data_6NZD
#
_model_server_result.job_id            NO6rY853WVAg5JlhJa037w 
_model_server_result.datetime_utc      '2025-08-31 10:07:14' 
_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          6nzd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":500}' 
#
_entry.id    6NZD 
#
_exptl.entry_id    6NZD 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              540.231 
_entity.id                          11 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione 
_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            6NZD 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6NZD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    nonameric 
_pdbx_struct_assembly.oligomeric_count      9 
_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 
_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    ? 
_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                      11 
_struct_asym.id                             K 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_struct_conn.conn_type_id                   disulf 
_struct_conn.details                        ? 
_struct_conn.id                             disulf1 
_struct_conn.ptnr1_label_asym_id            H 
_struct_conn.ptnr1_label_atom_id            SG 
_struct_conn.ptnr1_label_comp_id            CYS 
_struct_conn.ptnr1_label_seq_id             51 
_struct_conn.ptnr1_auth_asym_id             H 
_struct_conn.ptnr1_auth_comp_id             CYS 
_struct_conn.ptnr1_auth_seq_id              8 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            H 
_struct_conn.ptnr2_label_atom_id            SG 
_struct_conn.ptnr2_label_comp_id            CYS 
_struct_conn.ptnr2_label_seq_id             168 
_struct_conn.ptnr2_auth_asym_id             H 
_struct_conn.ptnr2_auth_comp_id             CYS 
_struct_conn.ptnr2_auth_seq_id              125 
_struct_conn.ptnr2_symmetry                 1_555 
_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                2.032 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C10 H15 N4 O14 P3 S' 
_chem_comp.formula_weight    540.231 
_chem_comp.id                L8S 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              9-{5-O-[(S)-hydroxy{[(R)-hydroxy(thiophosphonooxy)phosphoryl]oxy}phosphoryl]-alpha-L-arabinofuranosyl}-3,9-dihydro-1H-purine-2,6-dione 
_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
O6 C6 L8S doub 216 n n 
N7 C5 L8S sing 217 n y 
N7 C8 L8S doub 218 n y 
C6 C5 L8S sing 219 n n 
C6 N1 L8S sing 220 n n 
C5 C4 L8S doub 221 n y 
N1 C2 L8S sing 222 n n 
C8 N9 L8S sing 223 n y 
C4 N9 L8S sing 224 n y 
C4 N3 L8S sing 225 n n 
N9 C1' L8S sing 226 n n 
C2 N3 L8S sing 227 n n 
C2 O2 L8S doub 228 n n 
O2A PA L8S doub 229 n n 
O4' C1' L8S sing 230 n n 
O4' C4' L8S sing 231 n n 
C1' C2' L8S sing 232 n n 
O2B PB L8S doub 233 n n 
O1B PB L8S sing 234 n n 
C2' O2' L8S sing 235 n n 
C2' C3' L8S sing 236 n n 
C4' C3' L8S sing 237 n n 
C4' C5' L8S sing 238 n n 
PA O5' L8S sing 239 n n 
PA O3A L8S sing 240 n n 
PA O1A L8S sing 241 n n 
PB O3A L8S sing 242 n n 
PB O3B L8S sing 243 n n 
O5' C5' L8S sing 244 n n 
C3' O3' L8S sing 245 n n 
O1G PG L8S sing 246 n n 
O2G PG L8S sing 247 n n 
O3B PG L8S sing 248 n n 
PG S3G L8S doub 249 n n 
N1 H1 L8S sing 250 n n 
N3 H2 L8S sing 251 n n 
C8 H3 L8S sing 252 n n 
C1' H4 L8S sing 253 n n 
C2' H5 L8S sing 254 n n 
C3' H6 L8S sing 255 n n 
C4' H7 L8S sing 256 n n 
C5' H8 L8S sing 257 n n 
C5' H9 L8S sing 258 n n 
O1A H10 L8S sing 259 n n 
O1B H11 L8S sing 260 n n 
O2' H12 L8S sing 261 n n 
O2G H13 L8S sing 262 n n 
O3' H14 L8S sing 263 n n 
O1G H16 L8S sing 264 n n 
#
_atom_sites.entry_id                     6NZD 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
J 10 GDP F 1 500 500 GDP GDP . 
K 11 L8S G 1 500 500 L8S L8S . 
#
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 L8S . . . K 11 224.686 209.092 203.019 1 24.5 ? N1 L8S 500 G 1 
HETATM 2 N N3 L8S . . . K 11 224.413 207.64 204.856 1 24.5 ? N3 L8S 500 G 1 
HETATM 3 C C4 L8S . . . K 11 224.42 206.584 204.009 1 24.5 ? C4 L8S 500 G 1 
HETATM 4 C C5 L8S . . . K 11 224.556 206.76 202.655 1 24.5 ? C5 L8S 500 G 1 
HETATM 5 C C6 L8S . . . K 11 224.699 208.054 202.085 1 24.5 ? C6 L8S 500 G 1 
HETATM 6 C C8 L8S . . . K 11 224.376 204.639 203.026 1 24.5 ? C8 L8S 500 G 1 
HETATM 7 C C1' L8S . . . K 11 224.142 204.626 205.565 1 24.5 ? C1' L8S 500 G 1 
HETATM 8 C C2 L8S . . . K 11 224.547 208.916 204.374 1 24.5 ? C2 L8S 500 G 1 
HETATM 9 C C2' L8S . . . K 11 222.748 204.729 206.172 1 24.5 ? C2' L8S 500 G 1 
HETATM 10 C C3' L8S . . . K 11 222.881 203.651 207.248 1 24.5 ? C3' L8S 500 G 1 
HETATM 11 C C4' L8S . . . K 11 223.625 202.544 206.486 1 24.5 ? C4' L8S 500 G 1 
HETATM 12 C C5' L8S . . . K 11 224.542 201.68 207.316 1 24.5 ? C5' L8S 500 G 1 
HETATM 13 N N7 L8S . . . K 11 224.527 205.506 202.044 1 24.5 ? N7 L8S 500 G 1 
HETATM 14 N N9 L8S . . . K 11 224.3 205.238 204.26 1 24.5 ? N9 L8S 500 G 1 
HETATM 15 O O1A L8S . . . K 11 222.559 199.63 207.488 1 24.5 ? O1A L8S 500 G 1 
HETATM 16 O O1B L8S . . . K 11 226.732 198.051 206.072 1 24.5 ? O1B L8S 500 G 1 
HETATM 17 O O1G L8S . . . K 11 226.663 194.147 207.394 1 24.5 ? O1G L8S 500 G 1 
HETATM 18 O O2 L8S . . . K 11 224.542 209.865 205.141 1 24.5 ? O2 L8S 500 G 1 
HETATM 19 O O2' L8S . . . K 11 222.461 206.016 206.674 1 24.5 ? O2' L8S 500 G 1 
HETATM 20 O O2A L8S . . . K 11 223.305 199.127 205.078 1 24.5 ? O2A L8S 500 G 1 
HETATM 21 O O2B L8S . . . K 11 225.107 196.102 205.595 1 24.5 ? O2B L8S 500 G 1 
HETATM 22 O O2G L8S . . . K 11 228.417 195.896 207.521 1 24.5 ? O2G L8S 500 G 1 
HETATM 23 O O3' L8S . . . K 11 221.647 203.208 207.799 1 24.5 ? O3' L8S 500 G 1 
HETATM 24 O O3A L8S . . . K 11 224.419 198.033 207.058 1 24.5 ? O3A L8S 500 G 1 
HETATM 25 O O3B L8S . . . K 11 226.095 196.438 207.878 1 24.5 ? O3B L8S 500 G 1 
HETATM 26 O O4' L8S . . . K 11 224.39 203.238 205.464 1 24.5 ? O4' L8S 500 G 1 
HETATM 27 O O5' L8S . . . K 11 224.812 200.429 206.635 1 24.5 ? O5' L8S 500 G 1 
HETATM 28 O O6 L8S . . . K 11 224.83 208.325 200.888 1 24.5 ? O6 L8S 500 G 1 
HETATM 29 P PA L8S . . . K 11 223.65 199.329 206.515 1 24.5 ? PA L8S 500 G 1 
HETATM 30 P PB L8S . . . K 11 225.635 197.146 206.519 1 24.5 ? PB L8S 500 G 1 
HETATM 31 P PG L8S . . . K 11 227.202 195.309 208.182 1 24.5 ? PG L8S 500 G 1 
HETATM 32 S S3G L8S . . . K 11 227.317 195.052 210.106 1 24.5 ? S3G L8S 500 G 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           412 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           32 
#