data_6RGF
#
_model_server_result.job_id            Ux9a-fk5y34CWSFEEX7fSQ 
_model_server_result.datetime_utc      '2025-08-15 11:12:24' 
_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          6rgf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    6RGF 
#
_exptl.entry_id    6RGF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              663.536 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2~{R},3~{R},4~{R},5~{R})-2-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-amino]prop-1-ynyl]-6-azanyl-purin-9-yl]-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] dihydrogen 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            6RGF 
_cell.length_a            63.15 
_cell.length_b            75.17 
_cell.length_c            118.59 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6RGF 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D 1 1 
A,B,C,D 1 2 
A,B,C,D 1 3 
A,B,C,D 1 4 
#
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' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 63.15 0 0 
3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 63.15 0 0 
4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C24 H30 N11 O10 P' 
_chem_comp.formula_weight    663.536 
_chem_comp.id                K28 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2~{R},3~{R},4~{R},5~{R})-2-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-methyl-amino]prop-1-ynyl]-6-azanyl-purin-9-yl]-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] dihydrogen 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
N8 C21 K28 sing 193 n n 
N7 C20 K28 sing 194 n y 
N7 C19 K28 doub 195 n y 
C21 C20 K28 doub 196 n y 
C21 N9 K28 sing 197 n y 
C20 C23 K28 sing 198 n y 
C19 N6 K28 sing 199 n y 
O8 C17 K28 sing 200 n n 
C17 C18 K28 sing 201 n n 
C17 C16 K28 sing 202 n n 
N9 C22 K28 doub 203 n y 
O9 C18 K28 sing 204 n n 
C23 N6 K28 sing 205 n y 
C23 N10 K28 doub 206 n y 
N6 C16 K28 sing 207 n n 
C18 C15 K28 sing 208 n n 
C22 N10 K28 sing 209 n y 
C16 O7 K28 sing 210 n n 
C15 O7 K28 sing 211 n n 
C15 C14 K28 sing 212 n n 
C14 N K28 sing 213 n n 
N2 C6 K28 sing 214 n n 
C6 N3 K28 doub 215 n y 
C6 C5 K28 sing 216 n y 
N C K28 sing 217 n n 
N C1 K28 sing 218 n n 
N3 C7 K28 sing 219 n y 
N1 C5 K28 sing 220 n y 
N1 C4 K28 doub 221 n y 
C5 C8 K28 doub 222 n y 
C7 N4 K28 doub 223 n y 
C11 O1 K28 sing 224 n n 
C11 C10 K28 sing 225 n n 
C1 C2 K28 sing 226 n n 
C4 C3 K28 sing 227 n n 
C4 N5 K28 sing 228 n y 
C3 C2 K28 trip 229 n n 
C8 N4 K28 sing 230 n y 
C8 N5 K28 sing 231 n y 
O C10 K28 sing 232 n n 
O C9 K28 sing 233 n n 
N5 C9 K28 sing 234 n n 
C10 C12 K28 sing 235 n n 
C9 C13 K28 sing 236 n n 
C13 C12 K28 sing 237 n n 
C13 O3 K28 sing 238 n n 
C12 O2 K28 sing 239 n n 
O3 P K28 sing 240 n n 
O6 P K28 doub 241 n n 
P O4 K28 sing 242 n n 
P O5 K28 sing 243 n n 
O4 H1 K28 sing 244 n n 
C7 H2 K28 sing 245 n n 
N2 H3 K28 sing 246 n n 
N2 H4 K28 sing 247 n n 
C9 H5 K28 sing 248 n n 
O5 H6 K28 sing 249 n n 
C10 H7 K28 sing 250 n n 
C11 H8 K28 sing 251 n n 
C11 H9 K28 sing 252 n n 
C12 H10 K28 sing 253 n n 
C13 H11 K28 sing 254 n n 
C14 H12 K28 sing 255 n n 
C14 H13 K28 sing 256 n n 
O8 H14 K28 sing 257 n n 
C15 H15 K28 sing 258 n n 
C H17 K28 sing 259 n n 
C H18 K28 sing 260 n n 
C H19 K28 sing 261 n n 
C1 H20 K28 sing 262 n n 
C1 H21 K28 sing 263 n n 
C16 H22 K28 sing 264 n n 
C17 H23 K28 sing 265 n n 
C18 H24 K28 sing 266 n n 
C19 H25 K28 sing 267 n n 
C22 H26 K28 sing 268 n n 
N8 H27 K28 sing 269 n n 
N8 H28 K28 sing 270 n n 
O1 H29 K28 sing 271 n n 
O2 H30 K28 sing 272 n n 
O9 H31 K28 sing 273 n n 
#
_atom_sites.entry_id                     6RGF 
_atom_sites.fract_transf_matrix[1][1]    0.015835 
_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]    0.013303 
_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]    0.008432 
_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 CIT A 1 301 265 CIT CIT . 
C 3 K28 A 1 302 1 K28 XXX . 
D 4 HOH A 1 401 22 HOH HOH . 
D 4 HOH A 2 402 42 HOH HOH . 
D 4 HOH A 3 403 7 HOH HOH . 
D 4 HOH A 4 404 1 HOH HOH . 
D 4 HOH A 5 405 4 HOH HOH . 
D 4 HOH A 6 406 24 HOH HOH . 
D 4 HOH A 7 407 5 HOH HOH . 
D 4 HOH A 8 408 10 HOH HOH . 
D 4 HOH A 9 409 20 HOH HOH . 
D 4 HOH A 10 410 23 HOH HOH . 
D 4 HOH A 11 411 21 HOH HOH . 
D 4 HOH A 12 412 41 HOH HOH . 
D 4 HOH A 13 413 3 HOH HOH . 
D 4 HOH A 14 414 44 HOH HOH . 
D 4 HOH A 15 415 2 HOH HOH . 
D 4 HOH A 16 416 6 HOH HOH . 
D 4 HOH A 17 417 8 HOH HOH . 
D 4 HOH A 18 418 30 HOH HOH . 
D 4 HOH A 19 419 11 HOH HOH . 
D 4 HOH A 20 420 28 HOH HOH . 
D 4 HOH A 21 421 40 HOH HOH . 
D 4 HOH A 22 422 31 HOH HOH . 
D 4 HOH A 23 423 38 HOH HOH . 
D 4 HOH A 24 424 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 O3 K28 . . . C 3 18.402 9.685 16.295 1 97.06 ? O3 K28 302 A 1 
HETATM 2 C C4 K28 . . . C 3 18.355 11.48 12.8 1 56.83 ? C4 K28 302 A 1 
HETATM 3 C C5 K28 . . . C 3 20.206 12.419 12.302 1 52.93 ? C5 K28 302 A 1 
HETATM 4 O O4 K28 . . . C 3 17.189 8.461 18.1 1 109.62 ? O4 K28 302 A 1 
HETATM 5 C C6 K28 . . . C 3 21.27 13.207 11.809 1 48.87 ? C6 K28 302 A 1 
HETATM 6 N N1 K28 . . . C 3 18.828 12.559 12.206 1 55.47 ? N1 K28 302 A 1 
HETATM 7 C C7 K28 . . . C 3 22.706 11.62 12.684 1 46.37 ? C7 K28 302 A 1 
HETATM 8 C C8 K28 . . . C 3 20.555 11.255 12.97 1 52.66 ? C8 K28 302 A 1 
HETATM 9 N N2 K28 . . . C 3 21.097 14.347 11.134 1 49.35 ? N2 K28 302 A 1 
HETATM 10 C C9 K28 . . . C 3 19.227 9.369 13.993 1 75.21 ? C9 K28 302 A 1 
HETATM 11 O O5 K28 . . . C 3 17.95 10.837 18.481 1 107.23 ? O5 K28 302 A 1 
HETATM 12 C C10 K28 . . . C 3 18.243 7.284 13.597 1 76.75 ? C10 K28 302 A 1 
HETATM 13 O O6 K28 . . . C 3 16.052 10.36 16.889 1 107.71 ? O6 K28 302 A 1 
HETATM 14 C C11 K28 . . . C 3 17.053 6.996 12.71 1 72.98 ? C11 K28 302 A 1 
HETATM 15 C C12 K28 . . . C 3 17.895 7.725 15.02 1 80.7 ? C12 K28 302 A 1 
HETATM 16 N N3 K28 . . . C 3 22.528 12.767 12.022 1 47.58 ? N3 K28 302 A 1 
HETATM 17 C C13 K28 . . . C 3 18.056 9.241 14.964 1 84.65 ? C13 K28 302 A 1 
HETATM 18 O O7 K28 . . . C 3 16.036 8.46 9.915 1 70.6 ? O7 K28 302 A 1 
HETATM 19 C C14 K28 . . . C 3 14.013 9.641 10.531 1 71.67 ? C14 K28 302 A 1 
HETATM 20 O O8 K28 . . . C 3 17.645 10.532 7.861 1 62.64 ? O8 K28 302 A 1 
HETATM 21 C C15 K28 . . . C 3 15.388 9.745 9.894 1 69.54 ? C15 K28 302 A 1 
HETATM 22 N N4 K28 . . . C 3 21.788 10.799 13.2 1 47.46 ? N4 K28 302 A 1 
HETATM 23 N N K28 . . . C 3 14.042 9.439 11.978 1 71.37 ? N K28 302 A 1 
HETATM 24 C C K28 . . . C 3 12.806 8.82 12.461 1 71.11 ? C K28 302 A 1 
HETATM 25 O O K28 . . . C 3 19.027 8.357 13.025 1 76.35 ? O K28 302 A 1 
HETATM 26 C C1 K28 . . . C 3 14.364 10.635 12.755 1 71.54 ? C1 K28 302 A 1 
HETATM 27 C C16 K28 . . . C 3 16.98 8.42 8.859 1 67.51 ? C16 K28 302 A 1 
HETATM 28 C C17 K28 . . . C 3 16.624 9.542 7.867 1 63.04 ? C17 K28 302 A 1 
HETATM 29 C C18 K28 . . . C 3 15.296 10.084 8.414 1 61.43 ? C18 K28 302 A 1 
HETATM 30 C C19 K28 . . . C 3 15.937 6.466 7.624 1 61.91 ? C19 K28 302 A 1 
HETATM 31 C C2 K28 . . . C 3 15.802 10.913 12.875 1 70.68 ? C2 K28 302 A 1 
HETATM 32 C C20 K28 . . . C 3 17.541 5.072 7.578 1 59.95 ? C20 K28 302 A 1 
HETATM 33 C C21 K28 . . . C 3 18.433 4.001 7.409 1 54.61 ? C21 K28 302 A 1 
HETATM 34 C C22 K28 . . . C 3 19.995 5.271 8.55 1 55.77 ? C22 K28 302 A 1 
HETATM 35 C C23 K28 . . . C 3 18.009 6.186 8.254 1 60.66 ? C23 K28 302 A 1 
HETATM 36 C C3 K28 . . . C 3 16.976 11.152 12.867 1 62.9 ? C3 K28 302 A 1 
HETATM 37 N N10 K28 . . . C 3 19.236 6.347 8.77 1 56.94 ? N10 K28 302 A 1 
HETATM 38 N N5 K28 . . . C 3 19.355 10.646 13.3 1 60.76 ? N5 K28 302 A 1 
HETATM 39 N N6 K28 . . . C 3 16.973 7.083 8.279 1 64.99 ? N6 K28 302 A 1 
HETATM 40 N N7 K28 . . . C 3 16.22 5.265 7.184 1 64.79 ? N7 K28 302 A 1 
HETATM 41 N N8 K28 . . . C 3 18.126 2.868 6.77 1 52.38 ? N8 K28 302 A 1 
HETATM 42 N N9 K28 . . . C 3 19.678 4.137 7.918 1 54.32 ? N9 K28 302 A 1 
HETATM 43 O O1 K28 . . . C 3 15.952 7.847 13.006 1 69.86 ? O1 K28 302 A 1 
HETATM 44 O O2 K28 . . . C 3 18.808 7.146 15.945 1 79.97 ? O2 K28 302 A 1 
HETATM 45 O O9 K28 . . . C 3 15.189 11.49 8.225 1 58.48 ? O9 K28 302 A 1 
HETATM 46 P P K28 . . . C 3 17.334 9.848 17.514 1 106.28 ? P K28 302 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           46 
#