data_8FDV
#
_model_server_result.job_id            BN-j2a7M-H4BzS5taW9ITQ 
_model_server_result.datetime_utc      '2024-11-25 14:30:22' 
_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          8fdv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":901}' 
#
_entry.id    8FDV 
#
_exptl.entry_id    8FDV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              815.576 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate' 
_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            8FDV 
_cell.length_a            119.298 
_cell.length_b            180.388 
_cell.length_c            232.884 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8FDV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
#
_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 
#
_chem_comp.formula           'C28 H35 N9 O16 P2' 
_chem_comp.formula_weight    815.576 
_chem_comp.id                HUF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate' 
_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
O33 C19 HUF doub 150 n n 
C19 N29 HUF sing 151 n n 
O37 C26 HUF sing 152 n n 
C24 N32 HUF sing 153 n n 
C24 C25 HUF sing 154 n n 
N29 C15 HUF sing 155 n n 
N29 C20 HUF sing 156 n n 
N32 C21 HUF sing 157 n n 
N32 C14 HUF sing 158 n n 
C15 C14 HUF doub 159 n y 
C15 C16 HUF sing 160 n y 
C20 C21 HUF doub 161 n n 
C20 C23 HUF sing 162 n n 
C21 N30 HUF sing 163 n n 
C14 C13 HUF sing 164 n y 
C16 C17 HUF doub 165 n y 
N30 C22 HUF sing 166 n n 
C13 C12 HUF doub 167 n y 
C23 N31 HUF sing 168 n n 
C23 O35 HUF doub 169 n n 
C22 N31 HUF sing 170 n n 
C22 O34 HUF doub 171 n n 
C17 C12 HUF sing 172 n y 
C17 C18 HUF sing 173 n n 
C12 C11 HUF sing 174 n n 
C26 C25 HUF sing 175 n n 
C26 C27 HUF sing 176 n n 
C25 O36 HUF sing 177 n n 
O2B PB HUF doub 178 n n 
C28 C27 HUF sing 179 n n 
C28 O1B HUF sing 180 n n 
C27 O38 HUF sing 181 n n 
PB O3A HUF sing 182 n n 
PB O1B HUF sing 183 n n 
PB O3B HUF sing 184 n n 
O3A PA HUF sing 185 n n 
O2A PA HUF doub 186 n n 
PA O1A HUF sing 187 n n 
PA O5' HUF sing 188 n n 
C5' O5' HUF sing 189 n n 
C5' C4' HUF sing 190 n n 
N7 C8 HUF doub 191 n y 
N7 C5 HUF sing 192 n y 
C8 N9 HUF sing 193 n y 
N6 C6 HUF sing 194 n n 
O4' C4' HUF sing 195 n n 
O4' C1' HUF sing 196 n n 
C5 C6 HUF doub 197 n y 
C5 C4 HUF sing 198 n y 
C4' C3' HUF sing 199 n n 
N9 C1' HUF sing 200 n n 
N9 C4 HUF sing 201 n y 
C6 N1 HUF sing 202 n y 
C2' C3' HUF sing 203 n n 
C2' C1' HUF sing 204 n n 
C2' O2' HUF sing 205 n n 
C3' O3' HUF sing 206 n n 
C4 N3 HUF doub 207 n y 
N1 C2 HUF doub 208 n y 
N3 C2 HUF sing 209 n y 
O1A H1 HUF sing 210 n n 
O3B H2 HUF sing 211 n n 
C5' H3 HUF sing 212 n n 
C5' H4 HUF sing 213 n n 
C4' H5 HUF sing 214 n n 
C3' H6 HUF sing 215 n n 
O3' H7 HUF sing 216 n n 
C2' H8 HUF sing 217 n n 
O2' H9 HUF sing 218 n n 
C1' H10 HUF sing 219 n n 
C8 H11 HUF sing 220 n n 
C2 H12 HUF sing 221 n n 
N6 H13 HUF sing 222 n n 
N6 H14 HUF sing 223 n n 
C11 H15 HUF sing 224 n n 
C11 H16 HUF sing 225 n n 
C11 H17 HUF sing 226 n n 
C13 H18 HUF sing 227 n n 
C16 H19 HUF sing 228 n n 
C18 H20 HUF sing 229 n n 
C18 H21 HUF sing 230 n n 
C18 H22 HUF sing 231 n n 
C19 H23 HUF sing 232 n n 
C24 H24 HUF sing 233 n n 
C24 H25 HUF sing 234 n n 
C25 H26 HUF sing 235 n n 
C26 H27 HUF sing 236 n n 
C27 H28 HUF sing 237 n n 
C28 H29 HUF sing 238 n n 
C28 H30 HUF sing 239 n n 
N30 H31 HUF sing 240 n n 
N31 H32 HUF sing 241 n n 
O36 H33 HUF sing 242 n n 
O37 H34 HUF sing 243 n n 
O38 H35 HUF sing 244 n n 
#
_atom_sites.entry_id                     8FDV 
_atom_sites.fract_transf_matrix[1][1]    0.008382 
_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]    0.005544 
_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]    0.004294 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          D 
_pdbx_nonpoly_scheme.entity_id        4 
_pdbx_nonpoly_scheme.mon_id           HUF 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      901 
_pdbx_nonpoly_scheme.auth_seq_num     901 
_pdbx_nonpoly_scheme.pdb_mon_id       HUF 
_pdbx_nonpoly_scheme.auth_mon_id      DRG 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 O O2A HUF . . . D 4 -5.264 68.383 87.163 1 0.5 ? O2A HUF 901 A 1 
HETATM 2 P PA HUF . . . D 4 -6.618 68.265 87.687 1 0.5 ? PA HUF 901 A 1 
HETATM 3 O O1A HUF . . . D 4 -7.706 67.574 87.016 1 0.5 -1 O1A HUF 901 A 1 
HETATM 4 O O3A HUF . . . D 4 -6.569 67.649 89.104 1 0.5 ? O3A HUF 901 A 1 
HETATM 5 P PB HUF . . . D 4 -6.381 66.202 89.646 1 0.5 ? PB HUF 901 A 1 
HETATM 6 O O3B HUF . . . D 4 -7.257 66.067 90.81 1 0.5 ? O3B HUF 901 A 1 
HETATM 7 O O2B HUF . . . D 4 -4.94 66.011 89.798 1 0.5 -1 O2B HUF 901 A 1 
HETATM 8 O O1B HUF . . . D 4 -6.99 65.33 88.483 1 0.5 ? O1B HUF 901 A 1 
HETATM 9 O O5' HUF . . . D 4 -7.117 69.668 88.089 1 0.5 ? O5' HUF 901 A 1 
HETATM 10 C C5' HUF . . . D 4 -6.124 70.622 88.401 1 0.5 ? C5' HUF 901 A 1 
HETATM 11 C C4' HUF . . . D 4 -6.803 71.956 88.478 1 0.5 ? C4' HUF 901 A 1 
HETATM 12 C C3' HUF . . . D 4 -7.488 72.421 87.194 1 0.5 ? C3' HUF 901 A 1 
HETATM 13 O O3' HUF . . . D 4 -8.554 73.31 87.472 1 0.5 ? O3' HUF 901 A 1 
HETATM 14 C C2' HUF . . . D 4 -6.387 73.278 86.598 1 0.5 ? C2' HUF 901 A 1 
HETATM 15 O O2' HUF . . . D 4 -6.875 74.177 85.644 1 0.5 ? O2' HUF 901 A 1 
HETATM 16 C C1' HUF . . . D 4 -6.038 74.004 87.87 1 0.5 ? C1' HUF 901 A 1 
HETATM 17 O O4' HUF . . . D 4 -5.792 72.946 88.738 1 0.5 ? O4' HUF 901 A 1 
HETATM 18 N N9 HUF . . . D 4 -4.865 74.838 87.806 1 0.5 ? N9 HUF 901 A 1 
HETATM 19 C C4 HUF . . . D 4 -4.748 76.088 88.322 1 0.5 ? C4 HUF 901 A 1 
HETATM 20 C C5 HUF . . . D 4 -3.474 76.493 88.031 1 0.5 ? C5 HUF 901 A 1 
HETATM 21 N N7 HUF . . . D 4 -2.804 75.521 87.328 1 0.5 ? N7 HUF 901 A 1 
HETATM 22 C C8 HUF . . . D 4 -3.668 74.556 87.229 1 0.5 ? C8 HUF 901 A 1 
HETATM 23 N N3 HUF . . . D 4 -5.676 76.779 88.98 1 0.5 ? N3 HUF 901 A 1 
HETATM 24 C C2 HUF . . . D 4 -5.215 77.961 89.338 1 0.5 ? C2 HUF 901 A 1 
HETATM 25 N N1 HUF . . . D 4 -4.011 78.487 89.131 1 0.5 ? N1 HUF 901 A 1 
HETATM 26 C C6 HUF . . . D 4 -3.101 77.766 88.462 1 0.5 ? C6 HUF 901 A 1 
HETATM 27 N N6 HUF . . . D 4 -1.913 78.294 88.24 1 0.5 ? N6 HUF 901 A 1 
HETATM 28 C C11 HUF . . . D 4 -5.133 63.83 80.837 1 0.5 ? C11 HUF 901 A 1 
HETATM 29 C C12 HUF . . . D 4 -5.905 62.551 80.94 1 0.5 ? C12 HUF 901 A 1 
HETATM 30 C C13 HUF . . . D 4 -6.064 61.941 82.151 1 0.5 ? C13 HUF 901 A 1 
HETATM 31 C C14 HUF . . . D 4 -6.759 60.751 82.256 1 0.5 ? C14 HUF 901 A 1 
HETATM 32 C C15 HUF . . . D 4 -7.307 60.191 81.128 1 0.5 ? C15 HUF 901 A 1 
HETATM 33 C C16 HUF . . . D 4 -7.147 60.789 79.893 1 0.5 ? C16 HUF 901 A 1 
HETATM 34 C C17 HUF . . . D 4 -6.463 61.953 79.773 1 0.5 ? C17 HUF 901 A 1 
HETATM 35 C C18 HUF . . . D 4 -6.3 62.595 78.431 1 0.5 ? C18 HUF 901 A 1 
HETATM 36 C C19 HUF . . . D 4 -7.798 58.08 80.267 1 0.5 ? C19 HUF 901 A 1 
HETATM 37 C C20 HUF . . . D 4 -8.363 58.506 82.525 1 0.5 ? C20 HUF 901 A 1 
HETATM 38 C C21 HUF . . . D 4 -7.779 59.08 83.631 1 0.5 ? C21 HUF 901 A 1 
HETATM 39 C C22 HUF . . . D 4 -8.976 57.613 85.049 1 0.5 ? C22 HUF 901 A 1 
HETATM 40 C C23 HUF . . . D 4 -9.228 57.486 82.658 1 0.5 ? C23 HUF 901 A 1 
HETATM 41 C C24 HUF . . . D 4 -6.242 60.69 84.658 1 0.5 ? C24 HUF 901 A 1 
HETATM 42 C C25 HUF . . . D 4 -7.141 61.523 85.503 1 0.5 ? C25 HUF 901 A 1 
HETATM 43 C C26 HUF . . . D 4 -6.559 61.89 86.863 1 0.5 ? C26 HUF 901 A 1 
HETATM 44 C C27 HUF . . . D 4 -7.222 63.133 87.459 1 0.5 ? C27 HUF 901 A 1 
HETATM 45 C C28 HUF . . . D 4 -6.269 64.153 88.027 1 0.5 ? C28 HUF 901 A 1 
HETATM 46 N N29 HUF . . . D 4 -8.025 58.981 81.234 1 0.5 ? N29 HUF 901 A 1 
HETATM 47 N N30 HUF . . . D 4 -8.095 58.634 84.87 1 0.5 ? N30 HUF 901 A 1 
HETATM 48 N N31 HUF . . . D 4 -9.515 57.067 83.931 1 0.5 ? N31 HUF 901 A 1 
HETATM 49 N N32 HUF . . . D 4 -6.938 60.131 83.492 1 0.5 ? N32 HUF 901 A 1 
HETATM 50 O O33 HUF . . . D 4 -7.532 56.946 80.537 1 0.5 ? O33 HUF 901 A 1 
HETATM 51 O O34 HUF . . . D 4 -9.263 57.213 86.154 1 0.5 ? O34 HUF 901 A 1 
HETATM 52 O O35 HUF . . . D 4 -9.783 56.955 81.714 1 0.5 ? O35 HUF 901 A 1 
HETATM 53 O O36 HUF . . . D 4 -7.364 62.71 84.862 1 0.5 ? O36 HUF 901 A 1 
HETATM 54 O O37 HUF . . . D 4 -6.766 60.752 87.725 1 0.5 ? O37 HUF 901 A 1 
HETATM 55 O O38 HUF . . . D 4 -8.008 63.788 86.477 1 0.5 ? O38 HUF 901 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           244 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           55 
#