data_6YDB
#
_model_server_result.job_id            -XG1Jw9gjKYZubvapE906Q 
_model_server_result.datetime_utc      '2024-10-15 18:31:00' 
_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          6ydb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    6YDB 
#
_exptl.entry_id    6YDB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              694.393 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-azanyl-9-[(1~{R},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{R})-17-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-1~{H}-purin-6-one 
_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         90 
_cell.entry_id            6YDB 
_cell.length_a            111.073 
_cell.length_b            111.073 
_cell.length_c            35.836 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YDB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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' 8_554 -y,-x,-z-1/2 0 -1 0 -1 0 0 0 0 -1 0 0 -17.918 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C20 H22 F2 N10 O12 P2' 
_chem_comp.formula_weight    694.393 
_chem_comp.id                GGF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-azanyl-9-[(1~{R},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{R})-17-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-1~{H}-purin-6-one 
_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
O1P P1 GGF doub 83 n n 
O2P P1 GGF sing 84 n n 
P1 O5' GGF sing 85 n n 
P1 O3A GGF sing 86 n n 
O4' C1' GGF sing 87 n n 
O4' C4' GGF sing 88 n n 
O5' C5' GGF sing 89 n n 
C8 N7 GGF doub 90 n y 
C8 N9 GGF sing 91 n y 
N7 C5 GGF sing 92 n y 
C5' C4' GGF sing 93 n n 
N9 C1' GGF sing 94 n n 
N9 C4 GGF sing 95 n y 
C5 C6 GGF sing 96 n n 
C5 C4 GGF doub 97 n y 
O6 C6 GGF doub 98 n n 
C1' C2' GGF sing 99 n n 
C6 N1 GGF sing 100 n n 
C4 N3 GGF sing 101 n n 
C4' C3' GGF sing 102 n n 
O3A C3A GGF sing 103 n n 
N1 C2 GGF sing 104 n n 
N3 C2 GGF doub 105 n n 
C2 N2 GGF sing 106 n n 
F1 C2A GGF sing 107 n n 
C2A C3A GGF sing 108 n n 
C2A C1A GGF sing 109 n n 
C3A C4A GGF sing 110 n n 
C3' C2' GGF sing 111 n n 
C3' O3' GGF sing 112 n n 
C2' F2 GGF sing 113 n n 
N21 C21 GGF sing 114 n n 
C21 N31 GGF doub 115 n n 
C21 N11 GGF sing 116 n n 
N31 C41 GGF sing 117 n n 
N11 C61 GGF sing 118 n n 
O3' P11 GGF sing 119 n n 
C4A C5A GGF sing 120 n n 
C4A O4A GGF sing 121 n n 
C41 C51 GGF doub 122 n y 
C41 N91 GGF sing 123 n y 
C61 O61 GGF doub 124 n n 
C61 C51 GGF sing 125 n n 
C1A N91 GGF sing 126 n n 
C1A O4A GGF sing 127 n n 
C51 N71 GGF sing 128 n y 
N91 C81 GGF sing 129 n y 
C81 N71 GGF doub 130 n y 
C5A O5A GGF sing 131 n n 
O5A P11 GGF sing 132 n n 
P11 O21 GGF doub 133 n n 
P11 O11 GGF sing 134 n n 
C1' H1' GGF sing 135 n n 
C1A H1A GGF sing 136 n n 
C2' H2' GGF sing 137 n n 
C2A H2A GGF sing 138 n n 
C3' H3' GGF sing 139 n n 
C3A H3A GGF sing 140 n n 
C4' H4' GGF sing 141 n n 
C4A H4A GGF sing 142 n n 
C5' "H5'1" GGF sing 143 n n 
C5' "H5'2" GGF sing 144 n n 
C5A H5A1 GGF sing 145 n n 
C5A H5A2 GGF sing 146 n n 
C8 H8 GGF sing 147 n n 
C81 H81 GGF sing 148 n n 
N1 HN1 GGF sing 149 n n 
N11 HN11 GGF sing 150 n n 
N2 HN22 GGF sing 151 n n 
N2 HN21 GGF sing 152 n n 
N21 H212 GGF sing 153 n n 
N21 H211 GGF sing 154 n n 
O11 H1 GGF sing 155 n n 
O2P H2 GGF sing 156 n n 
#
_atom_sites.entry_id                     6YDB 
_atom_sites.fract_transf_matrix[1][1]    0.009003 
_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]    0.009003 
_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]    0.027905 
_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
B 2 GGF A 1 401 401 GGF GGF . 
C 3 HOH A 1 501 12 HOH HOH . 
C 3 HOH A 2 502 13 HOH HOH . 
C 3 HOH A 3 503 22 HOH HOH . 
C 3 HOH A 4 504 2 HOH HOH . 
C 3 HOH A 5 505 5 HOH HOH . 
C 3 HOH A 6 506 1 HOH HOH . 
C 3 HOH A 7 507 10 HOH HOH . 
C 3 HOH A 8 508 7 HOH HOH . 
C 3 HOH A 9 509 17 HOH HOH . 
C 3 HOH A 10 510 11 HOH HOH . 
C 3 HOH A 11 511 6 HOH HOH . 
C 3 HOH A 12 512 8 HOH HOH . 
C 3 HOH A 13 513 3 HOH HOH . 
C 3 HOH A 14 514 9 HOH HOH . 
C 3 HOH A 15 515 20 HOH HOH . 
C 3 HOH A 16 516 4 HOH HOH . 
C 3 HOH A 17 517 19 HOH HOH . 
C 3 HOH A 18 518 18 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 C1' GGF . . . B 2 -23.1 17.787 -10.373 0.5 49.28 ? C1' GGF 401 A 1 
HETATM 2 C C1A GGF . . . B 2 -17.783 23.119 -7.496 0.5 49.2 ? C1A GGF 401 A 1 
HETATM 3 C C2 GGF . . . B 2 -21.589 13.599 -9.807 0.5 54.67 ? C2 GGF 401 A 1 
HETATM 4 C C2' GGF . . . B 2 -23.291 18.182 -8.919 0.5 49.74 ? C2' GGF 401 A 1 
HETATM 5 C C21 GGF . . . B 2 -13.595 21.6 -8.058 0.5 54.67 ? C21 GGF 401 A 1 
HETATM 6 C C2A GGF . . . B 2 -18.186 23.295 -8.951 0.5 49.81 ? C2A GGF 401 A 1 
HETATM 7 C C3' GGF . . . B 2 -22.847 19.631 -8.92 0.5 47.68 ? C3' GGF 401 A 1 
HETATM 8 C C3A GGF . . . B 2 -19.638 22.862 -8.94 0.5 47.65 ? C3A GGF 401 A 1 
HETATM 9 C C4 GGF . . . B 2 -21.467 15.906 -10.267 0.5 51.49 ? C4 GGF 401 A 1 
HETATM 10 C C4' GGF . . . B 2 -23.418 20.105 -10.249 0.5 47.36 ? C4' GGF 401 A 1 
HETATM 11 C C41 GGF . . . B 2 -15.903 21.484 -7.598 0.5 51.48 ? C41 GGF 401 A 1 
HETATM 12 C C4A GGF . . . B 2 -20.106 23.435 -7.611 0.5 47.18 ? C4A GGF 401 A 1 
HETATM 13 C C5 GGF . . . B 2 -20.019 15.768 -10.461 0.5 52.21 ? C5 GGF 401 A 1 
HETATM 14 C C5' GGF . . . B 2 -22.757 21.37 -10.761 0.5 47.26 ? C5' GGF 401 A 1 
HETATM 15 C C51 GGF . . . B 2 -15.768 20.037 -7.399 0.5 52.22 ? C51 GGF 401 A 1 
HETATM 16 C C5A GGF . . . B 2 -21.365 22.771 -7.088 0.5 47.2 ? C5A GGF 401 A 1 
HETATM 17 C C6 GGF . . . B 2 -19.44 14.418 -10.29 0.5 54.23 ? C6 GGF 401 A 1 
HETATM 18 C C61 GGF . . . B 2 -14.418 19.455 -7.568 0.5 54.24 ? C61 GGF 401 A 1 
HETATM 19 C C8 GGF . . . B 2 -20.613 17.846 -10.768 0.5 50.83 ? C8 GGF 401 A 1 
HETATM 20 C C81 GGF . . . B 2 -17.845 20.634 -7.093 0.5 50.8 ? C81 GGF 401 A 1 
HETATM 21 F F1 GGF . . . B 2 -18.069 24.598 -9.334 0.5 50.81 ? F1 GGF 401 A 1 
HETATM 22 F F2 GGF . . . B 2 -24.602 18.088 -8.558 0.5 50.84 ? F2 GGF 401 A 1 
HETATM 23 N N1 GGF . . . B 2 -20.265 13.414 -9.973 0.5 57.84 ? N1 GGF 401 A 1 
HETATM 24 N N11 GGF . . . B 2 -13.413 20.277 -7.888 0.5 57.81 ? N11 GGF 401 A 1 
HETATM 25 N N2 GGF . . . B 2 -22.357 12.53 -9.487 0.5 55.02 ? N2 GGF 401 A 1 
HETATM 26 N N21 GGF . . . B 2 -12.524 22.365 -8.382 0.5 55.03 ? N21 GGF 401 A 1 
HETATM 27 N N3 GGF . . . B 2 -22.188 14.808 -9.947 0.5 52.57 ? N3 GGF 401 A 1 
HETATM 28 N N31 GGF . . . B 2 -14.803 22.202 -7.92 0.5 52.57 ? N31 GGF 401 A 1 
HETATM 29 N N7 GGF . . . B 2 -19.557 16.992 -10.766 0.5 52.13 ? N7 GGF 401 A 1 
HETATM 30 N N71 GGF . . . B 2 -16.992 19.577 -7.092 0.5 52.12 ? N71 GGF 401 A 1 
HETATM 31 N N9 GGF . . . B 2 -21.752 17.19 -10.481 0.5 48.53 ? N9 GGF 401 A 1 
HETATM 32 N N91 GGF . . . B 2 -17.187 21.771 -7.384 0.5 48.69 ? N91 GGF 401 A 1 
HETATM 33 O O11 GGF . . . B 2 -23.108 20.975 -5.33 0.5 47.08 ? O11 GGF 401 A 1 
HETATM 34 O O1P GGF . . . B 2 -20.977 23.117 -12.533 0.5 47.06 ? O1P GGF 401 A 1 
HETATM 35 O O21 GGF . . . B 2 -21.784 19.052 -6.205 0.5 45.7 ? O21 GGF 401 A 1 
HETATM 36 O O2P GGF . . . B 2 -19.041 21.805 -11.662 0.5 45.68 ? O2P GGF 401 A 1 
HETATM 37 O O3' GGF . . . B 2 -23.319 20.335 -7.788 0.5 47.8 ? O3' GGF 401 A 1 
HETATM 38 O O3A GGF . . . B 2 -20.337 23.33 -10.078 0.5 47.84 ? O3A GGF 401 A 1 
HETATM 39 O O4' GGF . . . B 2 -23.225 18.995 -11.137 0.5 50.72 ? O4' GGF 401 A 1 
HETATM 40 O O4A GGF . . . B 2 -18.991 23.236 -6.731 0.5 50.73 ? O4A GGF 401 A 1 
HETATM 41 O O5' GGF . . . B 2 -21.381 21.12 -11.011 0.5 43.22 ? O5' GGF 401 A 1 
HETATM 42 O O5A GGF . . . B 2 -21.114 21.393 -6.854 0.5 43.5 ? O5A GGF 401 A 1 
HETATM 43 O O6 GGF . . . B 2 -18.216 14.217 -10.436 0.5 53.16 ? O6 GGF 401 A 1 
HETATM 44 O O61 GGF . . . B 2 -14.221 18.231 -7.418 0.5 53.18 ? O61 GGF 401 A 1 
HETATM 45 P P1 GGF . . . B 2 -20.415 22.353 -11.357 0.5 46.76 ? P1 GGF 401 A 1 
HETATM 46 P P11 GGF . . . B 2 -22.343 20.422 -6.509 0.5 46.87 ? P11 GGF 401 A 1 
HETATM 47 H H1' GGF . . . B 2 -23.838 17.055 -10.73 0.5 59.17 ? H1' GGF 401 A 1 
HETATM 48 H H1A GGF . . . B 2 -17.054 23.865 -7.148 0.5 59.08 ? H1A GGF 401 A 1 
HETATM 49 H H2' GGF . . . B 2 -22.743 17.544 -8.212 0.5 59.72 ? H2' GGF 401 A 1 
HETATM 50 H H2A GGF . . . B 2 -17.56 22.729 -9.656 0.5 59.81 ? H2A GGF 401 A 1 
HETATM 51 H H3' GGF . . . B 2 -21.763 19.793 -8.838 0.5 57.25 ? H3' GGF 401 A 1 
HETATM 52 H H3A GGF . . . B 2 -19.813 21.78 -9.012 0.5 57.21 ? H3A GGF 401 A 1 
HETATM 53 H H4' GGF . . . B 2 -24.477 20.382 -10.158 0.5 56.86 ? H4' GGF 401 A 1 
HETATM 54 H H4A GGF . . . B 2 -20.385 24.494 -7.702 0.5 56.65 ? H4A GGF 401 A 1 
HETATM 55 H "H5'1" GGF . . . B 2 -23.247 21.698 -11.68 0.5 56.75 ? "H5'1" GGF 401 A 1 
HETATM 56 H "H5'2" GGF . . . B 2 -22.86 22.167 -10.022 0.5 56.75 ? "H5'2" GGF 401 A 1 
HETATM 57 H H5A1 GGF . . . B 2 -22.172 22.883 -7.814 0.5 56.67 ? H5A1 GGF 401 A 1 
HETATM 58 H H5A2 GGF . . . B 2 -21.679 23.253 -6.16 0.5 56.67 ? H5A2 GGF 401 A 1 
HETATM 59 H H8 GGF . . . B 2 -20.548 18.908 -10.972 0.5 61.03 ? H8 GGF 401 A 1 
HETATM 60 H H81 GGF . . . B 2 -18.906 20.571 -6.889 0.5 60.99 ? H81 GGF 401 A 1 
HETATM 61 H HN1 GGF . . . B 2 -19.871 12.459 -9.85 0.5 69.45 ? HN1 GGF 401 A 1 
HETATM 62 H HN11 GGF . . . B 2 -12.459 19.881 -8.01 0.5 69.41 ? HN11 GGF 401 A 1 
HETATM 63 H HN22 GGF . . . B 2 -21.935 11.619 -9.377 0.5 66.06 ? HN22 GGF 401 A 1 
HETATM 64 H HN21 GGF . . . B 2 -23.352 12.645 -9.356 0.5 66.06 ? HN21 GGF 401 A 1 
HETATM 65 H H212 GGF . . . B 2 -12.636 23.36 -8.514 0.5 66.07 ? H212 GGF 401 A 1 
HETATM 66 H H211 GGF . . . B 2 -11.615 21.94 -8.49 0.5 66.07 ? H211 GGF 401 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           66 
#