data_6F6Z # _model_server_result.job_id mIXAw4yMRV8ed9oTQMN5gw _model_server_result.datetime_utc '2024-11-24 09:09:18' _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 6f6z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 6F6Z # _exptl.entry_id 6F6Z _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 323.197 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate)" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.47 _cell.angle_gamma 90 _cell.entry_id 6F6Z _cell.length_a 160.36 _cell.length_b 89.16 _cell.length_c 66.56 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6F6Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _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,D,E,F,G,H _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 C N N ? 2 E N N # _chem_comp.formula 'C9 H14 N3 O8 P' _chem_comp.formula_weight 323.197 _chem_comp.id NOH _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate)" _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 OP2 P NOH doub 237 n n OP1 P NOH sing 238 n n P OP3 NOH sing 239 n n P O5' NOH sing 240 n n O5' C5' NOH sing 241 n n C5' C4' NOH sing 242 n n O4 N4 NOH sing 243 n n C5 C6 NOH doub 244 n n C5 C4 NOH sing 245 n n C4' C3' NOH sing 246 n n C4' O4' NOH sing 247 n n C6 N1 NOH sing 248 n n C3' C2' NOH sing 249 n n C3' O3' NOH sing 250 n n C2' C1' NOH sing 251 n n N4 C4 NOH sing 252 n n C4 N3 NOH doub 253 n n O4' C1' NOH sing 254 n n N1 C1' NOH sing 255 n n N1 C2 NOH sing 256 n n N3 C2 NOH sing 257 n n C2 O2 NOH doub 258 n n N4 H1 NOH sing 259 n n O4 H2 NOH sing 260 n n C5 H3 NOH sing 261 n n C6 H4 NOH sing 262 n n C1' H5 NOH sing 263 n n C2' H6 NOH sing 264 n n C2' H7 NOH sing 265 n n C3' H8 NOH sing 266 n n O3' H9 NOH sing 267 n n C4' H10 NOH sing 268 n n C5' H11 NOH sing 269 n n C5' H12 NOH sing 270 n n OP1 H13 NOH sing 271 n n OP3 H14 NOH sing 272 n n # _atom_sites.entry_id 6F6Z _atom_sites.fract_transf_matrix[1][1] 0.006236 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000818 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011216 _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] 0.015153 _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 C 2 NOH A 1 501 501 NOH NOH . D 3 TGQ A 1 502 502 TGQ TGQ . E 2 NOH B 1 501 501 NOH NOH . F 3 TGQ B 1 502 502 TGQ TGQ . G 4 HOH A 1 601 601 HOH HOH . G 4 HOH A 2 602 669 HOH HOH . G 4 HOH A 3 603 602 HOH HOH . G 4 HOH A 4 604 606 HOH HOH . G 4 HOH A 5 605 612 HOH HOH . G 4 HOH A 6 606 642 HOH HOH . G 4 HOH A 7 607 603 HOH HOH . G 4 HOH A 8 608 665 HOH HOH . G 4 HOH A 9 609 618 HOH HOH . G 4 HOH A 10 610 604 HOH HOH . G 4 HOH A 11 611 664 HOH HOH . G 4 HOH A 12 612 619 HOH HOH . G 4 HOH A 13 613 649 HOH HOH . G 4 HOH A 14 614 622 HOH HOH . G 4 HOH A 15 615 611 HOH HOH . G 4 HOH A 16 616 610 HOH HOH . G 4 HOH A 17 617 607 HOH HOH . G 4 HOH A 18 618 605 HOH HOH . G 4 HOH A 19 619 633 HOH HOH . G 4 HOH A 20 620 639 HOH HOH . G 4 HOH A 21 621 627 HOH HOH . G 4 HOH A 22 622 646 HOH HOH . G 4 HOH A 23 623 609 HOH HOH . G 4 HOH A 24 624 615 HOH HOH . G 4 HOH A 25 625 614 HOH HOH . G 4 HOH A 26 626 621 HOH HOH . G 4 HOH A 27 627 691 HOH HOH . G 4 HOH A 28 628 635 HOH HOH . G 4 HOH A 29 629 647 HOH HOH . G 4 HOH A 30 630 630 HOH HOH . G 4 HOH A 31 631 671 HOH HOH . G 4 HOH A 32 632 628 HOH HOH . G 4 HOH A 33 633 608 HOH HOH . G 4 HOH A 34 634 654 HOH HOH . G 4 HOH A 35 635 631 HOH HOH . G 4 HOH A 36 636 701 HOH HOH . G 4 HOH A 37 637 616 HOH HOH . G 4 HOH A 38 638 636 HOH HOH . G 4 HOH A 39 639 625 HOH HOH . G 4 HOH A 40 640 638 HOH HOH . G 4 HOH A 41 641 666 HOH HOH . G 4 HOH A 42 642 632 HOH HOH . G 4 HOH A 43 643 629 HOH HOH . G 4 HOH A 44 644 667 HOH HOH . G 4 HOH A 45 645 668 HOH HOH . G 4 HOH A 46 646 613 HOH HOH . G 4 HOH A 47 647 644 HOH HOH . G 4 HOH A 48 648 623 HOH HOH . G 4 HOH A 49 649 637 HOH HOH . G 4 HOH A 50 650 643 HOH HOH . G 4 HOH A 51 651 672 HOH HOH . G 4 HOH A 52 652 640 HOH HOH . G 4 HOH A 53 653 620 HOH HOH . G 4 HOH A 54 654 624 HOH HOH . G 4 HOH A 55 655 651 HOH HOH . G 4 HOH A 56 656 617 HOH HOH . G 4 HOH A 57 657 683 HOH HOH . G 4 HOH A 58 658 688 HOH HOH . G 4 HOH A 59 659 673 HOH HOH . G 4 HOH A 60 660 626 HOH HOH . G 4 HOH A 61 661 648 HOH HOH . G 4 HOH A 62 662 650 HOH HOH . G 4 HOH A 63 663 685 HOH HOH . G 4 HOH A 64 664 662 HOH HOH . G 4 HOH A 65 665 653 HOH HOH . G 4 HOH A 66 666 656 HOH HOH . G 4 HOH A 67 667 655 HOH HOH . G 4 HOH A 68 668 660 HOH HOH . G 4 HOH A 69 669 676 HOH HOH . G 4 HOH A 70 670 716 HOH HOH . G 4 HOH A 71 671 652 HOH HOH . G 4 HOH A 72 672 678 HOH HOH . G 4 HOH A 73 673 695 HOH HOH . G 4 HOH A 74 674 663 HOH HOH . G 4 HOH A 75 675 634 HOH HOH . G 4 HOH A 76 676 645 HOH HOH . G 4 HOH A 77 677 677 HOH HOH . G 4 HOH A 78 678 684 HOH HOH . G 4 HOH A 79 679 714 HOH HOH . G 4 HOH A 80 680 659 HOH HOH . G 4 HOH A 81 681 657 HOH HOH . G 4 HOH A 82 682 641 HOH HOH . G 4 HOH A 83 683 661 HOH HOH . G 4 HOH A 84 684 702 HOH HOH . G 4 HOH A 85 685 682 HOH HOH . G 4 HOH A 86 686 690 HOH HOH . G 4 HOH A 87 687 705 HOH HOH . G 4 HOH A 88 688 675 HOH HOH . G 4 HOH A 89 689 679 HOH HOH . G 4 HOH A 90 690 698 HOH HOH . G 4 HOH A 91 691 686 HOH HOH . G 4 HOH A 92 692 681 HOH HOH . G 4 HOH A 93 693 694 HOH HOH . G 4 HOH A 94 694 703 HOH HOH . G 4 HOH A 95 695 689 HOH HOH . G 4 HOH A 96 696 687 HOH HOH . G 4 HOH A 97 697 674 HOH HOH . G 4 HOH A 98 698 670 HOH HOH . G 4 HOH A 99 699 682 HOH HOH . G 4 HOH A 100 700 658 HOH HOH . G 4 HOH A 101 701 658 HOH HOH . G 4 HOH A 102 702 692 HOH HOH . G 4 HOH A 103 703 693 HOH HOH . G 4 HOH A 104 704 700 HOH HOH . G 4 HOH A 105 705 696 HOH HOH . G 4 HOH A 106 706 680 HOH HOH . G 4 HOH A 107 707 706 HOH HOH . G 4 HOH A 108 708 708 HOH HOH . G 4 HOH A 109 709 699 HOH HOH . G 4 HOH A 110 710 713 HOH HOH . G 4 HOH A 111 711 709 HOH HOH . G 4 HOH A 112 712 712 HOH HOH . G 4 HOH A 113 713 704 HOH HOH . G 4 HOH A 114 714 715 HOH HOH . G 4 HOH A 115 715 711 HOH HOH . G 4 HOH A 116 716 717 HOH HOH . G 4 HOH A 117 717 710 HOH HOH . G 4 HOH A 118 718 719 HOH HOH . G 4 HOH A 119 719 718 HOH HOH . G 4 HOH A 120 720 697 HOH HOH . G 4 HOH A 121 721 720 HOH HOH . G 4 HOH A 122 722 722 HOH HOH . G 4 HOH A 123 723 725 HOH HOH . G 4 HOH A 124 724 726 HOH HOH . G 4 HOH A 125 725 727 HOH HOH . G 4 HOH A 126 726 724 HOH HOH . G 4 HOH A 127 727 721 HOH HOH . G 4 HOH A 128 728 723 HOH HOH . G 4 HOH A 129 729 729 HOH HOH . G 4 HOH A 130 730 728 HOH HOH . G 4 HOH A 131 731 731 HOH HOH . G 4 HOH A 132 732 733 HOH HOH . G 4 HOH A 133 733 734 HOH HOH . G 4 HOH A 134 734 736 HOH HOH . G 4 HOH A 135 735 735 HOH HOH . H 4 HOH B 1 601 605 HOH HOH . H 4 HOH B 2 602 601 HOH HOH . H 4 HOH B 3 603 602 HOH HOH . H 4 HOH B 4 604 617 HOH HOH . H 4 HOH B 5 605 603 HOH HOH . H 4 HOH B 6 606 607 HOH HOH . H 4 HOH B 7 607 609 HOH HOH . H 4 HOH B 8 608 668 HOH HOH . H 4 HOH B 9 609 604 HOH HOH . H 4 HOH B 10 610 611 HOH HOH . H 4 HOH B 11 611 608 HOH HOH . H 4 HOH B 12 612 623 HOH HOH . H 4 HOH B 13 613 610 HOH HOH . H 4 HOH B 14 614 649 HOH HOH . H 4 HOH B 15 615 641 HOH HOH . H 4 HOH B 16 616 613 HOH HOH . H 4 HOH B 17 617 626 HOH HOH . H 4 HOH B 18 618 633 HOH HOH . H 4 HOH B 19 619 630 HOH HOH . H 4 HOH B 20 620 619 HOH HOH . H 4 HOH B 21 621 612 HOH HOH . H 4 HOH B 22 622 638 HOH HOH . H 4 HOH B 23 623 632 HOH HOH . H 4 HOH B 24 624 639 HOH HOH . H 4 HOH B 25 625 645 HOH HOH . H 4 HOH B 26 626 629 HOH HOH . H 4 HOH B 27 627 657 HOH HOH . H 4 HOH B 28 628 621 HOH HOH . H 4 HOH B 29 629 636 HOH HOH . H 4 HOH B 30 630 646 HOH HOH . H 4 HOH B 31 631 647 HOH HOH . H 4 HOH B 32 632 622 HOH HOH . H 4 HOH B 33 633 614 HOH HOH . H 4 HOH B 34 634 635 HOH HOH . H 4 HOH B 35 635 640 HOH HOH . H 4 HOH B 36 636 625 HOH HOH . H 4 HOH B 37 637 620 HOH HOH . H 4 HOH B 38 638 606 HOH HOH . H 4 HOH B 39 639 615 HOH HOH . H 4 HOH B 40 640 643 HOH HOH . H 4 HOH B 41 641 686 HOH HOH . H 4 HOH B 42 642 624 HOH HOH . H 4 HOH B 43 643 634 HOH HOH . H 4 HOH B 44 644 661 HOH HOH . H 4 HOH B 45 645 651 HOH HOH . H 4 HOH B 46 646 616 HOH HOH . H 4 HOH B 47 647 648 HOH HOH . H 4 HOH B 48 648 642 HOH HOH . H 4 HOH B 49 649 659 HOH HOH . H 4 HOH B 50 650 627 HOH HOH . H 4 HOH B 51 651 618 HOH HOH . H 4 HOH B 52 652 631 HOH HOH . H 4 HOH B 53 653 664 HOH HOH . H 4 HOH B 54 654 670 HOH HOH . H 4 HOH B 55 655 637 HOH HOH . H 4 HOH B 56 656 675 HOH HOH . H 4 HOH B 57 657 652 HOH HOH . H 4 HOH B 58 658 650 HOH HOH . H 4 HOH B 59 659 662 HOH HOH . H 4 HOH B 60 660 655 HOH HOH . H 4 HOH B 61 661 644 HOH HOH . H 4 HOH B 62 662 666 HOH HOH . H 4 HOH B 63 663 656 HOH HOH . H 4 HOH B 64 664 673 HOH HOH . H 4 HOH B 65 665 628 HOH HOH . H 4 HOH B 66 666 674 HOH HOH . H 4 HOH B 67 667 672 HOH HOH . H 4 HOH B 68 668 681 HOH HOH . H 4 HOH B 69 669 654 HOH HOH . H 4 HOH B 70 670 663 HOH HOH . H 4 HOH B 71 671 669 HOH HOH . H 4 HOH B 72 672 684 HOH HOH . H 4 HOH B 73 673 660 HOH HOH . H 4 HOH B 74 674 683 HOH HOH . H 4 HOH B 75 675 676 HOH HOH . H 4 HOH B 76 676 680 HOH HOH . H 4 HOH B 77 677 678 HOH HOH . H 4 HOH B 78 678 692 HOH HOH . H 4 HOH B 79 679 653 HOH HOH . H 4 HOH B 80 680 665 HOH HOH . H 4 HOH B 81 681 679 HOH HOH . H 4 HOH B 82 682 688 HOH HOH . H 4 HOH B 83 683 687 HOH HOH . H 4 HOH B 84 684 693 HOH HOH . H 4 HOH B 85 685 667 HOH HOH . H 4 HOH B 86 686 691 HOH HOH . H 4 HOH B 87 687 690 HOH HOH . H 4 HOH B 88 688 695 HOH HOH . H 4 HOH B 89 689 707 HOH HOH . H 4 HOH B 90 690 696 HOH HOH . H 4 HOH B 91 691 685 HOH HOH . H 4 HOH B 92 692 701 HOH HOH . H 4 HOH B 93 693 699 HOH HOH . H 4 HOH B 94 694 671 HOH HOH . H 4 HOH B 95 695 677 HOH HOH . H 4 HOH B 96 696 697 HOH HOH . H 4 HOH B 97 697 694 HOH HOH . H 4 HOH B 98 698 700 HOH HOH . H 4 HOH B 99 699 702 HOH HOH . H 4 HOH B 100 700 698 HOH HOH . H 4 HOH B 101 701 689 HOH HOH . H 4 HOH B 102 702 707 HOH HOH . H 4 HOH B 103 703 705 HOH HOH . H 4 HOH B 104 704 708 HOH HOH . H 4 HOH B 105 705 703 HOH HOH . H 4 HOH B 106 706 706 HOH HOH . H 4 HOH B 107 707 710 HOH HOH . H 4 HOH B 108 708 709 HOH HOH . H 4 HOH B 109 709 704 HOH HOH . H 4 HOH B 110 710 712 HOH HOH . H 4 HOH B 111 711 711 HOH HOH . H 4 HOH B 112 712 714 HOH HOH . H 4 HOH B 113 713 713 HOH HOH . H 4 HOH B 114 714 730 HOH HOH . H 4 HOH B 115 715 732 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 O2 NOH . . . E 2 117.705 -27.433 16.787 1 45.39 ? O2 NOH 501 B 1 HETATM 2 C C2 NOH . . . E 2 117.12 -27.288 15.738 1 45.11 ? C2 NOH 501 B 1 HETATM 3 N N3 NOH . . . E 2 117.031 -25.978 15.103 1 46.54 ? N3 NOH 501 B 1 HETATM 4 C C4 NOH . . . E 2 116.354 -25.823 13.878 1 45.61 ? C4 NOH 501 B 1 HETATM 5 N N4 NOH . . . E 2 116.284 -24.544 13.276 1 46.51 ? N4 NOH 501 B 1 HETATM 6 O O4 NOH . . . E 2 115.617 -24.414 12.087 1 52.2 ? O4 NOH 501 B 1 HETATM 7 C C5 NOH . . . E 2 115.726 -26.97 13.231 1 47.86 ? C5 NOH 501 B 1 HETATM 8 C C6 NOH . . . E 2 115.829 -28.299 13.854 1 52.96 ? C6 NOH 501 B 1 HETATM 9 N N1 NOH . . . E 2 116.497 -28.44 15.104 1 47.18 ? N1 NOH 501 B 1 HETATM 10 C C1' NOH . . . E 2 116.607 -29.75 15.74 1 47.07 ? C1' NOH 501 B 1 HETATM 11 C C2' NOH . . . E 2 115.708 -29.936 16.596 1 44.96 ? C2' NOH 501 B 1 HETATM 12 C C3' NOH . . . E 2 115.542 -31.544 16.56 1 46.21 ? C3' NOH 501 B 1 HETATM 13 O O3' NOH . . . E 2 116.775 -32.17 17.081 1 43.63 ? O3' NOH 501 B 1 HETATM 14 O O4' NOH . . . E 2 116.361 -30.796 14.647 1 46.41 ? O4' NOH 501 B 1 HETATM 15 C C4' NOH . . . E 2 115.416 -31.788 15.311 1 47.97 ? C4' NOH 501 B 1 HETATM 16 C C5' NOH . . . E 2 113.962 -31.479 14.858 1 45.41 ? C5' NOH 501 B 1 HETATM 17 O O5' NOH . . . E 2 113.207 -32.648 15.057 1 45.07 ? O5' NOH 501 B 1 HETATM 18 P P NOH . . . E 2 111.858 -32.587 15.875 1 41.7 ? P NOH 501 B 1 HETATM 19 O OP1 NOH . . . E 2 111.383 -33.999 16.043 1 42.22 ? OP1 NOH 501 B 1 HETATM 20 O OP2 NOH . . . E 2 110.839 -31.802 15.085 1 44.04 ? OP2 NOH 501 B 1 HETATM 21 O OP3 NOH . . . E 2 112.032 -31.931 17.226 1 41.95 ? OP3 NOH 501 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #