data_6RGD
#
_model_server_result.job_id            Q4iYE5_-C3nMDKLorGeKnw 
_model_server_result.datetime_utc      '2024-11-24 23:38:02' 
_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          6rgd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    6RGD 
#
_exptl.entry_id    6RGD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              583.557 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[4-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]but-3-ynylamino]methyl]oxolane-3,4-diol 
_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            6RGD 
_cell.length_a            63.282 
_cell.length_b            74.981 
_cell.length_c            118.959 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6RGD 
_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    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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
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 63.282 0 0 
3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 63.282 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 H29 N11 O7' 
_chem_comp.formula_weight    583.557 
_chem_comp.id                K2W 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[4-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]but-3-ynylamino]methyl]oxolane-3,4-diol 
_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
N3 C7 K2W sing 193 n n 
N2 C5 K2W doub 194 n y 
N2 C6 K2W sing 195 n y 
C7 C6 K2W doub 196 n y 
C7 N4 K2W sing 197 n y 
C5 N1 K2W sing 198 n y 
C6 C9 K2W sing 199 n y 
C1 O1 K2W sing 200 n n 
C1 C2 K2W sing 201 n n 
C1 C4 K2W sing 202 n n 
N4 C8 K2W doub 203 n y 
N1 C9 K2W sing 204 n y 
N1 C4 K2W sing 205 n n 
O7 C2 K2W sing 206 n n 
C2 C3 K2W sing 207 n n 
C9 N5 K2W doub 208 n y 
C8 N5 K2W sing 209 n y 
C4 O2 K2W sing 210 n n 
O2 C3 K2W sing 211 n n 
C3 C10 K2W sing 212 n n 
C10 N6 K2W sing 213 n n 
N11 C17 K2W sing 214 n n 
N6 C11 K2W sing 215 n n 
C17 N8 K2W doub 216 n y 
C17 C16 K2W sing 217 n y 
N8 C18 K2W sing 218 n y 
N7 C16 K2W sing 219 n y 
N7 C15 K2W doub 220 n y 
C16 C19 K2W doub 221 n y 
C11 C12 K2W sing 222 n n 
C18 N9 K2W doub 223 n y 
C15 C14 K2W sing 224 n n 
C15 N10 K2W sing 225 n y 
C19 N9 K2W sing 226 n y 
C19 N10 K2W sing 227 n y 
O6 C23 K2W sing 228 n n 
O6 C20 K2W sing 229 n n 
C24 C23 K2W sing 230 n n 
C24 O5 K2W sing 231 n n 
C14 C13 K2W trip 232 n n 
C13 C12 K2W sing 233 n n 
N10 C20 K2W sing 234 n n 
C23 C22 K2W sing 235 n n 
C20 C21 K2W sing 236 n n 
C21 C22 K2W sing 237 n n 
C21 O3 K2W sing 238 n n 
C22 O4 K2W sing 239 n n 
C2 H1 K2W sing 240 n n 
C3 H2 K2W sing 241 n n 
C4 H3 K2W sing 242 n n 
C5 H4 K2W sing 243 n n 
C10 H5 K2W sing 244 n n 
C10 H6 K2W sing 245 n n 
C11 H7 K2W sing 246 n n 
C11 H8 K2W sing 247 n n 
C12 H9 K2W sing 248 n n 
C12 H10 K2W sing 249 n n 
C18 H11 K2W sing 250 n n 
C20 H12 K2W sing 251 n n 
C21 H13 K2W sing 252 n n 
C1 H14 K2W sing 253 n n 
C22 H15 K2W sing 254 n n 
C23 H16 K2W sing 255 n n 
C24 H17 K2W sing 256 n n 
C24 H18 K2W sing 257 n n 
C8 H19 K2W sing 258 n n 
N11 H20 K2W sing 259 n n 
N11 H21 K2W sing 260 n n 
N3 H22 K2W sing 261 n n 
N3 H23 K2W sing 262 n n 
N6 H24 K2W sing 263 n n 
O1 H26 K2W sing 264 n n 
O3 H27 K2W sing 265 n n 
O4 H28 K2W sing 266 n n 
O5 H29 K2W sing 267 n n 
O7 H30 K2W sing 268 n n 
#
_atom_sites.entry_id                     6RGD 
_atom_sites.fract_transf_matrix[1][1]    0.015802 
_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]    0.013337 
_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]    0.008406 
_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 1 CIT CIT . 
C 3 K2W A 1 302 1 K2W PDB . 
D 4 HOH A 1 401 66 HOH HOH . 
D 4 HOH A 2 402 8 HOH HOH . 
D 4 HOH A 3 403 21 HOH HOH . 
D 4 HOH A 4 404 2 HOH HOH . 
D 4 HOH A 5 405 23 HOH HOH . 
D 4 HOH A 6 406 1 HOH HOH . 
D 4 HOH A 7 407 12 HOH HOH . 
D 4 HOH A 8 408 38 HOH HOH . 
D 4 HOH A 9 409 37 HOH HOH . 
D 4 HOH A 10 410 43 HOH HOH . 
D 4 HOH A 11 411 59 HOH HOH . 
D 4 HOH A 12 412 10 HOH HOH . 
D 4 HOH A 13 413 39 HOH HOH . 
D 4 HOH A 14 414 7 HOH HOH . 
D 4 HOH A 15 415 6 HOH HOH . 
D 4 HOH A 16 416 14 HOH HOH . 
D 4 HOH A 17 417 11 HOH HOH . 
D 4 HOH A 18 418 81 HOH HOH . 
D 4 HOH A 19 419 60 HOH HOH . 
D 4 HOH A 20 420 9 HOH HOH . 
D 4 HOH A 21 421 47 HOH HOH . 
D 4 HOH A 22 422 49 HOH HOH . 
D 4 HOH A 23 423 65 HOH HOH . 
D 4 HOH A 24 424 13 HOH HOH . 
D 4 HOH A 25 425 79 HOH HOH . 
D 4 HOH A 26 426 27 HOH HOH . 
D 4 HOH A 27 427 18 HOH HOH . 
D 4 HOH A 28 428 73 HOH HOH . 
D 4 HOH A 29 429 16 HOH HOH . 
D 4 HOH A 30 430 15 HOH HOH . 
D 4 HOH A 31 431 72 HOH HOH . 
D 4 HOH A 32 432 20 HOH HOH . 
D 4 HOH A 33 433 74 HOH HOH . 
D 4 HOH A 34 434 32 HOH HOH . 
D 4 HOH A 35 435 54 HOH HOH . 
D 4 HOH A 36 436 3 HOH HOH . 
D 4 HOH A 37 437 48 HOH HOH . 
D 4 HOH A 38 438 45 HOH HOH . 
D 4 HOH A 39 439 63 HOH HOH . 
D 4 HOH A 40 440 55 HOH HOH . 
D 4 HOH A 41 441 28 HOH HOH . 
D 4 HOH A 42 442 53 HOH HOH . 
D 4 HOH A 43 443 69 HOH HOH . 
D 4 HOH A 44 444 64 HOH HOH . 
D 4 HOH A 45 445 62 HOH HOH . 
D 4 HOH A 46 446 80 HOH HOH . 
D 4 HOH A 47 447 30 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 C C2 K2W . . . C 3 15.391 9.944 8.227 0.8 37.21 ? C2 K2W 302 A 1 
HETATM 2 C C3 K2W . . . C 3 15.229 9.471 9.629 0.8 39.54 ? C3 K2W 302 A 1 
HETATM 3 C C4 K2W . . . C 3 16.862 8.171 8.828 0.8 42.86 ? C4 K2W 302 A 1 
HETATM 4 C C5 K2W . . . C 3 16.034 6.241 7.472 0.8 43.91 ? C5 K2W 302 A 1 
HETATM 5 C C6 K2W . . . C 3 17.761 4.977 7.553 0.8 42.35 ? C6 K2W 302 A 1 
HETATM 6 C C7 K2W . . . C 3 18.678 4.03 7.452 0.8 37.99 ? C7 K2W 302 A 1 
HETATM 7 N N8 K2W . . . C 3 22.825 12.804 11.903 0.8 39.62 ? N8 K2W 302 A 1 
HETATM 8 N N9 K2W . . . C 3 22.157 10.839 12.954 0.8 37.58 ? N9 K2W 302 A 1 
HETATM 9 C C10 K2W . . . C 3 13.749 9.371 9.98 0.8 40.67 ? C10 K2W 302 A 1 
HETATM 10 C C11 K2W . . . C 3 14.374 9.293 12.338 0.8 39.18 ? C11 K2W 302 A 1 
HETATM 11 C C12 K2W . . . C 3 14.833 10.41 13.27 0.8 41.48 ? C12 K2W 302 A 1 
HETATM 12 C C14 K2W . . . C 3 17.407 10.992 12.921 0.8 40.85 ? C14 K2W 302 A 1 
HETATM 13 C C16 K2W . . . C 3 20.535 12.307 12.193 0.8 41.32 ? C16 K2W 302 A 1 
HETATM 14 C C18 K2W . . . C 3 23.156 11.684 12.498 0.8 36.68 ? C18 K2W 302 A 1 
HETATM 15 C C19 K2W . . . C 3 20.874 11.17 12.79 0.8 41.01 ? C19 K2W 302 A 1 
HETATM 16 C C20 K2W . . . C 3 19.788 9.259 13.822 0.8 42.35 ? C20 K2W 302 A 1 
HETATM 17 C C21 K2W . . . C 3 18.64 9.144 14.764 0.8 48.23 ? C21 K2W 302 A 1 
HETATM 18 C C1 K2W . . . C 3 16.682 9.278 7.823 0.8 38.78 ? C1 K2W 302 A 1 
HETATM 19 C C13 K2W . . . C 3 16.258 10.73 13.073 0.8 43.16 ? C13 K2W 302 A 1 
HETATM 20 C C15 K2W . . . C 3 18.755 11.294 12.746 0.8 39.68 ? C15 K2W 302 A 1 
HETATM 21 C C17 K2W . . . C 3 21.484 13.119 11.752 0.8 40.53 ? C17 K2W 302 A 1 
HETATM 22 C C22 K2W . . . C 3 18.671 7.679 14.984 0.8 50.56 ? C22 K2W 302 A 1 
HETATM 23 C C23 K2W . . . C 3 18.869 7.162 13.581 0.8 48.55 ? C23 K2W 302 A 1 
HETATM 24 C C24 K2W . . . C 3 17.518 7.001 12.892 0.8 54.77 ? C24 K2W 302 A 1 
HETATM 25 C C8 K2W . . . C 3 20.183 5.26 8.729 0.8 38.55 ? C8 K2W 302 A 1 
HETATM 26 C C9 K2W . . . C 3 18.03 6.08 8.236 0.8 43.21 ? C9 K2W 302 A 1 
HETATM 27 N N1 K2W . . . C 3 16.965 6.861 8.183 0.8 44.3 ? N1 K2W 302 A 1 
HETATM 28 N N10 K2W . . . C 3 19.766 10.541 13.135 0.8 40.19 ? N10 K2W 302 A 1 
HETATM 29 N N11 K2W . . . C 3 21.085 14.234 11.163 0.8 36.56 ? N11 K2W 302 A 1 
HETATM 30 N N2 K2W . . . C 3 16.527 5.076 7.081 0.8 45.53 ? N2 K2W 302 A 1 
HETATM 31 N N3 K2W . . . C 3 18.351 2.952 6.756 0.8 37.86 ? N3 K2W 302 A 1 
HETATM 32 N N4 K2W . . . C 3 19.919 4.169 8.053 0.8 37.81 ? N4 K2W 302 A 1 
HETATM 33 N N5 K2W . . . C 3 19.214 6.246 8.827 0.8 39.7 ? N5 K2W 302 A 1 
HETATM 34 N N6 K2W . . . C 3 13.454 9.843 11.337 0.8 43.49 ? N6 K2W 302 A 1 
HETATM 35 N N7 K2W . . . C 3 19.212 12.386 12.165 0.8 40.86 ? N7 K2W 302 A 1 
HETATM 36 O O1 K2W . . . C 3 17.739 10.197 7.99 0.8 42.07 ? O1 K2W 302 A 1 
HETATM 37 O O2 K2W . . . C 3 15.656 8.134 9.553 0.8 45.08 ? O2 K2W 302 A 1 
HETATM 38 O O3 K2W . . . C 3 18.968 9.809 15.983 0.8 48.46 ? O3 K2W 302 A 1 
HETATM 39 O O4 K2W . . . C 3 19.824 7.368 15.755 0.8 51.16 ? O4 K2W 302 A 1 
HETATM 40 O O5 K2W . . . C 3 16.568 6.46 13.802 0.8 62.03 ? O5 K2W 302 A 1 
HETATM 41 O O6 K2W . . . C 3 19.573 8.201 12.887 0.8 48.69 ? O6 K2W 302 A 1 
HETATM 42 O O7 K2W . . . C 3 15.558 11.36 8.227 0.8 33.54 ? O7 K2W 302 A 1 
#
_model_server_stats.io_time_ms              92 
_model_server_stats.parse_time_ms           30 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           1044 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           42 
#