data_6OB6
#
_model_server_result.job_id            gtol3azJDDkYxqzT-zh4sA 
_model_server_result.datetime_utc      '2024-11-04 18:16:20' 
_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          6ob6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    6OB6 
#
_exptl.entry_id    6OB6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              419.412 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            6-{[(4-nitrophenyl)methyl]sulfanyl}-9-beta-D-ribofuranosyl-9H-purine 
_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            6OB6 
_cell.length_a            72.532 
_cell.length_b            72.532 
_cell.length_c            335.458 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6OB6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C 1 1 
B,D 2 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 
#
_chem_comp.formula           'C17 H17 N5 O6 S' 
_chem_comp.formula_weight    419.412 
_chem_comp.id                NBM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              6-{[(4-nitrophenyl)methyl]sulfanyl}-9-beta-D-ribofuranosyl-9H-purine 
_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
C23 O24 NBM sing 235 n n 
C23 C21 NBM sing 236 n n 
C16 N15 NBM doub 237 n y 
C16 N17 NBM sing 238 n y 
N15 C14 NBM sing 239 n y 
O22 C21 NBM sing 240 n n 
O22 C18 NBM sing 241 n n 
C20 C21 NBM sing 242 n n 
C20 C19 NBM sing 243 n n 
C20 O25 NBM sing 244 n n 
N17 C18 NBM sing 245 n n 
N17 C13 NBM sing 246 n y 
S08 C09 NBM sing 247 n n 
S08 C07 NBM sing 248 n n 
C19 C18 NBM sing 249 n n 
C19 O26 NBM sing 250 n n 
C14 C13 NBM doub 251 n y 
C14 C09 NBM sing 252 n y 
C01 C02 NBM doub 253 n y 
C01 C06 NBM sing 254 n y 
C02 C03 NBM sing 255 n y 
O29 N27 NBM sing 256 n n 
C13 N12 NBM sing 257 n y 
C09 N10 NBM doub 258 n y 
C07 C06 NBM sing 259 n n 
C06 C05 NBM doub 260 n y 
C03 N27 NBM sing 261 n n 
C03 C04 NBM doub 262 n y 
N27 O28 NBM doub 263 n n 
N10 C11 NBM sing 264 n y 
N12 C11 NBM doub 265 n y 
C05 C04 NBM sing 266 n y 
C01 H011 NBM sing 267 n n 
C02 H021 NBM sing 268 n n 
C04 H041 NBM sing 269 n n 
C05 H051 NBM sing 270 n n 
C07 H071 NBM sing 271 n n 
C07 H072 NBM sing 272 n n 
C11 H111 NBM sing 273 n n 
C16 H161 NBM sing 274 n n 
C18 H181 NBM sing 275 n n 
C19 H191 NBM sing 276 n n 
C20 H201 NBM sing 277 n n 
C21 H211 NBM sing 278 n n 
C23 H231 NBM sing 279 n n 
C23 H232 NBM sing 280 n n 
O24 H241 NBM sing 281 n n 
O25 H251 NBM sing 282 n n 
O26 H261 NBM sing 283 n n 
#
_atom_sites.entry_id                     6OB6 
_atom_sites.fract_transf_matrix[1][1]    0.013787 
_atom_sites.fract_transf_matrix[1][2]    0.00796 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01592 
_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]    0.002981 
_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 NBM A 1 501 501 NBM NBM . 
D 2 NBM B 1 501 501 NBM NBM . 
#
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 C01 NBM . . . D 2 4.309 -7.775 28.231 1 30.19 ? C01 NBM 501 B 1 
HETATM 2 C C02 NBM . . . D 2 3.05 -7.267 28.07 1 38.09 ? C02 NBM 501 B 1 
HETATM 3 C C03 NBM . . . D 2 2.689 -6.684 26.844 1 36.01 ? C03 NBM 501 B 1 
HETATM 4 C C04 NBM . . . D 2 3.609 -6.617 25.776 1 44.51 ? C04 NBM 501 B 1 
HETATM 5 C C05 NBM . . . D 2 4.891 -7.142 25.942 1 41.08 ? C05 NBM 501 B 1 
HETATM 6 C C06 NBM . . . D 2 5.256 -7.694 27.154 1 27.38 ? C06 NBM 501 B 1 
HETATM 7 C C07 NBM . . . D 2 6.683 -8.319 27.329 1 46.73 ? C07 NBM 501 B 1 
HETATM 8 C C09 NBM . . . D 2 9.01 -6.666 27.718 1 24.77 ? C09 NBM 501 B 1 
HETATM 9 C C11 NBM . . . D 2 9.889 -5.835 25.707 1 46.89 ? C11 NBM 501 B 1 
HETATM 10 C C13 NBM . . . D 2 10.894 -5.165 27.735 1 26.09 ? C13 NBM 501 B 1 
HETATM 11 C C14 NBM . . . D 2 9.987 -5.926 28.467 1 38.3 ? C14 NBM 501 B 1 
HETATM 12 C C16 NBM . . . D 2 11.362 -4.927 29.892 1 25.18 ? C16 NBM 501 B 1 
HETATM 13 C C18 NBM . . . D 2 12.795 -3.683 28.226 1 35.29 ? C18 NBM 501 B 1 
HETATM 14 C C19 NBM . . . D 2 12.521 -2.427 28.592 1 25.16 ? C19 NBM 501 B 1 
HETATM 15 C C20 NBM . . . D 2 13.835 -1.811 28.912 1 28.82 ? C20 NBM 501 B 1 
HETATM 16 C C21 NBM . . . D 2 14.849 -3.023 28.918 1 30.14 ? C21 NBM 501 B 1 
HETATM 17 C C23 NBM . . . D 2 15.819 -3.01 30.132 1 43.04 ? C23 NBM 501 B 1 
HETATM 18 N N10 NBM . . . D 2 8.975 -6.597 26.376 1 27.61 ? N10 NBM 501 B 1 
HETATM 19 N N12 NBM . . . D 2 10.814 -5.146 26.362 1 25.38 ? N12 NBM 501 B 1 
HETATM 20 N N15 NBM . . . D 2 10.296 -5.759 29.813 1 43.66 ? N15 NBM 501 B 1 
HETATM 21 N N17 NBM . . . D 2 11.727 -4.559 28.614 1 24.78 ? N17 NBM 501 B 1 
HETATM 22 N N27 NBM . . . D 2 1.338 -6.142 26.669 1 37.79 ? N27 NBM 501 B 1 
HETATM 23 O O22 NBM . . . D 2 14.146 -4.079 28.981 1 46.44 ? O22 NBM 501 B 1 
HETATM 24 O O24 NBM . . . D 2 16.573 -4.18 29.995 1 56.58 ? O24 NBM 501 B 1 
HETATM 25 O O25 NBM . . . D 2 14.203 -0.923 27.93 1 47.21 ? O25 NBM 501 B 1 
HETATM 26 O O26 NBM . . . D 2 11.908 -1.693 27.468 1 29.97 ? O26 NBM 501 B 1 
HETATM 27 O O28 NBM . . . D 2 1.016 -5.632 25.588 1 48.66 ? O28 NBM 501 B 1 
HETATM 28 O O29 NBM . . . D 2 0.526 -6.197 27.602 1 44.22 ? O29 NBM 501 B 1 
HETATM 29 S S08 NBM . . . D 2 7.765 -7.667 28.615 1 52.4 ? S08 NBM 501 B 1 
HETATM 30 H H011 NBM . . . D 2 4.551 -8.171 29.037 1 36.23 ? H011 NBM 501 B 1 
HETATM 31 H H021 NBM . . . D 2 2.437 -7.306 28.768 1 45.7 ? H021 NBM 501 B 1 
HETATM 32 H H041 NBM . . . D 2 3.363 -6.226 24.969 1 53.41 ? H041 NBM 501 B 1 
HETATM 33 H H051 NBM . . . D 2 5.499 -7.121 25.238 1 49.3 ? H051 NBM 501 B 1 
HETATM 34 H H071 NBM . . . D 2 6.562 -9.264 27.512 1 56.08 ? H071 NBM 501 B 1 
HETATM 35 H H072 NBM . . . D 2 7.149 -8.212 26.485 1 56.08 ? H072 NBM 501 B 1 
HETATM 36 H H111 NBM . . . D 2 9.863 -5.798 24.778 1 56.26 ? H111 NBM 501 B 1 
HETATM 37 H H161 NBM . . . D 2 11.777 -4.65 30.676 1 30.21 ? H161 NBM 501 B 1 
HETATM 38 H H181 NBM . . . D 2 12.93 -3.719 27.266 1 42.35 ? H181 NBM 501 B 1 
HETATM 39 H H191 NBM . . . D 2 11.941 -2.425 29.37 1 30.19 ? H191 NBM 501 B 1 
HETATM 40 H H201 NBM . . . D 2 13.796 -1.37 29.775 1 34.59 ? H201 NBM 501 B 1 
HETATM 41 H H211 NBM . . . D 2 15.349 -2.966 28.09 1 36.17 ? H211 NBM 501 B 1 
HETATM 42 H H231 NBM . . . D 2 16.393 -2.229 30.101 1 51.65 ? H231 NBM 501 B 1 
HETATM 43 H H232 NBM . . . D 2 15.323 -3.019 30.965 1 51.65 ? H232 NBM 501 B 1 
HETATM 44 H H241 NBM . . . D 2 16.477 -4.487 29.208 1 67.89 ? H241 NBM 501 B 1 
HETATM 45 H H251 NBM . . . D 2 13.515 -0.509 27.653 1 56.65 ? H251 NBM 501 B 1 
HETATM 46 H H261 NBM . . . D 2 11.101 -1.945 27.374 1 35.96 ? H261 NBM 501 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           46 
#