data_2QQG # _model_server_result.job_id '_Me-qhkLF2iOJw88IY7TSg' _model_server_result.datetime_utc '2024-10-18 22:24:36' _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 2qqg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1001}' # _entry.id 2QQG # _exptl.entry_id 2QQG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 542.332 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]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 2QQG _cell.length_a 105.94 _cell.length_b 105.94 _cell.length_c 67.1 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QQG _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 2 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_675 x-y+1,-y+2,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 183.493463 22.366667 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 B C ALA 4 B ALA 15 1_555 B N ALY 5 B ALY 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 B C ALY 5 B ALY 16 1_555 B N ARG 6 B ARG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A SG CYS 157 A CYS 143 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc2 A SG CYS 160 A CYS 146 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc3 A SG CYS 184 A CYS 170 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc4 A SG CYS 187 A CYS 173 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? # _chem_comp.formula 'C15 H24 N6 O12 P2' _chem_comp.formula_weight 542.332 _chem_comp.id A1R _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]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 N1 C2 A1R doub 1 n y N1 C6 A1R sing 2 n y C2 N3 A1R sing 3 n y C2 H2 A1R sing 4 n n N3 C4 A1R doub 5 n y C4 C5 A1R sing 6 n y C4 N9 A1R sing 7 n y C5 C6 A1R doub 8 n y C5 N7 A1R sing 9 n y C6 N6 A1R sing 10 n n N6 HN61 A1R sing 11 n n N6 HN62 A1R sing 12 n n N7 C8 A1R doub 13 n y C8 N9 A1R sing 14 n y C8 H8 A1R sing 15 n n N9 C1' A1R sing 16 n n C1' O4' A1R sing 17 n n C1' C2' A1R sing 18 n n C1' H1' A1R sing 19 n n C2' O2' A1R sing 20 n n C2' C3' A1R sing 21 n n C2' H2' A1R sing 22 n n O2' HO2' A1R sing 23 n n C3' C4' A1R sing 24 n n C3' O3' A1R sing 25 n n C3' H3' A1R sing 26 n n O3' HO3' A1R sing 27 n n O4' C4' A1R sing 28 n n C4' C5' A1R sing 29 n n C4' H4' A1R sing 30 n n C5' O5' A1R sing 31 n n C5' "H5'1" A1R sing 32 n n C5' "H5'2" A1R sing 33 n n O5' PA A1R sing 34 n n PA O3A A1R sing 35 n n PA O1A A1R doub 36 n n PA O2A A1R sing 37 n n O2A HO2A A1R sing 38 n n O3A PB A1R sing 39 n n PB O2B A1R doub 40 n n PB O1B A1R sing 41 n n PB O5N A1R sing 42 n n O1B HO1B A1R sing 43 n n O5N C5N A1R sing 44 n n C5N C4N A1R sing 45 n n C5N H5N1 A1R sing 46 n n C5N H5N2 A1R sing 47 n n N4N C4N A1R sing 48 n n N4N C1N A1R sing 49 n n N4N HN4N A1R sing 50 n n C1N C2N A1R sing 51 n n C1N H1N1 A1R sing 52 n n C1N H1N2 A1R sing 53 n n O2N C2N A1R sing 54 n n O2N HO2N A1R sing 55 n n C2N C3N A1R sing 56 n n C2N H2N A1R sing 57 n n O3N C3N A1R sing 58 n n O3N HO3N A1R sing 59 n n C3N C4N A1R sing 60 n n C3N H3N A1R sing 61 n n C4N H4N A1R sing 62 n n # _atom_sites.entry_id 2QQG _atom_sites.fract_transf_matrix[1][1] 0.009439 _atom_sites.fract_transf_matrix[1][2] 0.00545 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0109 _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] 0.014903 _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 3 ZN A 1 701 701 ZN ZN . D 4 A1R A 1 1001 1001 A1R A1R . E 5 NCA A 1 3721 3721 NCA NCA . F 6 HOH A 1 3722 3722 HOH HOH . F 6 HOH A 2 3723 3723 HOH HOH . F 6 HOH A 3 3724 3724 HOH HOH . F 6 HOH A 4 3725 3725 HOH HOH . F 6 HOH A 5 3726 3726 HOH HOH . F 6 HOH A 6 3727 3727 HOH HOH . F 6 HOH A 7 3728 3728 HOH HOH . F 6 HOH A 8 3729 3729 HOH HOH . F 6 HOH A 9 3730 3730 HOH HOH . F 6 HOH A 10 3731 3731 HOH HOH . F 6 HOH A 11 3732 3732 HOH HOH . F 6 HOH A 12 3733 3733 HOH HOH . F 6 HOH A 13 3734 3734 HOH HOH . F 6 HOH A 14 3735 3735 HOH HOH . F 6 HOH A 15 3736 3736 HOH HOH . F 6 HOH A 16 3737 3737 HOH HOH . F 6 HOH A 17 3738 3738 HOH HOH . F 6 HOH A 18 3739 3739 HOH HOH . F 6 HOH A 19 3740 3740 HOH HOH . F 6 HOH A 20 3741 3741 HOH HOH . F 6 HOH A 21 3742 3742 HOH HOH . F 6 HOH A 22 3743 3743 HOH HOH . F 6 HOH A 23 3744 3744 HOH HOH . F 6 HOH A 24 3745 3745 HOH HOH . F 6 HOH A 25 3746 3746 HOH HOH . F 6 HOH A 26 3747 3747 HOH HOH . F 6 HOH A 27 3748 3748 HOH HOH . F 6 HOH A 28 3749 3749 HOH HOH . F 6 HOH A 29 3750 3750 HOH HOH . F 6 HOH A 30 3751 3751 HOH HOH . F 6 HOH A 31 3752 3752 HOH HOH . F 6 HOH A 32 3753 3753 HOH HOH . F 6 HOH A 33 3754 3754 HOH HOH . F 6 HOH A 34 3755 3755 HOH HOH . F 6 HOH A 35 3756 3756 HOH HOH . F 6 HOH A 36 3757 3757 HOH HOH . F 6 HOH A 37 3758 3758 HOH HOH . F 6 HOH A 38 3759 3759 HOH HOH . F 6 HOH A 39 3760 3760 HOH HOH . F 6 HOH A 40 3761 3761 HOH HOH . F 6 HOH A 41 3762 3762 HOH HOH . F 6 HOH A 42 3763 3763 HOH HOH . F 6 HOH A 43 3764 3764 HOH HOH . F 6 HOH A 44 3765 3765 HOH HOH . F 6 HOH A 45 3766 3766 HOH HOH . F 6 HOH A 46 3767 3767 HOH HOH . F 6 HOH A 47 3768 3768 HOH HOH . F 6 HOH A 48 3769 3769 HOH HOH . F 6 HOH A 49 3770 3770 HOH HOH . F 6 HOH A 50 3771 3771 HOH HOH . F 6 HOH A 51 3772 3772 HOH HOH . F 6 HOH A 52 3773 3773 HOH HOH . F 6 HOH A 53 3774 3774 HOH HOH . F 6 HOH A 54 3775 3775 HOH HOH . F 6 HOH A 55 3776 3776 HOH HOH . F 6 HOH A 56 3777 3777 HOH HOH . F 6 HOH A 57 3778 3778 HOH HOH . F 6 HOH A 58 3779 3779 HOH HOH . F 6 HOH A 59 3780 3780 HOH HOH . F 6 HOH A 60 3781 3781 HOH HOH . F 6 HOH A 61 3782 3782 HOH HOH . F 6 HOH A 62 3783 3783 HOH HOH . F 6 HOH A 63 3784 3784 HOH HOH . F 6 HOH A 64 3785 3785 HOH HOH . F 6 HOH A 65 3786 3786 HOH HOH . F 6 HOH A 66 3787 3787 HOH HOH . F 6 HOH A 67 3788 3788 HOH HOH . F 6 HOH A 68 3789 3789 HOH HOH . F 6 HOH A 69 3790 3790 HOH HOH . F 6 HOH A 70 3791 3791 HOH HOH . F 6 HOH A 71 3792 3792 HOH HOH . F 6 HOH A 72 3793 3793 HOH HOH . F 6 HOH A 73 3794 3794 HOH HOH . F 6 HOH A 74 3795 3795 HOH HOH . F 6 HOH A 75 3796 3796 HOH HOH . F 6 HOH A 76 3797 3797 HOH HOH . F 6 HOH A 77 3798 3798 HOH HOH . F 6 HOH A 78 3799 3799 HOH HOH . F 6 HOH A 79 3800 3800 HOH HOH . F 6 HOH A 80 3801 3801 HOH HOH . F 6 HOH A 81 3802 3802 HOH HOH . F 6 HOH A 82 3803 3803 HOH HOH . F 6 HOH A 83 3804 3804 HOH HOH . F 6 HOH A 84 3805 3805 HOH HOH . F 6 HOH A 85 3806 3806 HOH HOH . F 6 HOH A 86 3807 3807 HOH HOH . F 6 HOH A 87 3808 3808 HOH HOH . F 6 HOH A 88 3809 3809 HOH HOH . F 6 HOH A 89 3810 3810 HOH HOH . F 6 HOH A 90 3811 3811 HOH HOH . F 6 HOH A 91 3812 3812 HOH HOH . F 6 HOH A 92 3813 3813 HOH HOH . F 6 HOH A 93 3814 3814 HOH HOH . F 6 HOH A 94 3815 3815 HOH HOH . F 6 HOH A 95 3816 3816 HOH HOH . F 6 HOH A 96 3817 3817 HOH HOH . F 6 HOH A 97 3818 3818 HOH HOH . F 6 HOH A 98 3819 3819 HOH HOH . F 6 HOH A 99 3820 3820 HOH HOH . F 6 HOH A 100 3821 3821 HOH HOH . F 6 HOH A 101 3822 3822 HOH HOH . F 6 HOH A 102 3823 3823 HOH HOH . F 6 HOH A 103 3824 3824 HOH HOH . F 6 HOH A 104 3825 3825 HOH HOH . F 6 HOH A 105 3826 3826 HOH HOH . F 6 HOH A 106 3827 3827 HOH HOH . F 6 HOH A 107 3828 3828 HOH HOH . F 6 HOH A 108 3829 3829 HOH HOH . F 6 HOH A 109 3830 3830 HOH HOH . F 6 HOH A 110 3831 3831 HOH HOH . F 6 HOH A 111 3832 3832 HOH HOH . F 6 HOH A 112 3833 3833 HOH HOH . F 6 HOH A 113 3834 3834 HOH HOH . F 6 HOH A 114 3835 3835 HOH HOH . G 6 HOH B 1 28 28 HOH HOH . G 6 HOH B 2 46 46 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 N N1 A1R . . . D 4 18.128 87.064 1.298 1 29.62 ? N1 A1R 1001 A 1 HETATM 2 C C2 A1R . . . D 4 19.463 86.693 1.602 1 29.54 ? C2 A1R 1001 A 1 HETATM 3 N N3 A1R . . . D 4 19.968 86.652 2.974 1 26.92 ? N3 A1R 1001 A 1 HETATM 4 C C4 A1R . . . D 4 18.991 87.02 3.974 1 25.52 ? C4 A1R 1001 A 1 HETATM 5 C C5 A1R . . . D 4 17.65 87.406 3.787 1 26.29 ? C5 A1R 1001 A 1 HETATM 6 C C6 A1R . . . D 4 17.202 87.425 2.359 1 27.37 ? C6 A1R 1001 A 1 HETATM 7 N N6 A1R . . . D 4 15.884 87.784 1.969 1 30.56 ? N6 A1R 1001 A 1 HETATM 8 N N7 A1R . . . D 4 17.044 87.683 5.005 1 27.91 ? N7 A1R 1001 A 1 HETATM 9 C C8 A1R . . . D 4 17.991 87.467 5.928 1 27.26 ? C8 A1R 1001 A 1 HETATM 10 N N9 A1R . . . D 4 19.194 87.059 5.346 1 30.59 ? N9 A1R 1001 A 1 HETATM 11 C C1' A1R . . . D 4 20.497 86.694 5.922 1 28.67 ? C1' A1R 1001 A 1 HETATM 12 C C2' A1R . . . D 4 21.077 87.427 7.063 1 28.91 ? C2' A1R 1001 A 1 HETATM 13 O O2' A1R . . . D 4 22.069 88.395 6.621 1 32.65 ? O2' A1R 1001 A 1 HETATM 14 C C3' A1R . . . D 4 21.649 86.39 7.96 1 26.89 ? C3' A1R 1001 A 1 HETATM 15 O O3' A1R . . . D 4 23.086 86.226 7.892 1 30.25 ? O3' A1R 1001 A 1 HETATM 16 O O4' A1R . . . D 4 20.317 85.363 6.319 1 26.58 ? O4' A1R 1001 A 1 HETATM 17 C C4' A1R . . . D 4 20.979 85.083 7.571 1 28.59 ? C4' A1R 1001 A 1 HETATM 18 C C5' A1R . . . D 4 19.902 84.515 8.555 1 26.45 ? C5' A1R 1001 A 1 HETATM 19 O O5' A1R . . . D 4 20.529 84.244 9.856 1 27.3 ? O5' A1R 1001 A 1 HETATM 20 P PA A1R . . . D 4 19.752 83.658 11.053 1 28.24 ? PA A1R 1001 A 1 HETATM 21 O O1A A1R . . . D 4 18.549 84.44 11.39 1 33.13 ? O1A A1R 1001 A 1 HETATM 22 O O2A A1R . . . D 4 20.697 83.536 12.182 1 32.66 ? O2A A1R 1001 A 1 HETATM 23 O O3A A1R . . . D 4 19.382 82.19 10.8 1 28.08 ? O3A A1R 1001 A 1 HETATM 24 P PB A1R . . . D 4 20.026 80.899 10.41 1 27.37 ? PB A1R 1001 A 1 HETATM 25 O O1B A1R . . . D 4 21.455 81.085 10.183 1 30.16 ? O1B A1R 1001 A 1 HETATM 26 O O2B A1R . . . D 4 19.626 80.219 9.245 1 31.06 ? O2B A1R 1001 A 1 HETATM 27 O O5N A1R . . . D 4 19.89 80.299 11.819 1 29.03 ? O5N A1R 1001 A 1 HETATM 28 C C5N A1R . . . D 4 18.87 79.893 12.59 1 39.41 ? C5N A1R 1001 A 1 HETATM 29 N N4N A1R . . . D 4 17.312 80.027 14.039 1 41.17 ? N4N A1R 1001 A 1 HETATM 30 C C1N A1R . . . D 4 17.197 79.251 15.305 1 36.57 ? C1N A1R 1001 A 1 HETATM 31 O O2N A1R . . . D 4 18.198 80.269 16.753 1 39.82 ? O2N A1R 1001 A 1 HETATM 32 C C2N A1R . . . D 4 18.451 79.129 15.879 1 37.59 ? C2N A1R 1001 A 1 HETATM 33 O O3N A1R . . . D 4 20.499 80.647 15.606 1 47.9 ? O3N A1R 1001 A 1 HETATM 34 C C3N A1R . . . D 4 19.505 79.758 15.108 1 43.83 ? C3N A1R 1001 A 1 HETATM 35 C C4N A1R . . . D 4 18.78 80.358 13.92 1 41.81 ? C4N A1R 1001 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #