data_7DPK
#
_model_server_result.job_id            5pu6_U-df98C0_jsZLWSIQ 
_model_server_result.datetime_utc      '2024-11-15 15:25:25' 
_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          7dpk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    7DPK 
#
_exptl.entry_id    7DPK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              284.225 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2,3-dihydroxanthosine 
_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            7DPK 
_cell.length_a            119.027 
_cell.length_b            119.027 
_cell.length_c            38.919 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7DPK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    'P 61' 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_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
_struct_conn.pdbx_value_order
metalc ? metalc1 A ND1 HIS 56 A HIS 80 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
metalc ? metalc2 A SG CYS 86 A CYS 110 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc3 A SG CYS 89 A CYS 113 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc4 C O2 4UO . A 4UO 201 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? 
metalc ? metalc5 B ND1 HIS 56 D HIS 80 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc6 B SG CYS 86 D CYS 110 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc7 B SG CYS 89 D CYS 113 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
#
_chem_comp.formula           'C10 H12 N4 O6' 
_chem_comp.formula_weight    284.225 
_chem_comp.id                4UO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2,3-dihydroxanthosine 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Xanthosine 
#
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
N7 C8 4UO doub 1 n y 
N7 C5 4UO sing 2 n y 
C8 N9 4UO sing 3 n y 
O6 C6 4UO doub 4 n n 
C5 C6 4UO sing 5 n n 
C5 C4 4UO doub 6 n y 
C6 N1 4UO sing 7 n n 
N9 C4 4UO sing 8 n y 
N9 C1' 4UO sing 9 n n 
C4 N3 4UO sing 10 n n 
C1' C2' 4UO sing 11 n n 
C1' O4' 4UO sing 12 n n 
O2' C2' 4UO sing 13 n n 
N1 C2 4UO sing 14 n n 
C2' C3' 4UO sing 15 n n 
O4' C4' 4UO sing 16 n n 
N3 C2 4UO sing 17 n n 
C2 O2 4UO doub 18 n n 
C3' C4' 4UO sing 19 n n 
C3' O3' 4UO sing 20 n n 
C4' C5' 4UO sing 21 n n 
O5' C5' 4UO sing 22 n n 
N1 H1 4UO sing 23 n n 
N3 H2 4UO sing 24 n n 
C8 H3 4UO sing 25 n n 
C1' H4 4UO sing 26 n n 
C4' H5 4UO sing 27 n n 
C5' H6 4UO sing 28 n n 
C5' H7 4UO sing 29 n n 
O5' H8 4UO sing 30 n n 
C3' H9 4UO sing 31 n n 
O3' H10 4UO sing 32 n n 
C2' H11 4UO sing 33 n n 
O2' H12 4UO sing 34 n n 
#
_atom_sites.entry_id                     7DPK 
_atom_sites.fract_transf_matrix[1][1]    0.008401 
_atom_sites.fract_transf_matrix[1][2]    0.004851 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009701 
_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]    0.025694 
_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 4UO A 1 201 201 4UO 4UO . 
D 3 ZN A 1 202 2 ZN ZN . 
E 3 ZN D 1 201 1 ZN ZN . 
F 4 HOH A 1 301 1 HOH HOH . 
F 4 HOH A 2 302 164 HOH HOH . 
F 4 HOH A 3 303 61 HOH HOH . 
F 4 HOH A 4 304 188 HOH HOH . 
F 4 HOH A 5 305 55 HOH HOH . 
F 4 HOH A 6 306 79 HOH HOH . 
F 4 HOH A 7 307 112 HOH HOH . 
F 4 HOH A 8 308 40 HOH HOH . 
F 4 HOH A 9 309 166 HOH HOH . 
F 4 HOH A 10 310 7 HOH HOH . 
F 4 HOH A 11 311 53 HOH HOH . 
F 4 HOH A 12 312 23 HOH HOH . 
F 4 HOH A 13 313 4 HOH HOH . 
F 4 HOH A 14 314 43 HOH HOH . 
F 4 HOH A 15 315 27 HOH HOH . 
F 4 HOH A 16 316 186 HOH HOH . 
F 4 HOH A 17 317 11 HOH HOH . 
F 4 HOH A 18 318 149 HOH HOH . 
F 4 HOH A 19 319 34 HOH HOH . 
F 4 HOH A 20 320 178 HOH HOH . 
F 4 HOH A 21 321 113 HOH HOH . 
F 4 HOH A 22 322 111 HOH HOH . 
F 4 HOH A 23 323 106 HOH HOH . 
F 4 HOH A 24 324 63 HOH HOH . 
F 4 HOH A 25 325 62 HOH HOH . 
F 4 HOH A 26 326 10 HOH HOH . 
F 4 HOH A 27 327 15 HOH HOH . 
F 4 HOH A 28 328 130 HOH HOH . 
F 4 HOH A 29 329 88 HOH HOH . 
F 4 HOH A 30 330 48 HOH HOH . 
F 4 HOH A 31 331 81 HOH HOH . 
F 4 HOH A 32 332 56 HOH HOH . 
F 4 HOH A 33 333 51 HOH HOH . 
F 4 HOH A 34 334 50 HOH HOH . 
F 4 HOH A 35 335 12 HOH HOH . 
F 4 HOH A 36 336 52 HOH HOH . 
F 4 HOH A 37 337 89 HOH HOH . 
F 4 HOH A 38 338 68 HOH HOH . 
F 4 HOH A 39 339 14 HOH HOH . 
F 4 HOH A 40 340 33 HOH HOH . 
F 4 HOH A 41 341 70 HOH HOH . 
F 4 HOH A 42 342 122 HOH HOH . 
F 4 HOH A 43 343 83 HOH HOH . 
F 4 HOH A 44 344 147 HOH HOH . 
F 4 HOH A 45 345 31 HOH HOH . 
F 4 HOH A 46 346 9 HOH HOH . 
F 4 HOH A 47 347 24 HOH HOH . 
F 4 HOH A 48 348 169 HOH HOH . 
F 4 HOH A 49 349 16 HOH HOH . 
F 4 HOH A 50 350 139 HOH HOH . 
F 4 HOH A 51 351 142 HOH HOH . 
F 4 HOH A 52 352 66 HOH HOH . 
F 4 HOH A 53 353 126 HOH HOH . 
F 4 HOH A 54 354 146 HOH HOH . 
F 4 HOH A 55 355 20 HOH HOH . 
F 4 HOH A 56 356 82 HOH HOH . 
F 4 HOH A 57 357 157 HOH HOH . 
F 4 HOH A 58 358 35 HOH HOH . 
F 4 HOH A 59 359 76 HOH HOH . 
F 4 HOH A 60 360 73 HOH HOH . 
F 4 HOH A 61 361 117 HOH HOH . 
F 4 HOH A 62 362 45 HOH HOH . 
F 4 HOH A 63 363 17 HOH HOH . 
F 4 HOH A 64 364 84 HOH HOH . 
F 4 HOH A 65 365 78 HOH HOH . 
F 4 HOH A 66 366 170 HOH HOH . 
F 4 HOH A 67 367 141 HOH HOH . 
F 4 HOH A 68 368 30 HOH HOH . 
F 4 HOH A 69 369 29 HOH HOH . 
F 4 HOH A 70 370 109 HOH HOH . 
F 4 HOH A 71 371 136 HOH HOH . 
F 4 HOH A 72 372 98 HOH HOH . 
F 4 HOH A 73 373 114 HOH HOH . 
F 4 HOH A 74 374 120 HOH HOH . 
F 4 HOH A 75 375 185 HOH HOH . 
F 4 HOH A 76 376 104 HOH HOH . 
F 4 HOH A 77 377 77 HOH HOH . 
F 4 HOH A 78 378 145 HOH HOH . 
F 4 HOH A 79 379 177 HOH HOH . 
F 4 HOH A 80 380 123 HOH HOH . 
F 4 HOH A 81 381 172 HOH HOH . 
F 4 HOH A 82 382 108 HOH HOH . 
F 4 HOH A 83 383 150 HOH HOH . 
F 4 HOH A 84 384 67 HOH HOH . 
F 4 HOH A 85 385 134 HOH HOH . 
F 4 HOH A 86 386 72 HOH HOH . 
F 4 HOH A 87 387 92 HOH HOH . 
G 4 HOH D 1 301 158 HOH HOH . 
G 4 HOH D 2 302 171 HOH HOH . 
G 4 HOH D 3 303 187 HOH HOH . 
G 4 HOH D 4 304 179 HOH HOH . 
G 4 HOH D 5 305 42 HOH HOH . 
G 4 HOH D 6 306 115 HOH HOH . 
G 4 HOH D 7 307 105 HOH HOH . 
G 4 HOH D 8 308 71 HOH HOH . 
G 4 HOH D 9 309 175 HOH HOH . 
G 4 HOH D 10 310 160 HOH HOH . 
G 4 HOH D 11 311 182 HOH HOH . 
G 4 HOH D 12 312 2 HOH HOH . 
G 4 HOH D 13 313 21 HOH HOH . 
G 4 HOH D 14 314 137 HOH HOH . 
G 4 HOH D 15 315 118 HOH HOH . 
G 4 HOH D 16 316 6 HOH HOH . 
G 4 HOH D 17 317 25 HOH HOH . 
G 4 HOH D 18 318 5 HOH HOH . 
G 4 HOH D 19 319 44 HOH HOH . 
G 4 HOH D 20 320 128 HOH HOH . 
G 4 HOH D 21 321 99 HOH HOH . 
G 4 HOH D 22 322 49 HOH HOH . 
G 4 HOH D 23 323 173 HOH HOH . 
G 4 HOH D 24 324 13 HOH HOH . 
G 4 HOH D 25 325 64 HOH HOH . 
G 4 HOH D 26 326 38 HOH HOH . 
G 4 HOH D 27 327 39 HOH HOH . 
G 4 HOH D 28 328 127 HOH HOH . 
G 4 HOH D 29 329 181 HOH HOH . 
G 4 HOH D 30 330 168 HOH HOH . 
G 4 HOH D 31 331 91 HOH HOH . 
G 4 HOH D 32 332 22 HOH HOH . 
G 4 HOH D 33 333 132 HOH HOH . 
G 4 HOH D 34 334 85 HOH HOH . 
G 4 HOH D 35 335 97 HOH HOH . 
G 4 HOH D 36 336 65 HOH HOH . 
G 4 HOH D 37 337 90 HOH HOH . 
G 4 HOH D 38 338 87 HOH HOH . 
G 4 HOH D 39 339 8 HOH HOH . 
G 4 HOH D 40 340 46 HOH HOH . 
G 4 HOH D 41 341 152 HOH HOH . 
G 4 HOH D 42 342 18 HOH HOH . 
G 4 HOH D 43 343 57 HOH HOH . 
G 4 HOH D 44 344 80 HOH HOH . 
G 4 HOH D 45 345 159 HOH HOH . 
G 4 HOH D 46 346 138 HOH HOH . 
G 4 HOH D 47 347 3 HOH HOH . 
G 4 HOH D 48 348 37 HOH HOH . 
G 4 HOH D 49 349 116 HOH HOH . 
G 4 HOH D 50 350 135 HOH HOH . 
G 4 HOH D 51 351 41 HOH HOH . 
G 4 HOH D 52 352 124 HOH HOH . 
G 4 HOH D 53 353 183 HOH HOH . 
G 4 HOH D 54 354 32 HOH HOH . 
G 4 HOH D 55 355 36 HOH HOH . 
G 4 HOH D 56 356 94 HOH HOH . 
G 4 HOH D 57 357 133 HOH HOH . 
G 4 HOH D 58 358 121 HOH HOH . 
G 4 HOH D 59 359 165 HOH HOH . 
G 4 HOH D 60 360 47 HOH HOH . 
G 4 HOH D 61 361 60 HOH HOH . 
G 4 HOH D 62 362 95 HOH HOH . 
G 4 HOH D 63 363 96 HOH HOH . 
G 4 HOH D 64 364 103 HOH HOH . 
G 4 HOH D 65 365 151 HOH HOH . 
G 4 HOH D 66 366 19 HOH HOH . 
G 4 HOH D 67 367 54 HOH HOH . 
G 4 HOH D 68 368 75 HOH HOH . 
G 4 HOH D 69 369 110 HOH HOH . 
G 4 HOH D 70 370 154 HOH HOH . 
G 4 HOH D 71 371 26 HOH HOH . 
G 4 HOH D 72 372 74 HOH HOH . 
G 4 HOH D 73 373 140 HOH HOH . 
G 4 HOH D 74 374 86 HOH HOH . 
G 4 HOH D 75 375 129 HOH HOH . 
G 4 HOH D 76 376 125 HOH HOH . 
G 4 HOH D 77 377 189 HOH HOH . 
G 4 HOH D 78 378 101 HOH HOH . 
G 4 HOH D 79 379 93 HOH HOH . 
G 4 HOH D 80 380 155 HOH HOH . 
G 4 HOH D 81 381 143 HOH HOH . 
G 4 HOH D 82 382 102 HOH HOH . 
G 4 HOH D 83 383 107 HOH HOH . 
G 4 HOH D 84 384 184 HOH HOH . 
G 4 HOH D 85 385 180 HOH HOH . 
G 4 HOH D 86 386 153 HOH HOH . 
G 4 HOH D 87 387 131 HOH HOH . 
G 4 HOH D 88 388 144 HOH HOH . 
G 4 HOH D 89 389 176 HOH HOH . 
G 4 HOH D 90 390 119 HOH HOH . 
G 4 HOH D 91 391 59 HOH HOH . 
G 4 HOH D 92 392 156 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 O6 4UO . . . C 2 23.172 34.793 2.283 1 14.86 ? O6 4UO 201 A 1 
HETATM 2 C C6 4UO . . . C 2 22.139 34.537 2.807 1 14.47 ? C6 4UO 201 A 1 
HETATM 3 N N1 4UO . . . C 2 20.947 34.391 2.015 1 16.91 ? N1 4UO 201 A 1 
HETATM 4 C C2 4UO . . . C 2 19.693 34.09 2.664 1 18.97 ? C2 4UO 201 A 1 
HETATM 5 O O2 4UO . . . C 2 18.704 33.967 2.02 1 17.41 ? O2 4UO 201 A 1 
HETATM 6 N N3 4UO . . . C 2 19.643 33.928 4.128 1 18.86 ? N3 4UO 201 A 1 
HETATM 7 C C4 4UO . . . C 2 20.884 34.084 4.953 1 16.8 ? C4 4UO 201 A 1 
HETATM 8 C C5 4UO . . . C 2 22.069 34.376 4.332 1 13.72 ? C5 4UO 201 A 1 
HETATM 9 N N7 4UO . . . C 2 23.012 34.469 5.262 1 16.78 ? N7 4UO 201 A 1 
HETATM 10 C C8 4UO . . . C 2 22.438 34.237 6.466 1 17.16 ? C8 4UO 201 A 1 
HETATM 11 N N9 4UO . . . C 2 21.124 34.002 6.27 1 18.03 ? N9 4UO 201 A 1 
HETATM 12 C C1' 4UO . . . C 2 20.166 33.702 7.339 1 19.04 ? C1' 4UO 201 A 1 
HETATM 13 O O4' 4UO . . . C 2 19.944 32.308 7.361 1 19.22 ? O4' 4UO 201 A 1 
HETATM 14 C C4' 4UO . . . C 2 18.602 32.041 7.853 1 20.49 ? C4' 4UO 201 A 1 
HETATM 15 C C5' 4UO . . . C 2 17.904 31.09 6.911 1 20.54 ? C5' 4UO 201 A 1 
HETATM 16 O O5' 4UO . . . C 2 17.451 31.748 5.732 1 19.22 ? O5' 4UO 201 A 1 
HETATM 17 C C3' 4UO . . . C 2 17.93 33.407 8.028 1 18.67 ? C3' 4UO 201 A 1 
HETATM 18 O O3' 4UO . . . C 2 18.033 33.811 9.393 1 22.6 ? O3' 4UO 201 A 1 
HETATM 19 C C2' 4UO . . . C 2 18.789 34.326 7.161 1 16.91 ? C2' 4UO 201 A 1 
HETATM 20 O O2' 4UO . . . C 2 18.776 35.683 7.549 1 19.07 ? O2' 4UO 201 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           20 
#