data_6NR5
#
_model_server_result.job_id            '_I_aoSXPQyePjh5cC7LgLw' 
_model_server_result.datetime_utc      '2025-02-05 04:46:25' 
_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          6nr5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":901}' 
#
_entry.id    6NR5 
#
_exptl.entry_id    6NR5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              891.715 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R)-5-[(4aR)-7,8-dimethyl-2,4-dioxo-5-(2-phenylethyl)-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)' 
_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         120 
_cell.entry_id            6NR5 
_cell.length_a            189.361 
_cell.length_b            189.361 
_cell.length_c            109.031 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6NR5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C35 H43 N9 O15 P2' 
_chem_comp.formula_weight    891.715 
_chem_comp.id                KXM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R)-5-[(4aR)-7,8-dimethyl-2,4-dioxo-5-(2-phenylethyl)-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)' 
_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
C14 C15 KXM doub 171 n y 
C14 C13 KXM sing 172 n y 
C15 C16 KXM sing 173 n y 
C13 C12 KXM doub 174 n y 
C16 C11 KXM doub 175 n y 
C12 C11 KXM sing 176 n y 
C11 C10 KXM sing 177 n n 
C10 C9 KXM sing 178 n n 
O4 C23 KXM sing 179 n n 
C21 N4 KXM sing 180 n n 
C21 C22 KXM sing 181 n n 
N1 C5 KXM sing 182 n n 
N1 C9 KXM sing 183 n n 
N1 C17 KXM sing 184 n n 
N4 C4 KXM sing 185 n n 
N4 C20 KXM sing 186 n n 
C5 C4 KXM doub 187 n y 
C5 C6 KXM sing 188 n y 
N3 C20 KXM doub 189 n n 
N3 C19 KXM sing 190 n n 
C4 C3 KXM sing 191 n y 
C6 C7 KXM doub 192 n y 
C20 C17 KXM sing 193 n n 
C3 C2 KXM doub 194 n y 
N2 C19 KXM sing 195 n n 
N2 C18 KXM sing 196 n n 
C19 O2 KXM doub 197 n n 
C7 C2 KXM sing 198 n y 
C7 C8 KXM sing 199 n n 
C2 C1 KXM sing 200 n n 
C18 C17 KXM sing 201 n n 
C18 O1 KXM doub 202 n n 
C23 C22 KXM sing 203 n n 
C23 C24 KXM sing 204 n n 
C22 O3 KXM sing 205 n n 
O8 P1 KXM doub 206 n n 
C25 C24 KXM sing 207 n n 
C25 O6 KXM sing 208 n n 
C24 O5 KXM sing 209 n n 
O9 P1 KXM sing 210 n n 
O9 P2 KXM sing 211 n n 
P1 O6 KXM sing 212 n n 
P1 O7 KXM sing 213 n n 
O10 P2 KXM doub 214 n n 
P2 O11 KXM sing 215 n n 
P2 O12 KXM sing 216 n n 
N6 C29 KXM doub 217 n y 
N6 C30 KXM sing 218 n y 
C26 O12 KXM sing 219 n n 
C26 C27 KXM sing 220 n n 
C29 N5 KXM sing 221 n y 
N7 C31 KXM sing 222 n n 
C30 C31 KXM doub 223 n y 
C30 C33 KXM sing 224 n y 
C31 N8 KXM sing 225 n y 
O13 C27 KXM sing 226 n n 
O13 C28 KXM sing 227 n n 
N5 C33 KXM sing 228 n y 
N5 C28 KXM sing 229 n n 
C27 C35 KXM sing 230 n n 
C33 N9 KXM doub 231 n y 
C28 C34 KXM sing 232 n n 
C34 C35 KXM sing 233 n n 
C34 O14 KXM sing 234 n n 
C35 O15 KXM sing 235 n n 
N8 C32 KXM doub 236 n y 
N9 C32 KXM sing 237 n y 
C14 H1 KXM sing 238 n n 
C6 H2 KXM sing 239 n n 
C8 H3 KXM sing 240 n n 
C8 H4 KXM sing 241 n n 
C8 H5 KXM sing 242 n n 
C9 H6 KXM sing 243 n n 
C9 H7 KXM sing 244 n n 
C10 H8 KXM sing 245 n n 
C10 H9 KXM sing 246 n n 
C12 H10 KXM sing 247 n n 
C13 H11 KXM sing 248 n n 
N2 H12 KXM sing 249 n n 
C3 H13 KXM sing 250 n n 
C1 H14 KXM sing 251 n n 
C1 H15 KXM sing 252 n n 
C1 H16 KXM sing 253 n n 
C15 H17 KXM sing 254 n n 
C16 H18 KXM sing 255 n n 
C17 H19 KXM sing 256 n n 
C21 H20 KXM sing 257 n n 
C21 H21 KXM sing 258 n n 
C22 H22 KXM sing 259 n n 
C23 H23 KXM sing 260 n n 
C24 H24 KXM sing 261 n n 
C25 H25 KXM sing 262 n n 
C25 H26 KXM sing 263 n n 
C26 H27 KXM sing 264 n n 
C26 H28 KXM sing 265 n n 
C27 H29 KXM sing 266 n n 
C28 H30 KXM sing 267 n n 
C29 H31 KXM sing 268 n n 
C32 H32 KXM sing 269 n n 
C34 H33 KXM sing 270 n n 
C35 H34 KXM sing 271 n n 
N7 H35 KXM sing 272 n n 
N7 H36 KXM sing 273 n n 
O11 H37 KXM sing 274 n n 
O14 H38 KXM sing 275 n n 
O15 H39 KXM sing 276 n n 
O3 H40 KXM sing 277 n n 
O4 H41 KXM sing 278 n n 
O5 H42 KXM sing 279 n n 
O7 H43 KXM sing 280 n n 
#
_atom_sites.entry_id                     6NR5 
_atom_sites.fract_transf_matrix[1][1]    0.005281 
_atom_sites.fract_transf_matrix[1][2]    0.003049 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006098 
_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]    0.009172 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          B 
_pdbx_nonpoly_scheme.entity_id        2 
_pdbx_nonpoly_scheme.mon_id           KXM 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      901 
_pdbx_nonpoly_scheme.auth_seq_num     901 
_pdbx_nonpoly_scheme.pdb_mon_id       KXM 
_pdbx_nonpoly_scheme.auth_mon_id      DRG 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 C4 KXM . . . B 2 29.275 -49.423 15.777 1 43.21 ? C4 KXM 901 A 1 
HETATM 2 C C14 KXM . . . B 2 34.235 -51.699 12.217 1 79.81 ? C14 KXM 901 A 1 
HETATM 3 C C5 KXM . . . B 2 29.486 -50.775 15.751 1 37.69 ? C5 KXM 901 A 1 
HETATM 4 C C6 KXM . . . B 2 28.422 -51.655 15.877 1 37.19 ? C6 KXM 901 A 1 
HETATM 5 C C11 KXM . . . B 2 32.257 -52.832 13.792 1 73.98 ? C11 KXM 901 A 1 
HETATM 6 C C7 KXM . . . B 2 27.156 -51.184 16 1 34.27 ? C7 KXM 901 A 1 
HETATM 7 C C8 KXM . . . B 2 26.008 -52.134 16.13 1 31.92 ? C8 KXM 901 A 1 
HETATM 8 C C9 KXM . . . B 2 30.912 -52.668 15.896 1 62.23 ? C9 KXM 901 A 1 
HETATM 9 C C10 KXM . . . B 2 31.178 -53.457 14.637 1 90.63 ? C10 KXM 901 A 1 
HETATM 10 C C12 KXM . . . B 2 33.447 -53.493 13.567 1 77.2 ? C12 KXM 901 A 1 
HETATM 11 C C13 KXM . . . B 2 34.434 -52.927 12.786 1 71.91 ? C13 KXM 901 A 1 
HETATM 12 N N1 KXM . . . B 2 30.755 -51.275 15.624 1 47.31 ? N1 KXM 901 A 1 
HETATM 13 N N2 KXM . . . B 2 34.037 -49.971 15.967 1 58.23 ? N2 KXM 901 A 1 
HETATM 14 C C3 KXM . . . B 2 27.992 -48.928 15.904 1 40.19 ? C3 KXM 901 A 1 
HETATM 15 N N3 KXM . . . B 2 32.556 -48.214 15.764 1 41.78 ? N3 KXM 901 A 1 
HETATM 16 C C1 KXM . . . B 2 25.546 -49.245 16.164 1 48.71 ? C1 KXM 901 A 1 
HETATM 17 C C15 KXM . . . B 2 33.06 -51.037 12.425 1 78.55 ? C15 KXM 901 A 1 
HETATM 18 C C16 KXM . . . B 2 32.071 -51.601 13.204 1 59.2 ? C16 KXM 901 A 1 
HETATM 19 C C17 KXM . . . B 2 31.714 -50.451 16.336 1 60.32 ? C17 KXM 901 A 1 
HETATM 20 C C18 KXM . . . B 2 33.122 -50.9 16.208 1 60.39 ? C18 KXM 901 A 1 
HETATM 21 C C19 KXM . . . B 2 33.736 -48.661 15.983 1 59.04 ? C19 KXM 901 A 1 
HETATM 22 C C2 KXM . . . B 2 26.935 -49.78 16.016 1 36.26 ? C2 KXM 901 A 1 
HETATM 23 C C20 KXM . . . B 2 31.578 -49.019 15.893 1 42.55 ? C20 KXM 901 A 1 
HETATM 24 C C21 KXM . . . B 2 30.178 -47.173 15.266 1 50.23 ? C21 KXM 901 A 1 
HETATM 25 C C22 KXM . . . B 2 29.848 -46.246 16.396 1 61.71 ? C22 KXM 901 A 1 
HETATM 26 C C23 KXM . . . B 2 30.684 -44.976 16.295 1 77.14 ? C23 KXM 901 A 1 
HETATM 27 C C24 KXM . . . B 2 30.353 -43.913 17.337 1 54.43 ? C24 KXM 901 A 1 
HETATM 28 C C25 KXM . . . B 2 29.759 -42.645 16.784 1 48.3 ? C25 KXM 901 A 1 
HETATM 29 C C26 KXM . . . B 2 25.088 -39.146 19.393 1 64.11 ? C26 KXM 901 A 1 
HETATM 30 C C27 KXM . . . B 2 24.255 -38.935 20.626 1 71.2 ? C27 KXM 901 A 1 
HETATM 31 C C28 KXM . . . B 2 22.101 -38.319 21.126 1 70.04 ? C28 KXM 901 A 1 
HETATM 32 C C29 KXM . . . B 2 20.234 -38.212 19.505 1 81.07 ? C29 KXM 901 A 1 
HETATM 33 C C30 KXM . . . B 2 19.277 -36.414 20.091 1 79.04 ? C30 KXM 901 A 1 
HETATM 34 C C31 KXM . . . B 2 18.479 -35.288 20.289 1 88.24 ? C31 KXM 901 A 1 
HETATM 35 C C32 KXM . . . B 2 19.877 -34.753 22.04 1 81.31 ? C32 KXM 901 A 1 
HETATM 36 C C33 KXM . . . B 2 20.338 -36.583 20.935 1 88.66 ? C33 KXM 901 A 1 
HETATM 37 C C34 KXM . . . B 2 22.071 -39.833 21.155 1 68.63 ? C34 KXM 901 A 1 
HETATM 38 C C35 KXM . . . B 2 23.557 -40.182 21.168 1 77.74 ? C35 KXM 901 A 1 
HETATM 39 N N4 KXM . . . B 2 30.372 -48.572 15.665 1 47.74 ? N4 KXM 901 A 1 
HETATM 40 N N5 KXM . . . B 2 20.945 -37.736 20.539 1 73.51 ? N5 KXM 901 A 1 
HETATM 41 N N6 KXM . . . B 2 19.22 -37.451 19.185 1 77.22 ? N6 KXM 901 A 1 
HETATM 42 N N7 KXM . . . B 2 17.423 -35.003 19.544 1 98.18 ? N7 KXM 901 A 1 
HETATM 43 N N8 KXM . . . B 2 18.811 -34.458 21.296 1 87.2 ? N8 KXM 901 A 1 
HETATM 44 N N9 KXM . . . B 2 20.703 -35.782 21.94 1 85.08 ? N9 KXM 901 A 1 
HETATM 45 O O1 KXM . . . B 2 33.471 -52.038 16.389 1 57.63 ? O1 KXM 901 A 1 
HETATM 46 O O10 KXM . . . B 2 25.326 -41.696 18.492 1 67.27 ? O10 KXM 901 A 1 
HETATM 47 O O11 KXM . . . B 2 27.528 -41.982 19.697 1 66.99 -1 O11 KXM 901 A 1 
HETATM 48 O O12 KXM . . . B 2 26.29 -39.832 19.753 1 77.82 ? O12 KXM 901 A 1 
HETATM 49 O O13 KXM . . . B 2 23.198 -38.006 20.321 1 69.09 ? O13 KXM 901 A 1 
HETATM 50 O O14 KXM . . . B 2 21.429 -40.271 22.324 1 81.87 ? O14 KXM 901 A 1 
HETATM 51 O O15 KXM . . . B 2 24.041 -40.478 22.466 1 74.15 ? O15 KXM 901 A 1 
HETATM 52 O O2 KXM . . . B 2 34.608 -47.876 16.208 1 51.54 ? O2 KXM 901 A 1 
HETATM 53 O O3 KXM . . . B 2 30.157 -46.819 17.613 1 60.73 ? O3 KXM 901 A 1 
HETATM 54 O O4 KXM . . . B 2 30.531 -44.449 15.022 1 59.69 ? O4 KXM 901 A 1 
HETATM 55 O O5 KXM . . . B 2 29.453 -44.462 18.285 1 63.17 ? O5 KXM 901 A 1 
HETATM 56 O O6 KXM . . . B 2 29.443 -41.848 17.934 1 52.64 ? O6 KXM 901 A 1 
HETATM 57 O O7 KXM . . . B 2 29.294 -39.607 18.967 1 69.42 ? O7 KXM 901 A 1 
HETATM 58 O O8 KXM . . . B 2 29.402 -39.821 16.479 1 69.32 -1 O8 KXM 901 A 1 
HETATM 59 O O9 KXM . . . B 2 27.405 -40.535 17.748 1 59.79 ? O9 KXM 901 A 1 
HETATM 60 P P1 KXM . . . B 2 28.956 -40.364 17.761 1 65.65 ? P1 KXM 901 A 1 
HETATM 61 P P2 KXM . . . B 2 26.599 -41.132 18.941 1 75.03 ? P2 KXM 901 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           61 
#