data_3IAL # _model_server_result.job_id 5jv-fIT4BgM_Q8IZLE52gg _model_server_result.datetime_utc '2025-01-02 19:12:39' _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 3ial # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":601}' # _entry.id 3IAL # _exptl.entry_id 3IAL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 444.336 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine" _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 90 _cell.angle_gamma 90 _cell.entry_id 3IAL _cell.length_a 83.338 _cell.length_b 87.624 _cell.length_c 142.41 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IAL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,I,J,K,L _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 H N N # _chem_comp.formula 'C15 H21 N6 O8 P' _chem_comp.formula_weight 444.336 _chem_comp.id PR8 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(R)-hydroxy{[(2S)-pyrrolidin-2-ylcarbonyl]oxy}phosphoryl]adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms prolyl-adenylate # 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 O10 C PR8 sing 273 n n C O PR8 doub 274 n n C CA PR8 sing 275 n n CA N PR8 sing 276 n n CD N PR8 sing 277 n n N HN PR8 sing 278 n n O2P P PR8 doub 279 n n O5' P PR8 sing 280 n n P O1P PR8 sing 281 n n P O10 PR8 sing 282 n n C2 N1 PR8 doub 283 n y N1 C6 PR8 sing 284 n y C2 N3 PR8 sing 285 n y C2 H2 PR8 sing 286 n n N3 C4 PR8 doub 287 n y C4 N9 PR8 sing 288 n y C4 C5 PR8 sing 289 n y C6 C5 PR8 doub 290 n y C5 N7 PR8 sing 291 n y C6 N6 PR8 sing 292 n n N6 HN6 PR8 sing 293 n n N6 HN6A PR8 sing 294 n n C8 N7 PR8 doub 295 n y N9 C8 PR8 sing 296 n y C8 H8 PR8 sing 297 n n C1' N9 PR8 sing 298 n n CB CA PR8 sing 299 n n CA HA PR8 sing 300 n n CB CG PR8 sing 301 n n CB HB PR8 sing 302 n n CB HBA PR8 sing 303 n n CG CD PR8 sing 304 n n CD HD PR8 sing 305 n n CD HDA PR8 sing 306 n n CG HG PR8 sing 307 n n CG HGA PR8 sing 308 n n C2' C1' PR8 sing 309 n n C1' O4' PR8 sing 310 n n C1' H1' PR8 sing 311 n n O1P HO1P PR8 sing 312 n n O2' C2' PR8 sing 313 n n C2' C3' PR8 sing 314 n n C2' H2' PR8 sing 315 n n O2' HO2' PR8 sing 316 n n O3' C3' PR8 sing 317 n n C3' C4' PR8 sing 318 n n C3' H3' PR8 sing 319 n n O3' HO3' PR8 sing 320 n n C4' O4' PR8 sing 321 n n C4' C5' PR8 sing 322 n n C4' H4' PR8 sing 323 n n C5' O5' PR8 sing 324 n n C5' H5' PR8 sing 325 n n C5' "H5'A" PR8 sing 326 n n # _atom_sites.entry_id 3IAL _atom_sites.fract_transf_matrix[1][1] 0.011999 _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] 0.011412 _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] 0.007022 _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 PR8 A 1 601 601 PR8 PR8 . D 3 GOL A 1 602 602 GOL GOL . E 3 GOL A 1 603 603 GOL GOL . F 3 GOL A 1 604 604 GOL GOL . G 3 GOL A 1 605 605 GOL GOL . H 2 PR8 B 1 601 601 PR8 PR8 . I 3 GOL B 1 602 602 GOL GOL . J 3 GOL B 1 603 603 GOL GOL . K 4 HOH A 1 701 701 HOH HOH . K 4 HOH A 2 702 702 HOH HOH . K 4 HOH A 3 703 703 HOH HOH . K 4 HOH A 4 704 704 HOH HOH . K 4 HOH A 5 705 705 HOH HOH . K 4 HOH A 6 706 706 HOH HOH . K 4 HOH A 7 707 707 HOH HOH . K 4 HOH A 8 708 708 HOH HOH . K 4 HOH A 9 709 709 HOH HOH . K 4 HOH A 10 710 710 HOH HOH . K 4 HOH A 11 711 711 HOH HOH . K 4 HOH A 12 712 712 HOH HOH . K 4 HOH A 13 713 713 HOH HOH . K 4 HOH A 14 714 714 HOH HOH . K 4 HOH A 15 715 715 HOH HOH . K 4 HOH A 16 716 716 HOH HOH . K 4 HOH A 17 717 717 HOH HOH . K 4 HOH A 18 718 718 HOH HOH . K 4 HOH A 19 719 719 HOH HOH . K 4 HOH A 20 720 720 HOH HOH . K 4 HOH A 21 721 721 HOH HOH . K 4 HOH A 22 722 722 HOH HOH . K 4 HOH A 23 723 723 HOH HOH . K 4 HOH A 24 724 724 HOH HOH . K 4 HOH A 25 725 725 HOH HOH . K 4 HOH A 26 726 726 HOH HOH . K 4 HOH A 27 727 727 HOH HOH . K 4 HOH A 28 728 728 HOH HOH . K 4 HOH A 29 729 729 HOH HOH . K 4 HOH A 30 730 730 HOH HOH . K 4 HOH A 31 731 731 HOH HOH . K 4 HOH A 32 732 732 HOH HOH . K 4 HOH A 33 733 733 HOH HOH . K 4 HOH A 34 734 734 HOH HOH . K 4 HOH A 35 735 735 HOH HOH . K 4 HOH A 36 736 736 HOH HOH . K 4 HOH A 37 737 737 HOH HOH . K 4 HOH A 38 738 738 HOH HOH . K 4 HOH A 39 739 739 HOH HOH . K 4 HOH A 40 740 740 HOH HOH . K 4 HOH A 41 741 741 HOH HOH . K 4 HOH A 42 742 742 HOH HOH . K 4 HOH A 43 743 743 HOH HOH . K 4 HOH A 44 744 744 HOH HOH . K 4 HOH A 45 745 745 HOH HOH . K 4 HOH A 46 746 746 HOH HOH . K 4 HOH A 47 747 747 HOH HOH . K 4 HOH A 48 748 748 HOH HOH . K 4 HOH A 49 749 749 HOH HOH . K 4 HOH A 50 750 750 HOH HOH . K 4 HOH A 51 751 751 HOH HOH . K 4 HOH A 52 752 752 HOH HOH . K 4 HOH A 53 753 753 HOH HOH . K 4 HOH A 54 754 754 HOH HOH . K 4 HOH A 55 755 755 HOH HOH . K 4 HOH A 56 756 756 HOH HOH . K 4 HOH A 57 757 757 HOH HOH . K 4 HOH A 58 758 758 HOH HOH . K 4 HOH A 59 759 759 HOH HOH . K 4 HOH A 60 760 760 HOH HOH . K 4 HOH A 61 761 761 HOH HOH . K 4 HOH A 62 762 762 HOH HOH . K 4 HOH A 63 763 763 HOH HOH . K 4 HOH A 64 764 764 HOH HOH . K 4 HOH A 65 765 765 HOH HOH . K 4 HOH A 66 766 766 HOH HOH . K 4 HOH A 67 767 767 HOH HOH . K 4 HOH A 68 768 768 HOH HOH . K 4 HOH A 69 769 769 HOH HOH . K 4 HOH A 70 770 770 HOH HOH . K 4 HOH A 71 771 771 HOH HOH . K 4 HOH A 72 772 772 HOH HOH . K 4 HOH A 73 773 773 HOH HOH . K 4 HOH A 74 774 774 HOH HOH . K 4 HOH A 75 775 775 HOH HOH . K 4 HOH A 76 776 776 HOH HOH . K 4 HOH A 77 777 777 HOH HOH . K 4 HOH A 78 778 778 HOH HOH . K 4 HOH A 79 779 779 HOH HOH . K 4 HOH A 80 780 780 HOH HOH . K 4 HOH A 81 781 781 HOH HOH . K 4 HOH A 82 782 782 HOH HOH . K 4 HOH A 83 783 783 HOH HOH . K 4 HOH A 84 784 784 HOH HOH . K 4 HOH A 85 785 785 HOH HOH . K 4 HOH A 86 786 786 HOH HOH . K 4 HOH A 87 787 787 HOH HOH . K 4 HOH A 88 788 788 HOH HOH . K 4 HOH A 89 789 789 HOH HOH . K 4 HOH A 90 790 790 HOH HOH . K 4 HOH A 91 791 791 HOH HOH . K 4 HOH A 92 792 792 HOH HOH . K 4 HOH A 93 793 793 HOH HOH . K 4 HOH A 94 794 794 HOH HOH . K 4 HOH A 95 795 795 HOH HOH . K 4 HOH A 96 796 796 HOH HOH . L 4 HOH B 1 701 701 HOH HOH . L 4 HOH B 2 702 702 HOH HOH . L 4 HOH B 3 703 703 HOH HOH . L 4 HOH B 4 704 704 HOH HOH . L 4 HOH B 5 705 705 HOH HOH . L 4 HOH B 6 706 706 HOH HOH . L 4 HOH B 7 707 707 HOH HOH . L 4 HOH B 8 708 708 HOH HOH . L 4 HOH B 9 709 709 HOH HOH . L 4 HOH B 10 710 710 HOH HOH . L 4 HOH B 11 711 711 HOH HOH . L 4 HOH B 12 712 712 HOH HOH . L 4 HOH B 13 713 713 HOH HOH . L 4 HOH B 14 714 714 HOH HOH . L 4 HOH B 15 715 715 HOH HOH . L 4 HOH B 16 716 716 HOH HOH . L 4 HOH B 17 717 717 HOH HOH . L 4 HOH B 18 718 718 HOH HOH . L 4 HOH B 19 719 719 HOH HOH . L 4 HOH B 20 720 720 HOH HOH . L 4 HOH B 21 721 721 HOH HOH . L 4 HOH B 22 722 722 HOH HOH . L 4 HOH B 23 723 723 HOH HOH . L 4 HOH B 24 724 724 HOH HOH . L 4 HOH B 25 725 725 HOH HOH . L 4 HOH B 26 726 726 HOH HOH . L 4 HOH B 27 727 727 HOH HOH . L 4 HOH B 28 728 728 HOH HOH . L 4 HOH B 29 729 729 HOH HOH . L 4 HOH B 30 730 730 HOH HOH . L 4 HOH B 31 731 731 HOH HOH . L 4 HOH B 32 732 732 HOH HOH . L 4 HOH B 33 733 733 HOH HOH . L 4 HOH B 34 734 734 HOH HOH . L 4 HOH B 35 735 735 HOH HOH . L 4 HOH B 36 736 736 HOH HOH . L 4 HOH B 37 737 737 HOH HOH . L 4 HOH B 38 738 738 HOH HOH . L 4 HOH B 39 739 739 HOH HOH . L 4 HOH B 40 740 740 HOH HOH . L 4 HOH B 41 741 741 HOH HOH . L 4 HOH B 42 742 742 HOH HOH . L 4 HOH B 43 743 743 HOH HOH . L 4 HOH B 44 744 744 HOH HOH . L 4 HOH B 45 745 745 HOH HOH . L 4 HOH B 46 746 746 HOH HOH . L 4 HOH B 47 747 747 HOH HOH . L 4 HOH B 48 748 748 HOH HOH . L 4 HOH B 49 749 749 HOH HOH . L 4 HOH B 50 750 750 HOH HOH . L 4 HOH B 51 751 751 HOH HOH . L 4 HOH B 52 752 752 HOH HOH . L 4 HOH B 53 753 753 HOH HOH . L 4 HOH B 54 754 754 HOH HOH . L 4 HOH B 55 755 755 HOH HOH . L 4 HOH B 56 756 756 HOH HOH . L 4 HOH B 57 757 757 HOH HOH . L 4 HOH B 58 758 758 HOH HOH . L 4 HOH B 59 759 759 HOH HOH . L 4 HOH B 60 760 760 HOH HOH . L 4 HOH B 61 761 761 HOH HOH . L 4 HOH B 62 762 762 HOH HOH . L 4 HOH B 63 763 763 HOH HOH . L 4 HOH B 64 764 764 HOH HOH . L 4 HOH B 65 765 765 HOH HOH . L 4 HOH B 66 766 766 HOH HOH . L 4 HOH B 67 767 767 HOH HOH . L 4 HOH B 68 768 768 HOH HOH . L 4 HOH B 69 769 769 HOH HOH . L 4 HOH B 70 770 770 HOH HOH . L 4 HOH B 71 771 771 HOH HOH . L 4 HOH B 72 772 772 HOH HOH . L 4 HOH B 73 773 773 HOH HOH . L 4 HOH B 74 774 774 HOH HOH . L 4 HOH B 75 775 775 HOH HOH . L 4 HOH B 76 776 776 HOH HOH . L 4 HOH B 77 777 777 HOH HOH . L 4 HOH B 78 778 778 HOH HOH . L 4 HOH B 79 779 779 HOH HOH . L 4 HOH B 80 780 780 HOH HOH . L 4 HOH B 81 781 781 HOH HOH . L 4 HOH B 82 782 782 HOH HOH . L 4 HOH B 83 783 783 HOH HOH . L 4 HOH B 84 784 784 HOH HOH . L 4 HOH B 85 785 785 HOH HOH . L 4 HOH B 86 786 786 HOH HOH . L 4 HOH B 87 787 787 HOH HOH . L 4 HOH B 88 788 788 HOH HOH . L 4 HOH B 89 789 789 HOH HOH . L 4 HOH B 90 790 790 HOH HOH . L 4 HOH B 91 791 791 HOH HOH . L 4 HOH B 92 792 792 HOH HOH . L 4 HOH B 93 793 793 HOH HOH . L 4 HOH B 94 794 794 HOH HOH . L 4 HOH B 95 795 795 HOH HOH . L 4 HOH B 96 796 796 HOH HOH . L 4 HOH B 97 797 797 HOH HOH . L 4 HOH B 98 798 798 HOH HOH . L 4 HOH B 99 799 799 HOH HOH . L 4 HOH B 100 800 800 HOH HOH . L 4 HOH B 101 801 801 HOH HOH . L 4 HOH B 102 802 802 HOH HOH . L 4 HOH B 103 803 803 HOH HOH . L 4 HOH B 104 804 804 HOH HOH . L 4 HOH B 105 805 805 HOH HOH . L 4 HOH B 106 806 806 HOH HOH . L 4 HOH B 107 807 807 HOH HOH . L 4 HOH B 108 808 808 HOH HOH . L 4 HOH B 109 809 809 HOH HOH . L 4 HOH B 110 810 810 HOH HOH . L 4 HOH B 111 811 811 HOH HOH . L 4 HOH B 112 812 812 HOH HOH . L 4 HOH B 113 813 813 HOH HOH . L 4 HOH B 114 814 814 HOH HOH . L 4 HOH B 115 815 815 HOH HOH . L 4 HOH B 116 816 816 HOH HOH . L 4 HOH B 117 817 817 HOH HOH . L 4 HOH B 118 818 818 HOH HOH . L 4 HOH B 119 819 819 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 C C PR8 . . . H 2 86.479 83.701 16.646 1 41.68 ? C PR8 601 B 1 HETATM 2 N N PR8 . . . H 2 85.343 82.339 15.005 1 37.95 ? N PR8 601 B 1 HETATM 3 O O PR8 . . . H 2 85.603 83.291 17.41 1 39.8 ? O PR8 601 B 1 HETATM 4 P P PR8 . . . H 2 87.388 85.103 18.486 0.7 54.76 ? P PR8 601 B 1 HETATM 5 N N1 PR8 . . . H 2 81.031 88.283 25.108 0.7 38.84 ? N1 PR8 601 B 1 HETATM 6 C C2 PR8 . . . H 2 81.1 89.231 24.18 0.7 36.35 ? C2 PR8 601 B 1 HETATM 7 N N3 PR8 . . . H 2 81.945 89.155 23.149 0.7 36.19 ? N3 PR8 601 B 1 HETATM 8 C C4 PR8 . . . H 2 82.766 88.116 23.006 0.7 40.17 ? C4 PR8 601 B 1 HETATM 9 C C5 PR8 . . . H 2 82.729 87.108 23.964 0.7 44.07 ? C5 PR8 601 B 1 HETATM 10 C C6 PR8 . . . H 2 81.836 87.206 25.028 0.7 44.75 ? C6 PR8 601 B 1 HETATM 11 N N6 PR8 . . . H 2 81.782 86.244 25.95 0.7 47.85 ? N6 PR8 601 B 1 HETATM 12 N N7 PR8 . . . H 2 83.624 86.193 23.613 0.7 45.67 ? N7 PR8 601 B 1 HETATM 13 C C8 PR8 . . . H 2 84.206 86.601 22.483 0.7 49.61 ? C8 PR8 601 B 1 HETATM 14 N N9 PR8 . . . H 2 83.693 87.781 22.108 0.7 48.94 ? N9 PR8 601 B 1 HETATM 15 C CA PR8 . . . H 2 86.471 83.27 15.18 1 37.84 ? CA PR8 601 B 1 HETATM 16 C CB PR8 . . . H 2 86.183 84.483 14.311 1 35.99 ? CB PR8 601 B 1 HETATM 17 C CD PR8 . . . H 2 84.578 82.791 13.848 1 37.8 ? CD PR8 601 B 1 HETATM 18 C CG PR8 . . . H 2 84.71 84.318 13.912 1 35.6 ? CG PR8 601 B 1 HETATM 19 C C1' PR8 . . . H 2 84.11 88.544 20.888 0.7 52.31 ? C1' PR8 601 B 1 HETATM 20 O O10 PR8 . . . H 2 87.514 84.515 16.988 1 43.66 ? O10 PR8 601 B 1 HETATM 21 O O1P PR8 . . . H 2 87.647 84.088 19.539 0.7 56.6 ? O1P PR8 601 B 1 HETATM 22 C C2' PR8 . . . H 2 85.553 89.094 20.996 0.7 54.66 ? C2' PR8 601 B 1 HETATM 23 O O2' PR8 . . . H 2 85.616 90.417 20.442 0.7 47.98 ? O2' PR8 601 B 1 HETATM 24 O O2P PR8 . . . H 2 88.475 86.283 18.561 0.7 58.29 ? O2P PR8 601 B 1 HETATM 25 C C3' PR8 . . . H 2 86.329 88.181 20.076 0.7 55.14 ? C3' PR8 601 B 1 HETATM 26 O O3' PR8 . . . H 2 87.508 88.837 19.603 0.7 53.41 ? O3' PR8 601 B 1 HETATM 27 C C4' PR8 . . . H 2 85.295 88.088 18.969 0.7 55.14 ? C4' PR8 601 B 1 HETATM 28 O O4' PR8 . . . H 2 84.127 87.673 19.712 0.7 53.59 ? O4' PR8 601 B 1 HETATM 29 C C5' PR8 . . . H 2 85.745 87.06 17.954 0.7 54 ? C5' PR8 601 B 1 HETATM 30 O O5' PR8 . . . H 2 85.946 85.809 18.582 0.7 54.92 ? O5' PR8 601 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #