data_3I9O
#
_model_server_result.job_id            D4gdnC6Nj4jH8iOTRtRQ6Q 
_model_server_result.datetime_utc      '2025-08-31 11:55:26' 
_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          3i9o 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    3I9O 
#
_exptl.entry_id    3I9O 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              545.307 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4S)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' 
_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         120 
_cell.entry_id            3I9O 
_cell.length_a            56.726 
_cell.length_b            56.726 
_cell.length_c            360.333 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3I9O 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61' 
#
_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 
_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 D N 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
disulf ? disulf1 A SG CYS 15 A CYS 15 1_555 A SG CYS 34 A CYS 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
disulf ? disulf2 A SG CYS 51 A CYS 51 1_555 A SG CYS 131 A CYS 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
disulf ? disulf3 A SG CYS 112 A CYS 112 1_555 A SG CYS 125 A CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
disulf ? disulf4 A SG CYS 206 A CYS 206 1_555 A SG CYS 227 A CYS 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
disulf ? disulf5 A SG CYS 239 A CYS 239 1_555 A SG CYS 248 A CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf6 B SG CYS 15 B CYS 15 1_555 B SG CYS 34 B CYS 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
disulf ? disulf7 B SG CYS 51 B CYS 51 1_555 B SG CYS 131 B CYS 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
disulf ? disulf8 B SG CYS 112 B CYS 112 1_555 B SG CYS 125 B CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
disulf ? disulf9 B SG CYS 206 B CYS 206 1_555 B SG CYS 227 B CYS 227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
disulf ? disulf10 B SG CYS 239 B CYS 239 1_555 B SG CYS 248 B CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
#
_chem_comp.formula           'C15 H22 F N5 O12 P2' 
_chem_comp.formula_weight    545.307 
_chem_comp.id                AVW 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4S)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "ribosyl-2-fluoro-deoxy-adenosine diphosphate ribose;ribo-2'F-ADPR" 
#
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
O3 PA AVW sing 70 n n 
"O5'A" PA AVW sing 71 n n 
PA O1A AVW doub 72 n n 
PA O2A AVW sing 73 n n 
"O5'N" PN AVW sing 74 n n 
O1N PN AVW doub 75 n n 
O2N PN AVW sing 76 n n 
PN O3 AVW sing 77 n n 
C6A N1A AVW doub 78 n y 
C2A N1A AVW sing 79 n y 
N3A C2A AVW doub 80 n y 
C2A HC2 AVW sing 81 n n 
O2A HAO2 AVW sing 82 n n 
O2N HNO2 AVW sing 83 n n 
C4A N3A AVW sing 84 n y 
N9A C4A AVW sing 85 n y 
C4A C5A AVW doub 86 n y 
N7A C5A AVW sing 87 n y 
C5A C6A AVW sing 88 n y 
C6A N6A AVW sing 89 n n 
N6A HAN6 AVW sing 90 n n 
N6A HANA AVW sing 91 n n 
C8A N7A AVW doub 92 n y 
C8A N9A AVW sing 93 n y 
C8A HC8 AVW sing 94 n n 
"C1'A" N9A AVW sing 95 n n 
"C1'A" "C2'A" AVW sing 96 n n 
"C1'A" "O4'A" AVW sing 97 n n 
"C1'A" HC1' AVW sing 98 n n 
"C1'N" "C2'N" AVW sing 99 n n 
"C1'N" "O4'N" AVW sing 100 n n 
"C1'N" HC1A AVW sing 101 n n 
"C1'N" HC1B AVW sing 102 n n 
"O2'A" "C2'A" AVW sing 103 n n 
"C2'A" "C3'A" AVW sing 104 n n 
"C2'A" HC2' AVW sing 105 n n 
"O2'A" HO2' AVW sing 106 n n 
"F2'N" "C2'N" AVW sing 107 n n 
"C2'N" "C3'N" AVW sing 108 n n 
"C2'N" HC2A AVW sing 109 n n 
"O3'A" "C3'A" AVW sing 110 n n 
"C3'A" "C4'A" AVW sing 111 n n 
"C3'A" HC3' AVW sing 112 n n 
"O3'A" HO3' AVW sing 113 n n 
"O3'N" "C3'N" AVW sing 114 n n 
"C3'N" "C4'N" AVW sing 115 n n 
"C3'N" HC3A AVW sing 116 n n 
"O3'N" HO3A AVW sing 117 n n 
"O4'A" "C4'A" AVW sing 118 n n 
"C4'A" "C5'A" AVW sing 119 n n 
"C4'A" HC4' AVW sing 120 n n 
"O4'N" "C4'N" AVW sing 121 n n 
"C4'N" "C5'N" AVW sing 122 n n 
"C4'N" HC4A AVW sing 123 n n 
"C5'A" "O5'A" AVW sing 124 n n 
"C5'A" HC5' AVW sing 125 n n 
"C5'A" HC5A AVW sing 126 n n 
"C5'N" "O5'N" AVW sing 127 n n 
"C5'N" HC5B AVW sing 128 n n 
"C5'N" HC5C AVW sing 129 n n 
#
_atom_sites.entry_id                     3I9O 
_atom_sites.fract_transf_matrix[1][1]    0.017629 
_atom_sites.fract_transf_matrix[1][2]    0.010178 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020356 
_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]    0.002775 
_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 AVW A 1 301 301 AVW AVW . 
D 2 AVW B 1 301 301 AVW AVW . 
#
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 AVW . . . D 2 -3.142 -0.861 -19.381 1 76.85 ? PA AVW 301 B 1 
HETATM 2 P PN AVW . . . D 2 -5.242 0.817 -20.18 1 72.66 ? PN AVW 301 B 1 
HETATM 3 N N1A AVW . . . D 2 -9.622 -1.826 -16.302 1 120.55 ? N1A AVW 301 B 1 
HETATM 4 O O1A AVW . . . D 2 -1.648 -0.855 -19.489 1 75.64 ? O1A AVW 301 B 1 
HETATM 5 O O1N AVW . . . D 2 -5.487 2.296 -20.361 1 73.47 ? O1N AVW 301 B 1 
HETATM 6 C C2A AVW . . . D 2 -8.351 -1.681 -15.903 1 119.84 ? C2A AVW 301 B 1 
HETATM 7 O O2A AVW . . . D 2 -3.731 -1.277 -18.081 1 77.19 ? O2A AVW 301 B 1 
HETATM 8 O O2N AVW . . . D 2 -5.375 -0.06 -21.42 1 73.59 ? O2N AVW 301 B 1 
HETATM 9 O O3 AVW . . . D 2 -3.771 0.605 -19.568 1 74.85 ? O3 AVW 301 B 1 
HETATM 10 N N3A AVW . . . D 2 -7.378 -2.457 -16.353 1 119.17 ? N3A AVW 301 B 1 
HETATM 11 C C4A AVW . . . D 2 -7.679 -3.444 -17.218 1 118.46 ? C4A AVW 301 B 1 
HETATM 12 C C5A AVW . . . D 2 -8.975 -3.644 -17.654 1 119.99 ? C5A AVW 301 B 1 
HETATM 13 C C6A AVW . . . D 2 -9.966 -2.801 -17.18 1 121.02 ? C6A AVW 301 B 1 
HETATM 14 N N6A AVW . . . D 2 -11.263 -3 -17.569 1 123.04 ? N6A AVW 301 B 1 
HETATM 15 N N7A AVW . . . D 2 -8.961 -4.692 -18.51 1 120.06 ? N7A AVW 301 B 1 
HETATM 16 C C8A AVW . . . D 2 -7.671 -5.125 -18.588 1 118.32 ? C8A AVW 301 B 1 
HETATM 17 N N9A AVW . . . D 2 -6.921 -4.356 -17.786 1 116.62 ? N9A AVW 301 B 1 
HETATM 18 C "C1'A" AVW . . . D 2 -5.47 -4.395 -17.507 1 113.4 ? "C1'A" AVW 301 B 1 
HETATM 19 C "C1'N" AVW . . . D 2 -9.34 1.586 -16.657 1 72.76 ? "C1'N" AVW 301 B 1 
HETATM 20 C "C2'A" AVW . . . D 2 -4.782 -5.646 -18.001 1 112.07 ? "C2'A" AVW 301 B 1 
HETATM 21 O "O2'A" AVW . . . D 2 -3.885 -6.095 -16.957 1 111.41 ? "O2'A" AVW 301 B 1 
HETATM 22 C "C2'N" AVW . . . D 2 -8.425 1.809 -15.467 1 74.06 ? "C2'N" AVW 301 B 1 
HETATM 23 F "F2'N" AVW . . . D 2 -9.107 2.473 -14.467 1 74.95 ? "F2'N" AVW 301 B 1 
HETATM 24 C "C3'A" AVW . . . D 2 -4.053 -5.156 -19.245 1 109.79 ? "C3'A" AVW 301 B 1 
HETATM 25 O "O3'A" AVW . . . D 2 -2.752 -5.771 -19.236 1 110.47 ? "O3'A" AVW 301 B 1 
HETATM 26 C "C3'N" AVW . . . D 2 -7.216 2.526 -16.067 1 74.35 ? "C3'N" AVW 301 B 1 
HETATM 27 O "O3'N" AVW . . . D 2 -7.269 3.957 -15.95 1 74.94 ? "O3'N" AVW 301 B 1 
HETATM 28 C "C4'A" AVW . . . D 2 -4.072 -3.602 -19.19 1 106.24 ? "C4'A" AVW 301 B 1 
HETATM 29 O "O4'A" AVW . . . D 2 -4.969 -3.229 -18.133 1 110.13 ? "O4'A" AVW 301 B 1 
HETATM 30 C "C4'N" AVW . . . D 2 -7.219 2.106 -17.531 1 73.05 ? "C4'N" AVW 301 B 1 
HETATM 31 O "O4'N" AVW . . . D 2 -8.565 1.769 -17.842 1 72.6 ? "O4'N" AVW 301 B 1 
HETATM 32 C "C5'A" AVW . . . D 2 -4.572 -2.866 -20.437 1 97.37 ? "C5'A" AVW 301 B 1 
HETATM 33 O "O5'A" AVW . . . D 2 -3.82 -1.647 -20.621 1 85.34 ? "O5'A" AVW 301 B 1 
HETATM 34 C "C5'N" AVW . . . D 2 -6.306 0.879 -17.699 1 72.07 ? "C5'N" AVW 301 B 1 
HETATM 35 O "O5'N" AVW . . . D 2 -6.282 0.335 -19.022 1 72.08 ? "O5'N" AVW 301 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           340 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           35 
#