data_8YSJ # _model_server_result.job_id WDP9L7kDZO5zF0B5G25ZkQ _model_server_result.datetime_utc '2025-01-30 20:16:36' _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 8ysj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8YSJ # _exptl.entry_id 8YSJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 483.156 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 74.396 _cell.angle_beta 73.126 _cell.angle_gamma 84.271 _cell.entry_id 8YSJ _cell.length_a 35.346 _cell.length_b 46.244 _cell.length_c 61.058 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YSJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N # _chem_comp.formula 'C9 H16 N3 O14 P3' _chem_comp.formula_weight 483.156 _chem_comp.id 2KH _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine" _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 O2' C2' 2KH sing 1 n n O3' C3' 2KH sing 2 n n C2' C3' 2KH sing 3 n n C2' C1' 2KH sing 4 n n O2 C2 2KH doub 5 n n C3' C4' 2KH sing 6 n n C1' N1 2KH sing 7 n n C1' O4' 2KH sing 8 n n C2 N1 2KH sing 9 n n C2 N3 2KH sing 10 n n C4' O4' 2KH sing 11 n n C4' C5' 2KH sing 12 n n N1 C6 2KH sing 13 n n N3 C4 2KH sing 14 n n C5' O5' 2KH sing 15 n n C6 C5 2KH doub 16 n n C4 C5 2KH sing 17 n n C4 O4 2KH doub 18 n n O2B PB 2KH doub 19 n n O5' PA 2KH sing 20 n n N3A PB 2KH sing 21 n n N3A PA 2KH sing 22 n n PB O1B 2KH sing 23 n n PB O3B 2KH sing 24 n n PA O1A 2KH doub 25 n n PA O2A 2KH sing 26 n n O3B PG 2KH sing 27 n n PG O2G 2KH doub 28 n n PG O1G 2KH sing 29 n n PG O3G 2KH sing 30 n n O2A H1 2KH sing 31 n n N3A H2 2KH sing 32 n n O1B H3 2KH sing 33 n n O1G H4 2KH sing 34 n n O3G H5 2KH sing 35 n n C5' H6 2KH sing 36 n n C5' H7 2KH sing 37 n n C4' H8 2KH sing 38 n n C1' H9 2KH sing 39 n n C2' H10 2KH sing 40 n n O2' H11 2KH sing 41 n n C3' H12 2KH sing 42 n n O3' H13 2KH sing 43 n n C6 H14 2KH sing 44 n n N3 H15 2KH sing 45 n n C5 H16 2KH sing 46 n n # _atom_sites.entry_id 8YSJ _atom_sites.fract_transf_matrix[1][1] 0.028292 _atom_sites.fract_transf_matrix[1][2] -0.002838 _atom_sites.fract_transf_matrix[1][3] -0.008129 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021733 _atom_sites.fract_transf_matrix[2][3] -0.005661 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.017686 _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 2KH A 1 401 401 2KH LIG . C 2 2KH A 1 402 402 2KH LIG . D 3 HOH A 1 501 590 HOH HOH . D 3 HOH A 2 502 684 HOH HOH . D 3 HOH A 3 503 693 HOH HOH . D 3 HOH A 4 504 669 HOH HOH . D 3 HOH A 5 505 692 HOH HOH . D 3 HOH A 6 506 628 HOH HOH . D 3 HOH A 7 507 722 HOH HOH . D 3 HOH A 8 508 678 HOH HOH . D 3 HOH A 9 509 657 HOH HOH . D 3 HOH A 10 510 629 HOH HOH . D 3 HOH A 11 511 543 HOH HOH . D 3 HOH A 12 512 572 HOH HOH . D 3 HOH A 13 513 695 HOH HOH . D 3 HOH A 14 514 566 HOH HOH . D 3 HOH A 15 515 615 HOH HOH . D 3 HOH A 16 516 651 HOH HOH . D 3 HOH A 17 517 598 HOH HOH . D 3 HOH A 18 518 515 HOH HOH . D 3 HOH A 19 519 620 HOH HOH . D 3 HOH A 20 520 624 HOH HOH . D 3 HOH A 21 521 600 HOH HOH . D 3 HOH A 22 522 544 HOH HOH . D 3 HOH A 23 523 523 HOH HOH . D 3 HOH A 24 524 516 HOH HOH . D 3 HOH A 25 525 579 HOH HOH . D 3 HOH A 26 526 705 HOH HOH . D 3 HOH A 27 527 539 HOH HOH . D 3 HOH A 28 528 666 HOH HOH . D 3 HOH A 29 529 547 HOH HOH . D 3 HOH A 30 530 565 HOH HOH . D 3 HOH A 31 531 686 HOH HOH . D 3 HOH A 32 532 641 HOH HOH . D 3 HOH A 33 533 668 HOH HOH . D 3 HOH A 34 534 556 HOH HOH . D 3 HOH A 35 535 527 HOH HOH . D 3 HOH A 36 536 520 HOH HOH . D 3 HOH A 37 537 503 HOH HOH . D 3 HOH A 38 538 517 HOH HOH . D 3 HOH A 39 539 588 HOH HOH . D 3 HOH A 40 540 630 HOH HOH . D 3 HOH A 41 541 639 HOH HOH . D 3 HOH A 42 542 511 HOH HOH . D 3 HOH A 43 543 609 HOH HOH . D 3 HOH A 44 544 528 HOH HOH . D 3 HOH A 45 545 625 HOH HOH . D 3 HOH A 46 546 604 HOH HOH . D 3 HOH A 47 547 506 HOH HOH . D 3 HOH A 48 548 688 HOH HOH . D 3 HOH A 49 549 568 HOH HOH . D 3 HOH A 50 550 690 HOH HOH . D 3 HOH A 51 551 677 HOH HOH . D 3 HOH A 52 552 581 HOH HOH . D 3 HOH A 53 553 554 HOH HOH . D 3 HOH A 54 554 718 HOH HOH . D 3 HOH A 55 555 571 HOH HOH . D 3 HOH A 56 556 713 HOH HOH . D 3 HOH A 57 557 525 HOH HOH . D 3 HOH A 58 558 607 HOH HOH . D 3 HOH A 59 559 559 HOH HOH . D 3 HOH A 60 560 612 HOH HOH . D 3 HOH A 61 561 638 HOH HOH . D 3 HOH A 62 562 595 HOH HOH . D 3 HOH A 63 563 682 HOH HOH . D 3 HOH A 64 564 532 HOH HOH . D 3 HOH A 65 565 646 HOH HOH . D 3 HOH A 66 566 658 HOH HOH . D 3 HOH A 67 567 540 HOH HOH . D 3 HOH A 68 568 534 HOH HOH . D 3 HOH A 69 569 597 HOH HOH . D 3 HOH A 70 570 558 HOH HOH . D 3 HOH A 71 571 661 HOH HOH . D 3 HOH A 72 572 617 HOH HOH . D 3 HOH A 73 573 596 HOH HOH . D 3 HOH A 74 574 529 HOH HOH . D 3 HOH A 75 575 716 HOH HOH . D 3 HOH A 76 576 501 HOH HOH . D 3 HOH A 77 577 583 HOH HOH . D 3 HOH A 78 578 504 HOH HOH . D 3 HOH A 79 579 611 HOH HOH . D 3 HOH A 80 580 536 HOH HOH . D 3 HOH A 81 581 637 HOH HOH . D 3 HOH A 82 582 574 HOH HOH . D 3 HOH A 83 583 508 HOH HOH . D 3 HOH A 84 584 584 HOH HOH . D 3 HOH A 85 585 500 HOH HOH . D 3 HOH A 86 586 694 HOH HOH . D 3 HOH A 87 587 538 HOH HOH . D 3 HOH A 88 588 541 HOH HOH . D 3 HOH A 89 589 662 HOH HOH . D 3 HOH A 90 590 723 HOH HOH . D 3 HOH A 91 591 675 HOH HOH . D 3 HOH A 92 592 648 HOH HOH . D 3 HOH A 93 593 665 HOH HOH . D 3 HOH A 94 594 505 HOH HOH . D 3 HOH A 95 595 698 HOH HOH . D 3 HOH A 96 596 519 HOH HOH . D 3 HOH A 97 597 715 HOH HOH . D 3 HOH A 98 598 721 HOH HOH . D 3 HOH A 99 599 592 HOH HOH . D 3 HOH A 100 600 561 HOH HOH . D 3 HOH A 101 601 557 HOH HOH . D 3 HOH A 102 602 635 HOH HOH . D 3 HOH A 103 603 650 HOH HOH . D 3 HOH A 104 604 608 HOH HOH . D 3 HOH A 105 605 619 HOH HOH . D 3 HOH A 106 606 589 HOH HOH . D 3 HOH A 107 607 613 HOH HOH . D 3 HOH A 108 608 610 HOH HOH . D 3 HOH A 109 609 502 HOH HOH . D 3 HOH A 110 610 546 HOH HOH . D 3 HOH A 111 611 548 HOH HOH . D 3 HOH A 112 612 633 HOH HOH . D 3 HOH A 113 613 533 HOH HOH . D 3 HOH A 114 614 531 HOH HOH . D 3 HOH A 115 615 509 HOH HOH . D 3 HOH A 116 616 521 HOH HOH . D 3 HOH A 117 617 514 HOH HOH . D 3 HOH A 118 618 643 HOH HOH . D 3 HOH A 119 619 562 HOH HOH . D 3 HOH A 120 620 676 HOH HOH . D 3 HOH A 121 621 576 HOH HOH . D 3 HOH A 122 622 553 HOH HOH . D 3 HOH A 123 623 567 HOH HOH . D 3 HOH A 124 624 708 HOH HOH . D 3 HOH A 125 625 640 HOH HOH . D 3 HOH A 126 626 681 HOH HOH . D 3 HOH A 127 627 575 HOH HOH . D 3 HOH A 128 628 672 HOH HOH . D 3 HOH A 129 629 587 HOH HOH . D 3 HOH A 130 630 564 HOH HOH . D 3 HOH A 131 631 719 HOH HOH . D 3 HOH A 132 632 582 HOH HOH . D 3 HOH A 133 633 626 HOH HOH . D 3 HOH A 134 634 691 HOH HOH . D 3 HOH A 135 635 621 HOH HOH . D 3 HOH A 136 636 569 HOH HOH . D 3 HOH A 137 637 513 HOH HOH . D 3 HOH A 138 638 555 HOH HOH . D 3 HOH A 139 639 632 HOH HOH . D 3 HOH A 140 640 605 HOH HOH . D 3 HOH A 141 641 510 HOH HOH . D 3 HOH A 142 642 729 HOH HOH . D 3 HOH A 143 643 667 HOH HOH . D 3 HOH A 144 644 550 HOH HOH . D 3 HOH A 145 645 570 HOH HOH . D 3 HOH A 146 646 573 HOH HOH . D 3 HOH A 147 647 599 HOH HOH . D 3 HOH A 148 648 586 HOH HOH . D 3 HOH A 149 649 683 HOH HOH . D 3 HOH A 150 650 660 HOH HOH . D 3 HOH A 151 651 507 HOH HOH . D 3 HOH A 152 652 552 HOH HOH . D 3 HOH A 153 653 645 HOH HOH . D 3 HOH A 154 654 618 HOH HOH . D 3 HOH A 155 655 659 HOH HOH . D 3 HOH A 156 656 524 HOH HOH . D 3 HOH A 157 657 711 HOH HOH . D 3 HOH A 158 658 602 HOH HOH . D 3 HOH A 159 659 730 HOH HOH . D 3 HOH A 160 660 664 HOH HOH . D 3 HOH A 161 661 649 HOH HOH . D 3 HOH A 162 662 731 HOH HOH . D 3 HOH A 163 663 535 HOH HOH . D 3 HOH A 164 664 530 HOH HOH . D 3 HOH A 165 665 687 HOH HOH . D 3 HOH A 166 666 670 HOH HOH . D 3 HOH A 167 667 563 HOH HOH . D 3 HOH A 168 668 644 HOH HOH . D 3 HOH A 169 669 580 HOH HOH . D 3 HOH A 170 670 551 HOH HOH . D 3 HOH A 171 671 578 HOH HOH . D 3 HOH A 172 672 593 HOH HOH . D 3 HOH A 173 673 717 HOH HOH . D 3 HOH A 174 674 614 HOH HOH . D 3 HOH A 175 675 526 HOH HOH . D 3 HOH A 176 676 726 HOH HOH . D 3 HOH A 177 677 512 HOH HOH . D 3 HOH A 178 678 702 HOH HOH . D 3 HOH A 179 679 522 HOH HOH . D 3 HOH A 180 680 537 HOH HOH . D 3 HOH A 181 681 594 HOH HOH . D 3 HOH A 182 682 642 HOH HOH . D 3 HOH A 183 683 577 HOH HOH . D 3 HOH A 184 684 549 HOH HOH . D 3 HOH A 185 685 634 HOH HOH . D 3 HOH A 186 686 720 HOH HOH . D 3 HOH A 187 687 724 HOH HOH . D 3 HOH A 188 688 700 HOH HOH . D 3 HOH A 189 689 518 HOH HOH . D 3 HOH A 190 690 709 HOH HOH . D 3 HOH A 191 691 652 HOH HOH . D 3 HOH A 192 692 712 HOH HOH . D 3 HOH A 193 693 647 HOH HOH . D 3 HOH A 194 694 679 HOH HOH . D 3 HOH A 195 695 603 HOH HOH . D 3 HOH A 196 696 622 HOH HOH . D 3 HOH A 197 697 655 HOH HOH . D 3 HOH A 198 698 591 HOH HOH . D 3 HOH A 199 699 631 HOH HOH . D 3 HOH A 200 700 680 HOH HOH . D 3 HOH A 201 701 636 HOH HOH . D 3 HOH A 202 702 704 HOH HOH . D 3 HOH A 203 703 714 HOH HOH . D 3 HOH A 204 704 732 HOH HOH . D 3 HOH A 205 705 545 HOH HOH . D 3 HOH A 206 706 673 HOH HOH . D 3 HOH A 207 707 706 HOH HOH . D 3 HOH A 208 708 671 HOH HOH . D 3 HOH A 209 709 733 HOH HOH . D 3 HOH A 210 710 707 HOH HOH . D 3 HOH A 211 711 653 HOH HOH . D 3 HOH A 212 712 585 HOH HOH . D 3 HOH A 213 713 542 HOH HOH . D 3 HOH A 214 714 606 HOH HOH . D 3 HOH A 215 715 623 HOH HOH . D 3 HOH A 216 716 663 HOH HOH . D 3 HOH A 217 717 560 HOH HOH . D 3 HOH A 218 718 685 HOH HOH . D 3 HOH A 219 719 656 HOH HOH . D 3 HOH A 220 720 696 HOH HOH . D 3 HOH A 221 721 616 HOH HOH . D 3 HOH A 222 722 701 HOH HOH . D 3 HOH A 223 723 727 HOH HOH . D 3 HOH A 224 724 697 HOH HOH . D 3 HOH A 225 725 601 HOH HOH . D 3 HOH A 226 726 710 HOH HOH . D 3 HOH A 227 727 654 HOH HOH . D 3 HOH A 228 728 699 HOH HOH . D 3 HOH A 229 729 674 HOH HOH . D 3 HOH A 230 730 627 HOH HOH . D 3 HOH A 231 731 728 HOH HOH . D 3 HOH A 232 732 689 HOH HOH . D 3 HOH A 233 733 703 HOH HOH . D 3 HOH A 234 734 725 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 PA 2KH . . . B 2 -3.222 -7.351 9.607 1 101.19 0 PA 2KH 401 A 1 HETATM 2 O O1A 2KH . . . B 2 -2.268 -7.166 10.765 1 81.19 0 O1A 2KH 401 A 1 HETATM 3 O O2A 2KH . . . B 2 -2.939 -8.675 8.939 1 91.81 -1 O2A 2KH 401 A 1 HETATM 4 N N3A 2KH . . . B 2 -4.864 -7.267 10.153 1 111.15 0 N3A 2KH 401 A 1 HETATM 5 O O5' 2KH . . . B 2 -2.973 -6.132 8.513 1 99.66 0 O5' 2KH 401 A 1 HETATM 6 P PB 2KH . . . B 2 -5.844 -8.595 10.661 1 122.89 0 PB 2KH 401 A 1 HETATM 7 O O1B 2KH . . . B 2 -5.318 -9.878 10.065 1 133.31 0 O1B 2KH 401 A 1 HETATM 8 O O2B 2KH . . . B 2 -5.815 -8.692 12.172 1 107.82 -1 O2B 2KH 401 A 1 HETATM 9 O O3B 2KH . . . B 2 -7.425 -8.402 10.153 1 138.93 0 O3B 2KH 401 A 1 HETATM 10 P PG 2KH . . . B 2 -8.643 -9.547 10.105 1 150.11 0 PG 2KH 401 A 1 HETATM 11 O O1G 2KH . . . B 2 -9.682 -9.209 11.151 1 145.65 0 O1G 2KH 401 A 1 HETATM 12 O O2G 2KH . . . B 2 -9.314 -9.546 8.743 1 137.8 -1 O2G 2KH 401 A 1 HETATM 13 O O3G 2KH . . . B 2 -8.097 -10.931 10.393 1 145.49 -1 O3G 2KH 401 A 1 HETATM 14 C C5' 2KH . . . B 2 -1.693 -5.937 7.966 1 98.36 0 C5' 2KH 401 A 1 HETATM 15 C C4' 2KH . . . B 2 -0.987 -4.971 8.732 1 95.56 0 C4' 2KH 401 A 1 HETATM 16 O O4' 2KH . . . B 2 0.322 -5.552 9.208 1 91.2 0 O4' 2KH 401 A 1 HETATM 17 C C1' 2KH . . . B 2 1.19 -4.604 9.115 1 83.58 0 C1' 2KH 401 A 1 HETATM 18 C C2' 2KH . . . B 2 0.644 -3.603 7.921 1 90.67 0 C2' 2KH 401 A 1 HETATM 19 O O2' 2KH . . . B 2 1.092 -2.192 8.151 1 90.83 0 O2' 2KH 401 A 1 HETATM 20 C C3' 2KH . . . B 2 -0.6 -3.707 7.86 1 92.96 0 C3' 2KH 401 A 1 HETATM 21 O O3' 2KH . . . B 2 -1.275 -2.441 8.359 1 93.6 0 O3' 2KH 401 A 1 HETATM 22 N N1 2KH . . . B 2 2.497 -5.105 8.715 1 75.09 0 N1 2KH 401 A 1 HETATM 23 C C6 2KH . . . B 2 2.616 -6.356 8.249 1 64.27 0 C6 2KH 401 A 1 HETATM 24 C C2 2KH . . . B 2 3.561 -4.291 8.759 1 74.72 0 C2 2KH 401 A 1 HETATM 25 O O2 2KH . . . B 2 3.455 -3.148 9.164 1 71.88 0 O2 2KH 401 A 1 HETATM 26 N N3 2KH . . . B 2 4.766 -4.755 8.357 1 72.71 0 N3 2KH 401 A 1 HETATM 27 C C4 2KH . . . B 2 4.973 -6.007 7.899 1 64.16 0 C4 2KH 401 A 1 HETATM 28 O O4 2KH . . . B 2 6.086 -6.382 7.535 1 49.46 0 O4 2KH 401 A 1 HETATM 29 C C5 2KH . . . B 2 3.857 -6.846 7.826 1 58.45 0 C5 2KH 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #