data_7NDZ
#
_model_server_result.job_id            gztTpKgSIbpC6CntBB1N_g 
_model_server_result.datetime_utc      '2024-10-19 22:24:45' 
_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          7ndz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":302}' 
#
_entry.id    7NDZ 
#
_exptl.entry_id    7NDZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              815.576 
_entity.id                          3 
_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    3 
_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            7NDZ 
_cell.length_a            55.08 
_cell.length_b            117.56 
_cell.length_c            142.19 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7NDZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,E,F,G,H,I,J,K,L,M,N,O 
_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
? 3 F N N 
? 3 H N N 
? 3 J N 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 245 n n 
C19 N29 HUF sing 246 n n 
O37 C26 HUF sing 247 n n 
C24 N32 HUF sing 248 n n 
C24 C25 HUF sing 249 n n 
N29 C15 HUF sing 250 n n 
N29 C20 HUF sing 251 n n 
N32 C21 HUF sing 252 n n 
N32 C14 HUF sing 253 n n 
C15 C14 HUF doub 254 n y 
C15 C16 HUF sing 255 n y 
C20 C21 HUF doub 256 n n 
C20 C23 HUF sing 257 n n 
C21 N30 HUF sing 258 n n 
C14 C13 HUF sing 259 n y 
C16 C17 HUF doub 260 n y 
N30 C22 HUF sing 261 n n 
C13 C12 HUF doub 262 n y 
C23 N31 HUF sing 263 n n 
C23 O35 HUF doub 264 n n 
C22 N31 HUF sing 265 n n 
C22 O34 HUF doub 266 n n 
C17 C12 HUF sing 267 n y 
C17 C18 HUF sing 268 n n 
C12 C11 HUF sing 269 n n 
C26 C25 HUF sing 270 n n 
C26 C27 HUF sing 271 n n 
C25 O36 HUF sing 272 n n 
O2B PB HUF doub 273 n n 
C28 C27 HUF sing 274 n n 
C28 O1B HUF sing 275 n n 
C27 O38 HUF sing 276 n n 
PB O3A HUF sing 277 n n 
PB O1B HUF sing 278 n n 
PB O3B HUF sing 279 n n 
O3A PA HUF sing 280 n n 
O2A PA HUF doub 281 n n 
PA O1A HUF sing 282 n n 
PA O5' HUF sing 283 n n 
C5' O5' HUF sing 284 n n 
C5' C4' HUF sing 285 n n 
N7 C8 HUF doub 286 n y 
N7 C5 HUF sing 287 n y 
C8 N9 HUF sing 288 n y 
N6 C6 HUF sing 289 n n 
O4' C4' HUF sing 290 n n 
O4' C1' HUF sing 291 n n 
C5 C6 HUF doub 292 n y 
C5 C4 HUF sing 293 n y 
C4' C3' HUF sing 294 n n 
N9 C1' HUF sing 295 n n 
N9 C4 HUF sing 296 n y 
C6 N1 HUF sing 297 n y 
C2' C3' HUF sing 298 n n 
C2' C1' HUF sing 299 n n 
C2' O2' HUF sing 300 n n 
C3' O3' HUF sing 301 n n 
C4 N3 HUF doub 302 n y 
N1 C2 HUF doub 303 n y 
N3 C2 HUF sing 304 n y 
O1A H1 HUF sing 305 n n 
O3B H2 HUF sing 306 n n 
C5' H3 HUF sing 307 n n 
C5' H4 HUF sing 308 n n 
C4' H5 HUF sing 309 n n 
C3' H6 HUF sing 310 n n 
O3' H7 HUF sing 311 n n 
C2' H8 HUF sing 312 n n 
O2' H9 HUF sing 313 n n 
C1' H10 HUF sing 314 n n 
C8 H11 HUF sing 315 n n 
C2 H12 HUF sing 316 n n 
N6 H13 HUF sing 317 n n 
N6 H14 HUF sing 318 n n 
C11 H15 HUF sing 319 n n 
C11 H16 HUF sing 320 n n 
C11 H17 HUF sing 321 n n 
C13 H18 HUF sing 322 n n 
C16 H19 HUF sing 323 n n 
C18 H20 HUF sing 324 n n 
C18 H21 HUF sing 325 n n 
C18 H22 HUF sing 326 n n 
C19 H23 HUF sing 327 n n 
C24 H24 HUF sing 328 n n 
C24 H25 HUF sing 329 n n 
C25 H26 HUF sing 330 n n 
C26 H27 HUF sing 331 n n 
C27 H28 HUF sing 332 n n 
C28 H29 HUF sing 333 n n 
C28 H30 HUF sing 334 n n 
N30 H31 HUF sing 335 n n 
N31 H32 HUF sing 336 n n 
O36 H33 HUF sing 337 n n 
O37 H34 HUF sing 338 n n 
O38 H35 HUF sing 339 n n 
#
_atom_sites.entry_id                     7NDZ 
_atom_sites.fract_transf_matrix[1][1]    0.018155 
_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]    0.008506 
_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]    0.007033 
_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
E 2 PGE A 1 301 301 PGE PGE . 
F 3 HUF A 1 302 2 HUF FAC . 
G 4 FDA B 1 301 1 FDA FDA . 
H 3 HUF C 1 301 3 HUF FAC . 
I 5 PEG C 1 302 2 PEG PEG . 
J 3 HUF D 1 301 4 HUF FAC . 
K 5 PEG D 1 302 1 PEG PEG . 
L 6 HOH A 1 401 26 HOH HOH . 
L 6 HOH A 2 402 5 HOH HOH . 
L 6 HOH A 3 403 1 HOH HOH . 
L 6 HOH A 4 404 6 HOH HOH . 
L 6 HOH A 5 405 16 HOH HOH . 
L 6 HOH A 6 406 8 HOH HOH . 
M 6 HOH B 1 401 27 HOH HOH . 
M 6 HOH B 2 402 21 HOH HOH . 
M 6 HOH B 3 403 22 HOH HOH . 
M 6 HOH B 4 404 31 HOH HOH . 
M 6 HOH B 5 405 3 HOH HOH . 
M 6 HOH B 6 406 24 HOH HOH . 
M 6 HOH B 7 407 40 HOH HOH . 
M 6 HOH B 8 408 11 HOH HOH . 
M 6 HOH B 9 409 20 HOH HOH . 
M 6 HOH B 10 410 29 HOH HOH . 
N 6 HOH C 1 401 12 HOH HOH . 
N 6 HOH C 2 402 39 HOH HOH . 
N 6 HOH C 3 403 17 HOH HOH . 
N 6 HOH C 4 404 33 HOH HOH . 
N 6 HOH C 5 405 23 HOH HOH . 
N 6 HOH C 6 406 13 HOH HOH . 
N 6 HOH C 7 407 37 HOH HOH . 
N 6 HOH C 8 408 32 HOH HOH . 
N 6 HOH C 9 409 38 HOH HOH . 
O 6 HOH D 1 401 10 HOH HOH . 
O 6 HOH D 2 402 35 HOH HOH . 
O 6 HOH D 3 403 34 HOH HOH . 
O 6 HOH D 4 404 30 HOH HOH . 
O 6 HOH D 5 405 4 HOH HOH . 
O 6 HOH D 6 406 9 HOH HOH . 
O 6 HOH D 7 407 7 HOH HOH . 
O 6 HOH D 8 408 18 HOH HOH . 
O 6 HOH D 9 409 19 HOH HOH . 
O 6 HOH D 10 410 14 HOH HOH . 
O 6 HOH D 11 411 2 HOH HOH . 
O 6 HOH D 12 412 25 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 O O2A HUF . . . F 3 -12.854 12.397 -21.005 0.9 58.63 ? O2A HUF 302 A 1 
HETATM 2 P PA HUF . . . F 3 -13.671 13.635 -20.931 0.9 60.38 ? PA HUF 302 A 1 
HETATM 3 O O1A HUF . . . F 3 -12.979 14.709 -20.109 0.9 62.06 ? O1A HUF 302 A 1 
HETATM 4 O O3A HUF . . . F 3 -15.066 13.323 -20.237 0.9 59.94 ? O3A HUF 302 A 1 
HETATM 5 P PB HUF . . . F 3 -16.146 12.192 -20.522 0.9 59.71 ? PB HUF 302 A 1 
HETATM 6 O O3B HUF . . . F 3 -15.522 11.08 -21.281 0.9 58.19 ? O3B HUF 302 A 1 
HETATM 7 O O2B HUF . . . F 3 -17.309 12.784 -21.282 0.9 59.98 ? O2B HUF 302 A 1 
HETATM 8 O O1B HUF . . . F 3 -16.732 11.83 -19.108 0.9 62.86 ? O1B HUF 302 A 1 
HETATM 9 O O5' HUF . . . F 3 -14.02 14.294 -22.295 0.9 59.41 ? O5' HUF 302 A 1 
HETATM 10 C C5' HUF . . . F 3 -14.902 15.391 -22.608 0.9 57.59 ? C5' HUF 302 A 1 
HETATM 11 C C4' HUF . . . F 3 -15.541 15.128 -23.947 0.9 55.6 ? C4' HUF 302 A 1 
HETATM 12 C C3' HUF . . . F 3 -16.489 13.938 -23.972 0.9 56.49 ? C3' HUF 302 A 1 
HETATM 13 O O3' HUF . . . F 3 -17.814 14.351 -23.661 0.9 58.92 ? O3' HUF 302 A 1 
HETATM 14 C C2' HUF . . . F 3 -16.366 13.424 -25.407 0.9 56.17 ? C2' HUF 302 A 1 
HETATM 15 O O2' HUF . . . F 3 -17.255 14.093 -26.292 0.9 59.06 ? O2' HUF 302 A 1 
HETATM 16 C C1' HUF . . . F 3 -14.922 13.778 -25.763 0.9 54.21 ? C1' HUF 302 A 1 
HETATM 17 O O4' HUF . . . F 3 -14.509 14.824 -24.906 0.9 54.66 ? O4' HUF 302 A 1 
HETATM 18 N N9 HUF . . . F 3 -13.949 12.687 -25.7 0.9 51.93 ? N9 HUF 302 A 1 
HETATM 19 C C4 HUF . . . F 3 -13.836 11.644 -26.589 0.9 51.3 ? C4 HUF 302 A 1 
HETATM 20 C C5 HUF . . . F 3 -12.648 11.003 -26.268 0.9 52.24 ? C5 HUF 302 A 1 
HETATM 21 N N7 HUF . . . F 3 -12.004 11.658 -25.23 0.9 50.85 ? N7 HUF 302 A 1 
HETATM 22 C C8 HUF . . . F 3 -12.809 12.653 -24.942 0.9 50.33 ? C8 HUF 302 A 1 
HETATM 23 N N3 HUF . . . F 3 -14.699 11.295 -27.556 0.9 49.58 ? N3 HUF 302 A 1 
HETATM 24 C C2 HUF . . . F 3 -14.307 10.178 -28.174 0.9 49.11 ? C2 HUF 302 A 1 
HETATM 25 N N1 HUF . . . F 3 -13.197 9.46 -27.977 0.9 52.3 ? N1 HUF 302 A 1 
HETATM 26 C C6 HUF . . . F 3 -12.33 9.845 -27.01 0.9 54.08 ? C6 HUF 302 A 1 
HETATM 27 N N6 HUF . . . F 3 -11.247 9.085 -26.784 0.9 53.35 ? N6 HUF 302 A 1 
HETATM 28 C C11 HUF . . . F 3 -21.297 10.453 -14.313 0.9 71.34 ? C11 HUF 302 A 1 
HETATM 29 C C12 HUF . . . F 3 -20.991 8.981 -14.219 0.9 71.37 ? C12 HUF 302 A 1 
HETATM 30 C C13 HUF . . . F 3 -19.822 8.498 -14.801 0.9 71.06 ? C13 HUF 302 A 1 
HETATM 31 C C14 HUF . . . F 3 -19.499 7.143 -14.745 0.9 70.71 ? C14 HUF 302 A 1 
HETATM 32 C C15 HUF . . . F 3 -20.387 6.234 -14.091 0.9 71.25 ? C15 HUF 302 A 1 
HETATM 33 C C16 HUF . . . F 3 -21.555 6.727 -13.528 0.9 70.61 ? C16 HUF 302 A 1 
HETATM 34 C C17 HUF . . . F 3 -21.873 8.08 -13.573 0.9 70.02 ? C17 HUF 302 A 1 
HETATM 35 C C18 HUF . . . F 3 -23.161 8.553 -12.949 0.9 67.75 ? C18 HUF 302 A 1 
HETATM 36 C C19 HUF . . . F 3 -19.881 4.341 -12.443 0.9 70.77 ? C19 HUF 302 A 1 
HETATM 37 C C20 HUF . . . F 3 -18.975 4.356 -14.838 0.9 68.85 ? C20 HUF 302 A 1 
HETATM 38 C C21 HUF . . . F 3 -18.114 5.247 -15.447 0.9 68.63 ? C21 HUF 302 A 1 
HETATM 39 C C22 HUF . . . F 3 -16.818 3.423 -16.389 0.9 64.75 ? C22 HUF 302 A 1 
HETATM 40 C C23 HUF . . . F 3 -18.797 2.888 -15.017 0.9 67.93 ? C23 HUF 302 A 1 
HETATM 41 C C24 HUF . . . F 3 -17.333 7.531 -15.944 0.9 69.16 ? C24 HUF 302 A 1 
HETATM 42 C C25 HUF . . . F 3 -17.673 7.893 -17.389 0.9 69.27 ? C25 HUF 302 A 1 
HETATM 43 C C26 HUF . . . F 3 -16.682 8.908 -17.96 0.9 67.06 ? C26 HUF 302 A 1 
HETATM 44 C C27 HUF . . . F 3 -16.741 10.28 -17.286 0.9 66.75 ? C27 HUF 302 A 1 
HETATM 45 C C28 HUF . . . F 3 -15.932 11.325 -18.022 0.9 65.8 ? C28 HUF 302 A 1 
HETATM 46 N N29 HUF . . . F 3 -20.1 4.797 -13.984 0.9 70.79 ? N29 HUF 302 A 1 
HETATM 47 N N30 HUF . . . F 3 -17.068 4.756 -16.194 0.9 66.73 ? N30 HUF 302 A 1 
HETATM 48 N N31 HUF . . . F 3 -17.697 2.553 -15.792 0.9 67.02 ? N31 HUF 302 A 1 
HETATM 49 N N32 HUF . . . F 3 -18.305 6.619 -15.324 0.9 69.3 ? N32 HUF 302 A 1 
HETATM 50 O O33 HUF . . . F 3 -19.067 5.295 -11.826 0.9 70.89 ? O33 HUF 302 A 1 
HETATM 51 O O34 HUF . . . F 3 -15.867 3.033 -17.053 0.9 62.6 ? O34 HUF 302 A 1 
HETATM 52 O O35 HUF . . . F 3 -19.496 1.999 -14.54 0.9 67.46 ? O35 HUF 302 A 1 
HETATM 53 O O36 HUF . . . F 3 -17.69 6.73 -18.217 0.9 71.54 ? O36 HUF 302 A 1 
HETATM 54 O O37 HUF . . . F 3 -15.359 8.396 -17.834 0.9 66.44 ? O37 HUF 302 A 1 
HETATM 55 O O38 HUF . . . F 3 -18.098 10.7 -17.125 0.9 67.02 ? O38 HUF 302 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           55 
#