data_4DXL # _model_server_result.job_id AfEzAbSNKD4Fdr2ULiSLNg _model_server_result.datetime_utc '2025-06-27 06:02:17' _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 4dxl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4DXL # _exptl.entry_id 4DXL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 4DXL _cell.length_a 46.59 _cell.length_b 110.09 _cell.length_c 53.29 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DXL _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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,E _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 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 4DXL _atom_sites.fract_transf_matrix[1][1] 0.021464 _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] 0.009083 _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] 0.018765 _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 C5P A 1 401 1 C5P C5P . C 3 ATP A 1 402 1 ATP ATP . D 4 CL A 1 403 1 CL CL . E 5 HOH A 1 501 2 HOH HOH . E 5 HOH A 2 502 4 HOH HOH . E 5 HOH A 3 503 5 HOH HOH . E 5 HOH A 4 504 6 HOH HOH . E 5 HOH A 5 505 7 HOH HOH . E 5 HOH A 6 506 8 HOH HOH . E 5 HOH A 7 507 9 HOH HOH . E 5 HOH A 8 508 10 HOH HOH . E 5 HOH A 9 509 11 HOH HOH . E 5 HOH A 10 510 12 HOH HOH . E 5 HOH A 11 511 13 HOH HOH . E 5 HOH A 12 512 14 HOH HOH . E 5 HOH A 13 513 15 HOH HOH . E 5 HOH A 14 514 16 HOH HOH . E 5 HOH A 15 515 17 HOH HOH . E 5 HOH A 16 516 18 HOH HOH . E 5 HOH A 17 517 19 HOH HOH . E 5 HOH A 18 518 20 HOH HOH . E 5 HOH A 19 519 21 HOH HOH . E 5 HOH A 20 520 22 HOH HOH . E 5 HOH A 21 521 23 HOH HOH . E 5 HOH A 22 522 24 HOH HOH . E 5 HOH A 23 523 25 HOH HOH . E 5 HOH A 24 524 26 HOH HOH . E 5 HOH A 25 525 27 HOH HOH . E 5 HOH A 26 526 28 HOH HOH . E 5 HOH A 27 527 29 HOH HOH . E 5 HOH A 28 528 30 HOH HOH . E 5 HOH A 29 529 31 HOH HOH . E 5 HOH A 30 530 32 HOH HOH . E 5 HOH A 31 531 33 HOH HOH . E 5 HOH A 32 532 34 HOH HOH . E 5 HOH A 33 533 35 HOH HOH . E 5 HOH A 34 534 36 HOH HOH . E 5 HOH A 35 535 37 HOH HOH . E 5 HOH A 36 536 38 HOH HOH . E 5 HOH A 37 537 39 HOH HOH . E 5 HOH A 38 538 40 HOH HOH . E 5 HOH A 39 539 41 HOH HOH . E 5 HOH A 40 540 42 HOH HOH . E 5 HOH A 41 541 43 HOH HOH . E 5 HOH A 42 542 44 HOH HOH . E 5 HOH A 43 543 45 HOH HOH . E 5 HOH A 44 544 46 HOH HOH . E 5 HOH A 45 545 47 HOH HOH . E 5 HOH A 46 546 48 HOH HOH . E 5 HOH A 47 547 49 HOH HOH . E 5 HOH A 48 548 50 HOH HOH . E 5 HOH A 49 549 51 HOH HOH . E 5 HOH A 50 550 52 HOH HOH . E 5 HOH A 51 551 53 HOH HOH . E 5 HOH A 52 552 54 HOH HOH . E 5 HOH A 53 553 55 HOH HOH . E 5 HOH A 54 554 56 HOH HOH . E 5 HOH A 55 555 57 HOH HOH . E 5 HOH A 56 556 58 HOH HOH . E 5 HOH A 57 557 59 HOH HOH . E 5 HOH A 58 558 60 HOH HOH . E 5 HOH A 59 559 61 HOH HOH . E 5 HOH A 60 560 62 HOH HOH . E 5 HOH A 61 561 63 HOH HOH . E 5 HOH A 62 562 64 HOH HOH . E 5 HOH A 63 563 65 HOH HOH . E 5 HOH A 64 564 66 HOH HOH . E 5 HOH A 65 565 67 HOH HOH . E 5 HOH A 66 566 68 HOH HOH . E 5 HOH A 67 567 69 HOH HOH . E 5 HOH A 68 568 70 HOH HOH . E 5 HOH A 69 569 71 HOH HOH . E 5 HOH A 70 570 72 HOH HOH . E 5 HOH A 71 571 73 HOH HOH . E 5 HOH A 72 572 74 HOH HOH . E 5 HOH A 73 573 75 HOH HOH . E 5 HOH A 74 574 76 HOH HOH . E 5 HOH A 75 575 77 HOH HOH . E 5 HOH A 76 576 78 HOH HOH . E 5 HOH A 77 577 79 HOH HOH . E 5 HOH A 78 578 80 HOH HOH . E 5 HOH A 79 579 81 HOH HOH . E 5 HOH A 80 580 82 HOH HOH . E 5 HOH A 81 581 83 HOH HOH . E 5 HOH A 82 582 84 HOH HOH . E 5 HOH A 83 583 85 HOH HOH . E 5 HOH A 84 584 86 HOH HOH . E 5 HOH A 85 585 87 HOH HOH . E 5 HOH A 86 586 88 HOH HOH . E 5 HOH A 87 587 89 HOH HOH . E 5 HOH A 88 588 90 HOH HOH . E 5 HOH A 89 589 91 HOH HOH . E 5 HOH A 90 590 92 HOH HOH . E 5 HOH A 91 591 93 HOH HOH . E 5 HOH A 92 592 94 HOH HOH . E 5 HOH A 93 593 95 HOH HOH . E 5 HOH A 94 594 96 HOH HOH . E 5 HOH A 95 595 97 HOH HOH . E 5 HOH A 96 596 98 HOH HOH . E 5 HOH A 97 597 99 HOH HOH . E 5 HOH A 98 598 100 HOH HOH . E 5 HOH A 99 599 101 HOH HOH . E 5 HOH A 100 600 102 HOH HOH . E 5 HOH A 101 601 103 HOH HOH . E 5 HOH A 102 602 104 HOH HOH . E 5 HOH A 103 603 105 HOH HOH . E 5 HOH A 104 604 106 HOH HOH . E 5 HOH A 105 605 107 HOH HOH . E 5 HOH A 106 606 108 HOH HOH . E 5 HOH A 107 607 110 HOH HOH . E 5 HOH A 108 608 111 HOH HOH . E 5 HOH A 109 609 112 HOH HOH . E 5 HOH A 110 610 113 HOH HOH . E 5 HOH A 111 611 114 HOH HOH . E 5 HOH A 112 612 115 HOH HOH . E 5 HOH A 113 613 116 HOH HOH . E 5 HOH A 114 614 117 HOH HOH . E 5 HOH A 115 615 118 HOH HOH . E 5 HOH A 116 616 119 HOH HOH . E 5 HOH A 117 617 120 HOH HOH . E 5 HOH A 118 618 121 HOH HOH . E 5 HOH A 119 619 122 HOH HOH . E 5 HOH A 120 620 123 HOH HOH . E 5 HOH A 121 621 124 HOH HOH . E 5 HOH A 122 622 125 HOH HOH . E 5 HOH A 123 623 126 HOH HOH . E 5 HOH A 124 624 127 HOH HOH . E 5 HOH A 125 625 128 HOH HOH . E 5 HOH A 126 626 129 HOH HOH . E 5 HOH A 127 627 130 HOH HOH . E 5 HOH A 128 628 131 HOH HOH . E 5 HOH A 129 629 132 HOH HOH . E 5 HOH A 130 630 133 HOH HOH . E 5 HOH A 131 631 135 HOH HOH . E 5 HOH A 132 632 136 HOH HOH . E 5 HOH A 133 633 137 HOH HOH . E 5 HOH A 134 634 138 HOH HOH . E 5 HOH A 135 635 139 HOH HOH . E 5 HOH A 136 636 140 HOH HOH . E 5 HOH A 137 637 141 HOH HOH . E 5 HOH A 138 638 142 HOH HOH . E 5 HOH A 139 639 143 HOH HOH . E 5 HOH A 140 640 144 HOH HOH . E 5 HOH A 141 641 145 HOH HOH . E 5 HOH A 142 642 146 HOH HOH . E 5 HOH A 143 643 147 HOH HOH . E 5 HOH A 144 644 148 HOH HOH . E 5 HOH A 145 645 149 HOH HOH . E 5 HOH A 146 646 150 HOH HOH . E 5 HOH A 147 647 151 HOH HOH . E 5 HOH A 148 648 152 HOH HOH . E 5 HOH A 149 649 153 HOH HOH . E 5 HOH A 150 650 154 HOH HOH . E 5 HOH A 151 651 156 HOH HOH . E 5 HOH A 152 652 157 HOH HOH . E 5 HOH A 153 653 158 HOH HOH . E 5 HOH A 154 654 159 HOH HOH . E 5 HOH A 155 655 160 HOH HOH . E 5 HOH A 156 656 161 HOH HOH . E 5 HOH A 157 657 163 HOH HOH . E 5 HOH A 158 658 164 HOH HOH . E 5 HOH A 159 659 167 HOH HOH . E 5 HOH A 160 660 168 HOH HOH . E 5 HOH A 161 661 169 HOH HOH . E 5 HOH A 162 662 170 HOH HOH . E 5 HOH A 163 663 171 HOH HOH . E 5 HOH A 164 664 172 HOH HOH . E 5 HOH A 165 665 173 HOH HOH . E 5 HOH A 166 666 174 HOH HOH . E 5 HOH A 167 667 175 HOH HOH . E 5 HOH A 168 668 176 HOH HOH . E 5 HOH A 169 669 177 HOH HOH . E 5 HOH A 170 670 178 HOH HOH . E 5 HOH A 171 671 179 HOH HOH . E 5 HOH A 172 672 180 HOH HOH . E 5 HOH A 173 673 181 HOH HOH . E 5 HOH A 174 674 182 HOH HOH . E 5 HOH A 175 675 183 HOH HOH . E 5 HOH A 176 676 184 HOH HOH . E 5 HOH A 177 677 185 HOH HOH . E 5 HOH A 178 678 186 HOH HOH . E 5 HOH A 179 679 187 HOH HOH . E 5 HOH A 180 680 188 HOH HOH . E 5 HOH A 181 681 189 HOH HOH . E 5 HOH A 182 682 190 HOH HOH . E 5 HOH A 183 683 191 HOH HOH . E 5 HOH A 184 684 192 HOH HOH . E 5 HOH A 185 685 193 HOH HOH . E 5 HOH A 186 686 194 HOH HOH . E 5 HOH A 187 687 195 HOH HOH . E 5 HOH A 188 688 196 HOH HOH . E 5 HOH A 189 689 197 HOH HOH . E 5 HOH A 190 690 198 HOH HOH . E 5 HOH A 191 691 199 HOH HOH . E 5 HOH A 192 692 200 HOH HOH . E 5 HOH A 193 693 201 HOH HOH . E 5 HOH A 194 694 202 HOH HOH . E 5 HOH A 195 695 204 HOH HOH . E 5 HOH A 196 696 205 HOH HOH . E 5 HOH A 197 697 206 HOH HOH . E 5 HOH A 198 698 207 HOH HOH . E 5 HOH A 199 699 208 HOH HOH . E 5 HOH A 200 700 209 HOH HOH . E 5 HOH A 201 701 210 HOH HOH . E 5 HOH A 202 702 211 HOH HOH . E 5 HOH A 203 703 213 HOH HOH . E 5 HOH A 204 704 214 HOH HOH . E 5 HOH A 205 705 215 HOH HOH . E 5 HOH A 206 706 216 HOH HOH . E 5 HOH A 207 707 217 HOH HOH . E 5 HOH A 208 708 218 HOH HOH . E 5 HOH A 209 709 219 HOH HOH . E 5 HOH A 210 710 220 HOH HOH . E 5 HOH A 211 711 221 HOH HOH . E 5 HOH A 212 712 222 HOH HOH . E 5 HOH A 213 713 223 HOH HOH . E 5 HOH A 214 714 224 HOH HOH . E 5 HOH A 215 715 225 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 PG ATP . . . C 3 -12.127 18.586 -6.738 0.5 9.83 ? PG ATP 402 A 1 HETATM 2 O O1G ATP . . . C 3 -11.21 18.958 -7.858 0.5 8.95 ? O1G ATP 402 A 1 HETATM 3 O O2G ATP . . . C 3 -13.613 18.648 -7.024 0.5 9.25 ? O2G ATP 402 A 1 HETATM 4 O O3G ATP . . . C 3 -11.722 17.368 -5.925 0.5 8.33 ? O3G ATP 402 A 1 HETATM 5 P PB ATP . . . C 3 -11.18 21.229 -6.017 1 13.09 ? PB ATP 402 A 1 HETATM 6 O O1B ATP . . . C 3 -9.701 21.211 -5.52 1 11.18 ? O1B ATP 402 A 1 HETATM 7 O O2B ATP . . . C 3 -11.638 21.818 -7.328 1 11.72 ? O2B ATP 402 A 1 HETATM 8 O O3B ATP . . . C 3 -11.901 19.824 -5.703 1 11.05 ? O3B ATP 402 A 1 HETATM 9 P PA ATP . . . C 3 -11.071 22.195 -3.421 1 11.69 ? PA ATP 402 A 1 HETATM 10 O O1A ATP . . . C 3 -10.755 20.822 -2.825 1 10.86 ? O1A ATP 402 A 1 HETATM 11 O O2A ATP . . . C 3 -10.167 23.395 -3.241 1 11 ? O2A ATP 402 A 1 HETATM 12 O O3A ATP . . . C 3 -11.799 22.174 -4.864 1 11.4 ? O3A ATP 402 A 1 HETATM 13 O O5' ATP . . . C 3 -12.445 22.577 -2.641 1 13.86 ? O5' ATP 402 A 1 HETATM 14 C C5' ATP . . . C 3 -13.079 23.865 -2.823 1 15.08 ? C5' ATP 402 A 1 HETATM 15 C C4' ATP . . . C 3 -14.407 23.967 -2.05 1 16.54 ? C4' ATP 402 A 1 HETATM 16 O O4' ATP . . . C 3 -14.387 23.283 -0.766 1 16.13 ? O4' ATP 402 A 1 HETATM 17 C C3' ATP . . . C 3 -14.721 25.402 -1.673 1 17.44 ? C3' ATP 402 A 1 HETATM 18 O O3' ATP . . . C 3 -16.135 25.47 -1.52 1 18.25 ? O3' ATP 402 A 1 HETATM 19 C C2' ATP . . . C 3 -13.999 25.592 -0.335 1 17.65 ? C2' ATP 402 A 1 HETATM 20 O O2' ATP . . . C 3 -14.547 26.613 0.512 1 19.19 ? O2' ATP 402 A 1 HETATM 21 C C1' ATP . . . C 3 -14.191 24.233 0.302 1 16.45 ? C1' ATP 402 A 1 HETATM 22 N N9 ATP . . . C 3 -13.074 23.727 1.134 1 16.1 ? N9 ATP 402 A 1 HETATM 23 C C8 ATP . . . C 3 -13.299 23.041 2.28 1 15.41 ? C8 ATP 402 A 1 HETATM 24 N N7 ATP . . . C 3 -12.123 22.629 2.806 1 16.18 ? N7 ATP 402 A 1 HETATM 25 C C5 ATP . . . C 3 -11.122 23.068 2.005 1 14.67 ? C5 ATP 402 A 1 HETATM 26 C C6 ATP . . . C 3 -9.653 22.933 2.009 1 13.62 ? C6 ATP 402 A 1 HETATM 27 N N6 ATP . . . C 3 -9.028 22.29 3.053 1 12.47 ? N6 ATP 402 A 1 HETATM 28 N N1 ATP . . . C 3 -8.975 23.483 0.976 1 13.39 ? N1 ATP 402 A 1 HETATM 29 C C2 ATP . . . C 3 -9.598 24.138 -0.037 1 14.42 ? C2 ATP 402 A 1 HETATM 30 N N3 ATP . . . C 3 -10.944 24.289 -0.095 1 15.49 ? N3 ATP 402 A 1 HETATM 31 C C4 ATP . . . C 3 -11.75 23.782 0.891 1 15.6 ? C4 ATP 402 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #