data_2OD9
#
_model_server_result.job_id            nOnOn5ZwZ56bGhCk-HbGMA 
_model_server_result.datetime_utc      '2024-11-15 03:57:04' 
_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          2od9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1001}' 
#
_entry.id    2OD9 
#
_exptl.entry_id    2OD9 
_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            2OD9 
_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                 2OD9 
_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
PISA dimeric 2 author_and_software_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                     2OD9 
_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 1 HOH HOH . 
F 6 HOH A 2 3723 2 HOH HOH . 
F 6 HOH A 3 3724 3 HOH HOH . 
F 6 HOH A 4 3725 4 HOH HOH . 
F 6 HOH A 5 3726 5 HOH HOH . 
F 6 HOH A 6 3727 6 HOH HOH . 
F 6 HOH A 7 3728 7 HOH HOH . 
F 6 HOH A 8 3729 8 HOH HOH . 
F 6 HOH A 9 3730 9 HOH HOH . 
F 6 HOH A 10 3731 10 HOH HOH . 
F 6 HOH A 11 3732 11 HOH HOH . 
F 6 HOH A 12 3733 12 HOH HOH . 
F 6 HOH A 13 3734 13 HOH HOH . 
F 6 HOH A 14 3735 14 HOH HOH . 
F 6 HOH A 15 3736 15 HOH HOH . 
F 6 HOH A 16 3737 16 HOH HOH . 
F 6 HOH A 17 3738 17 HOH HOH . 
F 6 HOH A 18 3739 18 HOH HOH . 
F 6 HOH A 19 3740 19 HOH HOH . 
F 6 HOH A 20 3741 20 HOH HOH . 
F 6 HOH A 21 3742 21 HOH HOH . 
F 6 HOH A 22 3743 22 HOH HOH . 
F 6 HOH A 23 3744 23 HOH HOH . 
F 6 HOH A 24 3745 24 HOH HOH . 
F 6 HOH A 25 3746 25 HOH HOH . 
F 6 HOH A 26 3747 26 HOH HOH . 
F 6 HOH A 27 3748 27 HOH HOH . 
F 6 HOH A 28 3749 29 HOH HOH . 
F 6 HOH A 29 3750 30 HOH HOH . 
F 6 HOH A 30 3751 31 HOH HOH . 
F 6 HOH A 31 3752 32 HOH HOH . 
F 6 HOH A 32 3753 33 HOH HOH . 
F 6 HOH A 33 3754 34 HOH HOH . 
F 6 HOH A 34 3755 35 HOH HOH . 
F 6 HOH A 35 3756 36 HOH HOH . 
F 6 HOH A 36 3757 37 HOH HOH . 
F 6 HOH A 37 3758 38 HOH HOH . 
F 6 HOH A 38 3759 39 HOH HOH . 
F 6 HOH A 39 3760 40 HOH HOH . 
F 6 HOH A 40 3761 41 HOH HOH . 
F 6 HOH A 41 3762 42 HOH HOH . 
F 6 HOH A 42 3763 43 HOH HOH . 
F 6 HOH A 43 3764 44 HOH HOH . 
F 6 HOH A 44 3765 45 HOH HOH . 
F 6 HOH A 45 3766 47 HOH HOH . 
F 6 HOH A 46 3767 48 HOH HOH . 
F 6 HOH A 47 3768 49 HOH HOH . 
F 6 HOH A 48 3769 50 HOH HOH . 
F 6 HOH A 49 3770 51 HOH HOH . 
F 6 HOH A 50 3771 52 HOH HOH . 
F 6 HOH A 51 3772 53 HOH HOH . 
F 6 HOH A 52 3773 54 HOH HOH . 
F 6 HOH A 53 3774 55 HOH HOH . 
F 6 HOH A 54 3775 56 HOH HOH . 
F 6 HOH A 55 3776 57 HOH HOH . 
F 6 HOH A 56 3777 58 HOH HOH . 
F 6 HOH A 57 3778 59 HOH HOH . 
F 6 HOH A 58 3779 60 HOH HOH . 
F 6 HOH A 59 3780 61 HOH HOH . 
F 6 HOH A 60 3781 62 HOH HOH . 
F 6 HOH A 61 3782 63 HOH HOH . 
F 6 HOH A 62 3783 64 HOH HOH . 
F 6 HOH A 63 3784 65 HOH HOH . 
F 6 HOH A 64 3785 66 HOH HOH . 
F 6 HOH A 65 3786 67 HOH HOH . 
F 6 HOH A 66 3787 68 HOH HOH . 
F 6 HOH A 67 3788 69 HOH HOH . 
F 6 HOH A 68 3789 70 HOH HOH . 
F 6 HOH A 69 3790 71 HOH HOH . 
F 6 HOH A 70 3791 72 HOH HOH . 
F 6 HOH A 71 3792 73 HOH HOH . 
F 6 HOH A 72 3793 74 HOH HOH . 
F 6 HOH A 73 3794 75 HOH HOH . 
F 6 HOH A 74 3795 76 HOH HOH . 
F 6 HOH A 75 3796 77 HOH HOH . 
F 6 HOH A 76 3797 78 HOH HOH . 
F 6 HOH A 77 3798 79 HOH HOH . 
F 6 HOH A 78 3799 80 HOH HOH . 
F 6 HOH A 79 3800 81 HOH HOH . 
F 6 HOH A 80 3801 82 HOH HOH . 
F 6 HOH A 81 3802 83 HOH HOH . 
F 6 HOH A 82 3803 84 HOH HOH . 
F 6 HOH A 83 3804 85 HOH HOH . 
F 6 HOH A 84 3805 86 HOH HOH . 
F 6 HOH A 85 3806 87 HOH HOH . 
F 6 HOH A 86 3807 88 HOH HOH . 
F 6 HOH A 87 3808 89 HOH HOH . 
F 6 HOH A 88 3809 90 HOH HOH . 
F 6 HOH A 89 3810 91 HOH HOH . 
F 6 HOH A 90 3811 92 HOH HOH . 
F 6 HOH A 91 3812 93 HOH HOH . 
F 6 HOH A 92 3813 94 HOH HOH . 
F 6 HOH A 93 3814 95 HOH HOH . 
F 6 HOH A 94 3815 96 HOH HOH . 
F 6 HOH A 95 3816 97 HOH HOH . 
F 6 HOH A 96 3817 98 HOH HOH . 
F 6 HOH A 97 3818 99 HOH HOH . 
F 6 HOH A 98 3819 100 HOH HOH . 
F 6 HOH A 99 3820 101 HOH HOH . 
F 6 HOH A 100 3821 102 HOH HOH . 
F 6 HOH A 101 3822 103 HOH HOH . 
F 6 HOH A 102 3823 104 HOH HOH . 
F 6 HOH A 103 3824 105 HOH HOH . 
F 6 HOH A 104 3825 106 HOH HOH . 
F 6 HOH A 105 3826 107 HOH HOH . 
F 6 HOH A 106 3827 108 HOH HOH . 
F 6 HOH A 107 3828 109 HOH HOH . 
F 6 HOH A 108 3829 110 HOH HOH . 
F 6 HOH A 109 3830 111 HOH HOH . 
F 6 HOH A 110 3831 112 HOH HOH . 
F 6 HOH A 111 3832 113 HOH HOH . 
F 6 HOH A 112 3833 114 HOH HOH . 
F 6 HOH A 113 3834 115 HOH HOH . 
F 6 HOH A 114 3835 116 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              8 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           35 
#