4 504 504 HOH HOH . D 4 HOH A 5 505 505 HOH HOH . D 4 HOH A 6 506 506 HOH HOH . D 4 HOH A 7 507 507 HOH HOH . D 4 HOH A 8 508 508 HOH HOH . D 4 HOH A 9 509 509 HOH HOH . D 4 HOH A 10 510 510 HOH HOH . D 4 HOH A 11 511 511 HOH HOH . D 4 HOH A 12 512 512 HOH HOH . D 4 HOH A 13 513 513 HOH HOH . D 4 HOH A 14 514 514 HOH HOH . D 4 HOH A 15 515 515 HOH HOH . D 4 HOH A 16 516 516 HOH HOH . D 4 HOH A 17 517 517 HOH HOH . D 4 HOH A 18 518 518 HOH HOH . D 4 HOH A 19 519 519 HOH HOH . D 4 HOH A 20 520 520 HOH HOH . D 4 HOH A 21 521 521 HOH HOH . D 4 HOH A 22 522 522 HOH HOH . D 4 HOH A 23 523 523 HOH HOH . D 4 HOH A 24 524 524 HOH HOH . D 4 HOH A 25 525 525 HOH HOH . D 4 HOH A 26 526 526 HOH HOH . D 4 HOH A 27 527 527 HOH HOH . D 4 HOH A 28 528 528 HOH HOH . D 4 HOH A 29 529 529 HOH HOH . D 4 HOH A 30 530 530 HOH HOH . D 4 HOH A 31 531 531 HOH HOH . D 4 HOH A 32 532 532 HOH HOH . D 4 HOH A 33 533 533 HOH HOH . D 4 HOH A 34 534 534 HOH HOH . D 4 HOH A 35 535 535 HOH HOH . D 4 HOH A 36 536 536 HOH HOH . D 4 HOH A 37 537 537 HOH HOH . D 4 HOH A 38 538 538 HOH HOH . D 4 HOH A 39 539 539 HOH HOH . D 4 HOH A 40 540 540 HOH HOH . D 4 HOH A 41 541 541 HOH HOH . D 4 HOH A 42 542 542 HOH HOH . D 4 HOH A 43 543 543 HOH HOH . D 4 HOH A 44 544 544 HOH HOH . D 4 HOH A 45 545 545 HOH HOH . D 4 HOH A 46 546 546 HOH HOH . D 4 HOH A 47 547 547 HOH HOH . D 4 HOH A 48 548 548 HOH HOH . D 4 HOH A 49 549 549 HOH HOH . D 4 HOH A 50 550 550 HOH HOH . D 4 HOH A 51 551 551 HOH HOH . D 4 HOH A 52 552 552 HOH HOH . D 4 HOH A 53 553 553 HOH HOH . D 4 HOH A 54 554 554 HOH HOH . D 4 HOH A 55 555 555 HOH HOH . D 4 HOH A 56 556 556 HOH HOH . D 4 HOH A 57 557 557 HOH HOH . D 4 HOH A 58 558 558 HOH HOH . D 4 HOH A 59 559 559 HOH HOH . D 4 HOH A 60 560 560 HOH HOH . D 4 HOH A 61 561 561 HOH HOH . D 4 HOH A 62 562 562 HOH HOH . D 4 HOH A 63 563 563 HOH HOH . D 4 HOH A 64 564 564 HOH HOH . D 4 HOH A 65 565 565 HOH HOH . D 4 HOH A 66 566 566 HOH HOH . D 4 HOH A 67 567 567 HOH HOH . D 4 HOH A 68 568 568 HOH HOH . D 4 HOH A 69 569 569 HOH HOH . D 4 HOH A 70 570 570 HOH HOH . D 4 HOH A 71 571 571 HOH HOH . D 4 HOH A 72 572 572 HOH HOH . D 4 HOH A 73 573 573 HOH HOH . D 4 HOH A 74 574 574 HOH HOH . D 4 HOH A 75 575 575 HOH HOH . D 4 HOH A 76 576 576 HOH HOH . D 4 HOH A 77 577 577 HOH HOH . D 4 HOH A 78 578 578 HOH HOH . D 4 HOH A 79 579 579 HOH HOH . D 4 HOH A 80 580 580 HOH HOH . D 4 HOH A 81 581 581 HOH HOH . D 4 HOH A 82 582 582 HOH HOH . D 4 HOH A 83 583 583 HOH HOH . D 4 HOH A 84 584 584 HOH HOH . D 4 HOH A 85 585 585 HOH HOH . D 4 HOH A 86 586 586 HOH HOH . D 4 HOH A 87 587 587 HOH HOH . D 4 HOH A 88 588 588 HOH HOH . D 4 HOH A 89 589 589 HOH HOH . D 4 HOH A 90 590 590 HOH HOH . D 4 HOH A 91 591 591 HOH HOH . D 4 HOH A 92 592 592 HOH HOH . D 4 HOH A 93 593 593 HOH HOH . D 4 HOH A 94 594 594 HOH HOH . D 4 HOH A 95 595 595 HOH HOH . D 4 HOH A 96 596 596 HOH HOH . D 4 HOH A 97 597 597 HOH HOH . D 4 HOH A 98 598 598 HOH HOH . D 4 HOH A 99 599 599 HOH HOH . D 4 HOH A 100 600 600 HOH HOH . D 4 HOH A 101 601 601 HOH HOH . D 4 HOH A 102 602 602 HOH HOH . D 4 HOH A 103 603 603 HOH HOH . D 4 HOH A 104 604 604 HOH HOH . D 4 HOH A 105 605 605 HOH HOH . D 4 HOH A 106 606 606 HOH HOH . D 4 HOH A 107 607 607 HOH HOH . D 4 HOH A 108 608 608 HOH HOH . D 4 HOH A 109 609 609 HOH HOH . D 4 HOH A 110 610 610 HOH HOH . D 4 HOH A 111 611 611 HOH HOH . D 4 HOH A 112 612 612 HOH HOH . D 4 HOH A 113 613 613 HOH HOH . D 4 HOH A 114 614 614 HOH HOH . D 4 HOH A 115 615 615 HOH HOH . D 4 HOH A 116 616 616 HOH HOH . D 4 HOH A 117 617 617 HOH HOH . D 4 HOH A 118 618 618 HOH HOH . D 4 HOH A 119 619 619 HOH HOH . D 4 HOH A 120 620 620 HOH HOH . D 4 HOH A 121 621 621 HOH HOH . D 4 HOH A 122 622 622 HOH HOH . D 4 HOH A 123 623 623 HOH HOH . D 4 HOH A 124 624 624 HOH HOH . D 4 HOH A 125 625 625 HOH HOH . D 4 HOH A 126 626 626 HOH HOH . D 4 HOH A 127 627 627 HOH HOH . D 4 HOH A 128 628 628 HOH HOH . D 4 HOH A 129 629 629 HOH HOH . D 4 HOH A 130 630 630 HOH HOH . D 4 HOH A 131 631 631 HOH HOH . D 4 HOH A 132 632 632 HOH HOH . D 4 HOH A 133 633 633 HOH HOH . D 4 HOH A 134 634 634 HOH HOH . D 4 HOH A 135 635 635 HOH HOH . D 4 HOH A 136 636 636 HOH HOH . D 4 HOH A 137 637 637 HOH HOH . D 4 HOH A 138 638 638 HOH HOH . D 4 HOH A 139 639 639 HOH HOH . D 4 HOH A 140 640 640 HOH HOH . D 4 HOH A 141 641 641 HOH HOH . D 4 HOH A 142 642 642 HOH HOH . D 4 HOH A 143 643 643 HOH HOH . D 4 HOH A 144 644 644 HOH HOH . D 4 HOH A 145 645 645 HOH HOH . D 4 HOH A 146 646 646 HOH HOH . D 4 HOH A 147 647 647 HOH HOH . D 4 HOH A 148 648 648 HOH HOH . D 4 HOH A 149 649 649 HOH HOH . D 4 HOH A 150 650 650 HOH HOH . D 4 HOH A 151 651 651 HOH HOH . D 4 HOH A 152 652 652 HOH HOH . D 4 HOH A 153 653 653 HOH HOH . D 4 HOH A 154 654 654 HOH HOH . D 4 HOH A 155 655 655 HOH HOH . D 4 HOH A 156 656 656 HOH HOH . D 4 HOH A 157 657 657 HOH HOH . D 4 HOH A 158 658 658 HOH HOH . D 4 HOH A 159 659 659 HOH HOH . D 4 HOH A 160 660 660 HOH HOH . D 4 HOH A 161 661 661 HOH HOH . D 4 HOH A 162 662 662 HOH HOH . D 4 HOH A 163 663 663 HOH HOH . D 4 HOH A 164 664 664 HOH HOH . D 4 HOH A 165 665 665 HOH HOH . D 4 HOH A 166 666 666 HOH HOH . D 4 HOH A 167 667 667 HOH HOH . D 4 HOH A 168 668 668 HOH HOH . D 4 HOH A 169 669 669 HOH HOH . D 4 HOH A 170 670 670 HOH HOH . D 4 HOH A 171 671 671 HOH HOH . D 4 HOH A 172 672 672 HOH HOH . D 4 HOH A 173 673 673 HOH HOH . D 4 HOH A 174 674 674 HOH HOH . D 4 HOH A 175 675 675 HOH HOH . D 4 HOH A 176 676 676 HOH HOH . D 4 HOH A 177 677 677 HOH HOH . D 4 HOH A 178 678 678 HOH HOH . D 4 HOH A 179 679 679 HOH HOH . D 4 HOH A 180 680 680 HOH HOH . D 4 HOH A 181 681 681 HOH HOH . D 4 HOH A 182 682 682 HOH HOH . D 4 HOH A 183 683 683 HOH HOH . D 4 HOH A 184 684 684 HOH HOH . D 4 HOH A 185 685 685 HOH HOH . D 4 HOH A 186 686 686 HOH HOH . D 4 HOH A 187 687 687 HOH HOH . D 4 HOH A 188 688 688 HOH HOH . D 4 HOH A 189 689 689 HOH HOH . D 4 HOH A 190 690 690 HOH HOH . D 4 HOH A 191 691 691 HOH HOH . D 4 HOH A 192 692 692 HOH HOH . D 4 HOH A 193 693 693 HOH HOH . D 4 HOH A 194 694 694 HOH HOH . D 4 HOH A 195 695 695 HOH HOH . D 4 HOH A 196 696 696 HOH HOH . D 4 HOH A 197 697 697 HOH HOH . D 4 HOH A 198 698 698 HOH HOH . D 4 HOH A 199 699 699 HOH HOH . D 4 HOH A 200 700 700 HOH HOH . D 4 HOH A 201 701 701 HOH HOH . D 4 HOH A 202 702 702 HOH HOH . D 4 HOH A 203 703 703 HOH HOH . D 4 HOH A 204 704 704 HOH HOH . D 4 HOH A 205 705 705 HOH HOH . D 4 HOH A 206 706 706 HOH HOH . D 4 HOH A 207 707 707 HOH HOH . D 4 HOH A 208 708 708 HOH HOH . D 4 HOH A 209 709 709 HOH HOH . D 4 HOH A 210 710 710 HOH HOH . D 4 HOH A 211 711 711 HOH HOH . D 4 HOH A 212 712 712 HOH HOH . D 4 HOH A 213 713 713 HOH HOH . D 4 HOH A 214 714 714 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 . . . C 3 -14.971 6.178 18.426 1 17.08 ? P1 A3P 402 A 1 HETATM 2 O O1P A3P . . . C 3 -15.451 6.007 16.929 1 18.19 ? O1P A3P 402 A 1 HETATM 3 O O2P A3P . . . C 3 -16.184 6.501 19.365 1 18.11 ? O2P A3P 402 A 1 HETATM 4 O O3P A3P . . . C 3 -13.85 7.146 18.506 1 18.82 ? O3P A3P 402 A 1 HETATM 5 P P2 A3P . . . C 3 -12.559 -0.306 16.025 1 17.38 ? P2 A3P 402 A 1 HETATM 6 O O4P A3P . . . C 3 -13.173 0.185 14.635 1 19.51 ? O4P A3P 402 A 1 HETATM 7 O O5P A3P . . . C 3 -13.155 -1.722 16.427 1 19.57 ? O5P A3P 402 A 1 HETATM 8 O O6P A3P . . . C 3 -11.082 -0.33 15.957 1 17.24 ? O6P A3P 402 A 1 HETATM 9 O O5' A3P . . . C 3 -13.008 0.608 17.275 1 17.69 ? O5' A3P 402 A 1 HETATM 10 C C5' A3P . . . C 3 -12.638 2.004 17.226 1 15.94 ? C5' A3P 402 A 1 HETATM 11 C C4' A3P . . . C 3 -13.366 2.69 18.374 1 16.33 ? C4' A3P 402 A 1 HETATM 12 O O4' A3P . . . C 3 -12.774 2.305 19.642 1 16.94 ? O4' A3P 402 A 1 HETATM 13 C C3' A3P . . . C 3 -13.288 4.216 18.336 1 17.01 ? C3' A3P 402 A 1 HETATM 14 O O3' A3P . . . C 3 -14.491 4.71 18.981 1 16.01 ? O3' A3P 402 A 1 HETATM 15 C C2' A3P . . . C 3 -12.052 4.481 19.187 1 16.26 ? C2' A3P 402 A 1 HETATM 16 O O2' A3P . . . C 3 -11.956 5.808 19.689 1 18.68 ? O2' A3P 402 A 1 HETATM 17 C C1' A3P . . . C 3 -12.299 3.47 20.302 1 16.47 ? C1' A3P 402 A 1 HETATM 18 N N9 A3P . . . C 3 -11.106 3.121 21.057 1 16.91 ? N9 A3P 402 A 1 HETATM 19 C C8 A3P . . . C 3 -10.08 2.325 20.617 1 17.57 ? C8 A3P 402 A 1 HETATM 20 N N7 A3P . . . C 3 -9.117 2.169 21.486 1 19.09 ? N7 A3P 402 A 1 HETATM 21 C C5 A3P . . . C 3 -9.536 2.903 22.582 1 20.11 ? C5 A3P 402 A 1 HETATM 22 C C6 A3P . . . C 3 -8.962 3.124 23.846 1 21.17 ? C6 A3P 402 A 1 HETATM 23 N N6 A3P . . . C 3 -7.784 2.612 24.225 1 23.6 ? N6 A3P 402 A 1 HETATM 24 N N1 A3P . . . C 3 -9.641 3.913 24.717 1 22.53 ? N1 A3P 402 A 1 HETATM 25 C C2 A3P . . . C 3 -10.815 4.426 24.338 1 22.28 ? C2 A3P 402 A 1 HETATM 26 N N3 A3P . . . C 3 -11.455 4.275 23.175 1 21.64 ? N3 A3P 402 A 1 HETATM 27 C C4 A3P . . . C 3 -10.761 3.498 22.334 1 20.18 ? C4 A3P 402 A 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #