data_2PKM # _model_server_result.job_id FYw_8pNWLidcvMJ8ZLyHRQ _model_server_result.datetime_utc '2024-11-22 05:57:42' _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 2pkm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 2PKM # _exptl.entry_id 2PKM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE _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 120 _cell.entry_id 2PKM _cell.length_a 71.9 _cell.length_b 71.9 _cell.length_c 110.8 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 73.866667 # _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 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id ADN _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE _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 O5' C5' ADN sing 1 n n O5' HO5' ADN sing 2 n n C5' C4' ADN sing 3 n n C5' "H5'1" ADN sing 4 n n C5' "H5'2" ADN sing 5 n n C4' O4' ADN sing 6 n n C4' C3' ADN sing 7 n n C4' H4' ADN sing 8 n n O4' C1' ADN sing 9 n n C3' O3' ADN sing 10 n n C3' C2' ADN sing 11 n n C3' H3' ADN sing 12 n n O3' HO3' ADN sing 13 n n C2' O2' ADN sing 14 n n C2' C1' ADN sing 15 n n C2' H2' ADN sing 16 n n O2' HO2' ADN sing 17 n n C1' N9 ADN sing 18 n n C1' H1' ADN sing 19 n n N9 C8 ADN sing 20 n y N9 C4 ADN sing 21 n y C8 N7 ADN doub 22 n y C8 H8 ADN sing 23 n n N7 C5 ADN sing 24 n y C5 C6 ADN sing 25 n y C5 C4 ADN doub 26 n y C6 N6 ADN sing 27 n n C6 N1 ADN doub 28 n y N6 HN61 ADN sing 29 n n N6 HN62 ADN sing 30 n n N1 C2 ADN sing 31 n y C2 N3 ADN doub 32 n y C2 H2 ADN sing 33 n n N3 C4 ADN sing 34 n y # _atom_sites.entry_id 2PKM _atom_sites.fract_transf_matrix[1][1] 0.013908 _atom_sites.fract_transf_matrix[1][2] 0.00803 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01606 _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] 0.009025 _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 ADN A 1 501 501 ADN ADN . C 3 HOH A 1 502 1 HOH HOH . C 3 HOH A 2 503 2 HOH HOH . C 3 HOH A 3 504 3 HOH HOH . C 3 HOH A 4 505 4 HOH HOH . C 3 HOH A 5 506 5 HOH HOH . C 3 HOH A 6 507 6 HOH HOH . C 3 HOH A 7 508 7 HOH HOH . C 3 HOH A 8 509 8 HOH HOH . C 3 HOH A 9 510 9 HOH HOH . C 3 HOH A 10 511 10 HOH HOH . C 3 HOH A 11 512 11 HOH HOH . C 3 HOH A 12 513 12 HOH HOH . C 3 HOH A 13 514 13 HOH HOH . C 3 HOH A 14 515 14 HOH HOH . C 3 HOH A 15 516 15 HOH HOH . C 3 HOH A 16 517 16 HOH HOH . C 3 HOH A 17 518 17 HOH HOH . C 3 HOH A 18 519 18 HOH HOH . C 3 HOH A 19 520 19 HOH HOH . C 3 HOH A 20 521 20 HOH HOH . C 3 HOH A 21 522 21 HOH HOH . C 3 HOH A 22 523 22 HOH HOH . C 3 HOH A 23 524 23 HOH HOH . C 3 HOH A 24 525 24 HOH HOH . C 3 HOH A 25 526 25 HOH HOH . C 3 HOH A 26 527 26 HOH HOH . C 3 HOH A 27 528 27 HOH HOH . C 3 HOH A 28 529 28 HOH HOH . C 3 HOH A 29 530 29 HOH HOH . C 3 HOH A 30 531 30 HOH HOH . C 3 HOH A 31 532 31 HOH HOH . C 3 HOH A 32 533 32 HOH HOH . C 3 HOH A 33 534 33 HOH HOH . C 3 HOH A 34 535 34 HOH HOH . C 3 HOH A 35 536 35 HOH HOH . C 3 HOH A 36 537 36 HOH HOH . C 3 HOH A 37 538 37 HOH HOH . C 3 HOH A 38 539 38 HOH HOH . C 3 HOH A 39 540 39 HOH HOH . C 3 HOH A 40 541 40 HOH HOH . C 3 HOH A 41 542 41 HOH HOH . C 3 HOH A 42 543 42 HOH HOH . C 3 HOH A 43 544 43 HOH HOH . C 3 HOH A 44 545 44 HOH HOH . C 3 HOH A 45 546 45 HOH HOH . C 3 HOH A 46 547 46 HOH HOH . C 3 HOH A 47 548 47 HOH HOH . C 3 HOH A 48 549 48 HOH HOH . C 3 HOH A 49 550 49 HOH HOH . C 3 HOH A 50 551 50 HOH HOH . C 3 HOH A 51 552 51 HOH HOH . C 3 HOH A 52 553 52 HOH HOH . C 3 HOH A 53 554 53 HOH HOH . C 3 HOH A 54 555 54 HOH HOH . C 3 HOH A 55 556 55 HOH HOH . C 3 HOH A 56 557 56 HOH HOH . C 3 HOH A 57 558 57 HOH HOH . C 3 HOH A 58 559 58 HOH HOH . C 3 HOH A 59 560 59 HOH HOH . C 3 HOH A 60 561 60 HOH HOH . C 3 HOH A 61 562 61 HOH HOH . C 3 HOH A 62 563 62 HOH HOH . C 3 HOH A 63 564 63 HOH HOH . C 3 HOH A 64 565 64 HOH HOH . C 3 HOH A 65 566 65 HOH HOH . C 3 HOH A 66 567 66 HOH HOH . C 3 HOH A 67 568 67 HOH HOH . C 3 HOH A 68 569 68 HOH HOH . C 3 HOH A 69 570 69 HOH HOH . C 3 HOH A 70 571 70 HOH HOH . C 3 HOH A 71 572 71 HOH HOH . C 3 HOH A 72 573 72 HOH HOH . C 3 HOH A 73 574 73 HOH HOH . C 3 HOH A 74 575 74 HOH HOH . C 3 HOH A 75 576 75 HOH HOH . C 3 HOH A 76 577 76 HOH HOH . C 3 HOH A 77 578 77 HOH HOH . C 3 HOH A 78 579 78 HOH HOH . C 3 HOH A 79 580 79 HOH HOH . C 3 HOH A 80 581 80 HOH HOH . C 3 HOH A 81 582 81 HOH HOH . C 3 HOH A 82 583 82 HOH HOH . C 3 HOH A 83 584 83 HOH HOH . C 3 HOH A 84 585 84 HOH HOH . C 3 HOH A 85 586 85 HOH HOH . C 3 HOH A 86 587 86 HOH HOH . C 3 HOH A 87 588 87 HOH HOH . C 3 HOH A 88 589 88 HOH HOH . C 3 HOH A 89 590 89 HOH HOH . C 3 HOH A 90 591 90 HOH HOH . C 3 HOH A 91 592 91 HOH HOH . C 3 HOH A 92 593 92 HOH HOH . C 3 HOH A 93 594 93 HOH HOH . C 3 HOH A 94 595 94 HOH HOH . C 3 HOH A 95 596 95 HOH HOH . C 3 HOH A 96 597 96 HOH HOH . C 3 HOH A 97 598 97 HOH HOH . C 3 HOH A 98 599 98 HOH HOH . C 3 HOH A 99 600 99 HOH HOH . C 3 HOH A 100 601 100 HOH HOH . C 3 HOH A 101 602 101 HOH HOH . C 3 HOH A 102 603 102 HOH HOH . C 3 HOH A 103 604 103 HOH HOH . C 3 HOH A 104 605 104 HOH HOH . C 3 HOH A 105 606 105 HOH HOH . C 3 HOH A 106 607 106 HOH HOH . C 3 HOH A 107 608 107 HOH HOH . C 3 HOH A 108 609 108 HOH HOH . C 3 HOH A 109 610 109 HOH HOH . C 3 HOH A 110 611 110 HOH HOH . C 3 HOH A 111 612 111 HOH HOH . C 3 HOH A 112 613 112 HOH HOH . C 3 HOH A 113 614 113 HOH HOH . C 3 HOH A 114 615 114 HOH HOH . C 3 HOH A 115 616 115 HOH HOH . C 3 HOH A 116 617 116 HOH HOH . C 3 HOH A 117 618 117 HOH HOH . C 3 HOH A 118 619 118 HOH HOH . C 3 HOH A 119 620 119 HOH HOH . C 3 HOH A 120 621 120 HOH HOH . C 3 HOH A 121 622 121 HOH HOH . C 3 HOH A 122 623 122 HOH HOH . C 3 HOH A 123 624 123 HOH HOH . C 3 HOH A 124 625 124 HOH HOH . C 3 HOH A 125 626 125 HOH HOH . C 3 HOH A 126 627 126 HOH HOH . C 3 HOH A 127 628 127 HOH HOH . C 3 HOH A 128 629 128 HOH HOH . C 3 HOH A 129 630 129 HOH HOH . C 3 HOH A 130 631 130 HOH HOH . C 3 HOH A 131 632 131 HOH HOH . C 3 HOH A 132 633 132 HOH HOH . C 3 HOH A 133 634 133 HOH HOH . C 3 HOH A 134 635 134 HOH HOH . C 3 HOH A 135 636 135 HOH HOH . C 3 HOH A 136 637 136 HOH HOH . C 3 HOH A 137 638 137 HOH HOH . C 3 HOH A 138 639 138 HOH HOH . C 3 HOH A 139 640 139 HOH HOH . C 3 HOH A 140 641 140 HOH HOH . C 3 HOH A 141 642 141 HOH HOH . C 3 HOH A 142 643 142 HOH HOH . C 3 HOH A 143 644 143 HOH HOH . C 3 HOH A 144 645 144 HOH HOH . C 3 HOH A 145 646 145 HOH HOH . C 3 HOH A 146 647 146 HOH HOH . C 3 HOH A 147 648 147 HOH HOH . C 3 HOH A 148 649 148 HOH HOH . C 3 HOH A 149 650 149 HOH HOH . C 3 HOH A 150 651 150 HOH HOH . C 3 HOH A 151 652 151 HOH HOH . C 3 HOH A 152 653 152 HOH HOH . C 3 HOH A 153 654 153 HOH HOH . C 3 HOH A 154 655 154 HOH HOH . C 3 HOH A 155 656 155 HOH HOH . C 3 HOH A 156 657 156 HOH HOH . C 3 HOH A 157 658 157 HOH HOH . C 3 HOH A 158 659 158 HOH HOH . C 3 HOH A 159 660 159 HOH HOH . C 3 HOH A 160 661 160 HOH HOH . C 3 HOH A 161 662 161 HOH HOH . C 3 HOH A 162 663 162 HOH HOH . C 3 HOH A 163 664 163 HOH HOH . C 3 HOH A 164 665 164 HOH HOH . C 3 HOH A 165 666 165 HOH HOH . C 3 HOH A 166 667 166 HOH HOH . C 3 HOH A 167 668 167 HOH HOH . C 3 HOH A 168 669 168 HOH HOH . C 3 HOH A 169 670 169 HOH HOH . C 3 HOH A 170 671 170 HOH HOH . C 3 HOH A 171 672 171 HOH HOH . C 3 HOH A 172 673 172 HOH HOH . C 3 HOH A 173 674 173 HOH HOH . C 3 HOH A 174 675 174 HOH HOH . C 3 HOH A 175 676 175 HOH HOH . C 3 HOH A 176 677 176 HOH HOH . C 3 HOH A 177 678 177 HOH HOH . C 3 HOH A 178 679 178 HOH HOH . C 3 HOH A 179 680 179 HOH HOH . C 3 HOH A 180 681 180 HOH HOH . C 3 HOH A 181 682 181 HOH HOH . C 3 HOH A 182 683 182 HOH HOH . C 3 HOH A 183 684 183 HOH HOH . C 3 HOH A 184 685 184 HOH HOH . C 3 HOH A 185 686 185 HOH HOH . C 3 HOH A 186 687 186 HOH HOH . C 3 HOH A 187 688 187 HOH HOH . C 3 HOH A 188 689 188 HOH HOH . C 3 HOH A 189 690 189 HOH HOH . C 3 HOH A 190 691 190 HOH HOH . C 3 HOH A 191 692 191 HOH HOH . C 3 HOH A 192 693 192 HOH HOH . C 3 HOH A 193 694 193 HOH HOH . C 3 HOH A 194 695 194 HOH HOH . C 3 HOH A 195 696 195 HOH HOH . C 3 HOH A 196 697 196 HOH HOH . C 3 HOH A 197 698 197 HOH HOH . C 3 HOH A 198 699 198 HOH HOH . C 3 HOH A 199 700 199 HOH HOH . C 3 HOH A 200 701 201 HOH HOH . C 3 HOH A 201 702 202 HOH HOH . C 3 HOH A 202 703 204 HOH HOH . C 3 HOH A 203 704 205 HOH HOH . C 3 HOH A 204 705 206 HOH HOH . C 3 HOH A 205 706 207 HOH HOH . C 3 HOH A 206 707 208 HOH HOH . C 3 HOH A 207 708 209 HOH HOH . C 3 HOH A 208 709 210 HOH HOH . C 3 HOH A 209 710 211 HOH HOH . C 3 HOH A 210 711 213 HOH HOH . C 3 HOH A 211 712 214 HOH HOH . C 3 HOH A 212 713 215 HOH HOH . C 3 HOH A 213 714 216 HOH HOH . C 3 HOH A 214 715 217 HOH HOH . C 3 HOH A 215 716 218 HOH HOH . C 3 HOH A 216 717 219 HOH HOH . C 3 HOH A 217 718 220 HOH HOH . C 3 HOH A 218 719 221 HOH HOH . C 3 HOH A 219 720 222 HOH HOH . C 3 HOH A 220 721 223 HOH HOH . C 3 HOH A 221 722 224 HOH HOH . C 3 HOH A 222 723 225 HOH HOH . C 3 HOH A 223 724 226 HOH HOH . C 3 HOH A 224 725 228 HOH HOH . C 3 HOH A 225 726 229 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' ADN . . . B 2 21.259 2.503 21.936 1 29.32 ? O5' ADN 501 A 1 HETATM 2 C C5' ADN . . . B 2 22.48 1.852 22.398 1 30.89 ? C5' ADN 501 A 1 HETATM 3 C C4' ADN . . . B 2 22.899 2.42 23.752 1 31.17 ? C4' ADN 501 A 1 HETATM 4 O O4' ADN . . . B 2 22.712 3.827 23.846 1 23.76 ? O4' ADN 501 A 1 HETATM 5 C C3' ADN . . . B 2 24.283 2.075 24.36 1 21.99 ? C3' ADN 501 A 1 HETATM 6 O O3' ADN . . . B 2 25.398 1.798 23.492 1 22.86 ? O3' ADN 501 A 1 HETATM 7 C C2' ADN . . . B 2 24.599 3.265 25.247 1 20.54 ? C2' ADN 501 A 1 HETATM 8 O O2' ADN . . . B 2 26.002 3.57 25.248 1 22.54 ? O2' ADN 501 A 1 HETATM 9 C C1' ADN . . . B 2 23.76 4.393 24.673 1 22.73 ? C1' ADN 501 A 1 HETATM 10 N N9 ADN . . . B 2 22.979 5.024 25.727 1 23.15 ? N9 ADN 501 A 1 HETATM 11 C C8 ADN . . . B 2 22.149 4.425 26.61 1 28.41 ? C8 ADN 501 A 1 HETATM 12 N N7 ADN . . . B 2 21.571 5.326 27.413 1 23.03 ? N7 ADN 501 A 1 HETATM 13 C C5 ADN . . . B 2 22.045 6.511 27.017 1 24.96 ? C5 ADN 501 A 1 HETATM 14 C C6 ADN . . . B 2 21.846 7.882 27.425 1 25.75 ? C6 ADN 501 A 1 HETATM 15 N N6 ADN . . . B 2 21.013 8.123 28.443 1 24.56 ? N6 ADN 501 A 1 HETATM 16 N N1 ADN . . . B 2 22.519 8.843 26.764 1 22.1 ? N1 ADN 501 A 1 HETATM 17 C C2 ADN . . . B 2 23.348 8.608 25.736 1 22.51 ? C2 ADN 501 A 1 HETATM 18 N N3 ADN . . . B 2 23.58 7.373 25.287 1 23.73 ? N3 ADN 501 A 1 HETATM 19 C C4 ADN . . . B 2 22.961 6.32 25.901 1 20.57 ? C4 ADN 501 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 19 #