data_7DGC # _model_server_result.job_id PgbVR8L-thcjbTZdEXRYDg _model_server_result.datetime_utc '2024-12-19 11:06:51' _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 7dgc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 7DGC # _exptl.entry_id 7DGC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 298.252 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 9-[(2R,3R,4R)-5-(hydroxymethyl)-3-methoxy-4-oxidanyl-oxolan-2-yl]-3H-purine-2,6-dione _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 7DGC _cell.length_a 119.052 _cell.length_b 119.052 _cell.length_c 39.809 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DGC _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,H,I _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 # 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 F N 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 O SER 42 A SER 66 1_555 E NA NA . A NA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc2 A ND1 HIS 56 A HIS 80 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc3 A SG CYS 86 A CYS 110 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc4 A SG CYS 89 A CYS 113 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc5 C O21 H5C . A H5C 201 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc6 E NA NA . A NA 203 1_555 H O HOH . A HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc7 E NA NA . A NA 203 1_555 H O HOH . A HOH 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc8 B ND1 HIS 56 D HIS 80 1_555 G ZN ZN . D ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc9 B SG CYS 86 D CYS 110 1_555 G ZN ZN . D ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc10 B SG CYS 89 D CYS 113 1_555 G ZN ZN . D ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc11 F O21 H5C . D H5C 201 1_555 G ZN ZN . D ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? # _chem_comp.formula 'C11 H14 N4 O6' _chem_comp.formula_weight 298.252 _chem_comp.id H5C _chem_comp.mon_nstd_flag . _chem_comp.name 9-[(2R,3R,4R)-5-(hydroxymethyl)-3-methoxy-4-oxidanyl-oxolan-2-yl]-3H-purine-2,6-dione _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 C02 C03 H5C sing 129 n n C02 N20 H5C sing 130 n n C02 O01 H5C doub 131 n n C03 C17 H5C doub 132 n y C03 N04 H5C sing 133 n y C05 N04 H5C doub 134 n y C05 N06 H5C sing 135 n y C07 C08 H5C sing 136 n n C07 N06 H5C sing 137 n n C07 O16 H5C sing 138 n n C08 C11 H5C sing 139 n n C08 O09 H5C sing 140 n n C10 O09 H5C sing 141 n n C11 C13 H5C sing 142 n n C11 O12 H5C sing 143 n n C13 C14 H5C sing 144 n n C14 O15 H5C sing 145 n n C17 N06 H5C sing 146 n y C17 N18 H5C sing 147 n n C19 N18 H5C sing 148 n n C19 N20 H5C sing 149 n n C19 O21 H5C doub 150 n n C05 H1 H5C sing 151 n n C07 H2 H5C sing 152 n n C08 H3 H5C sing 153 n n C10 H4 H5C sing 154 n n C10 H5 H5C sing 155 n n C10 H6 H5C sing 156 n n C11 H7 H5C sing 157 n n C13 H8 H5C sing 158 n n C14 H10 H5C sing 159 n n C14 H11 H5C sing 160 n n N18 H12 H5C sing 161 n n N20 H13 H5C sing 162 n n O12 H14 H5C sing 163 n n O15 H15 H5C sing 164 n n O16 C13 H5C sing 165 n n # _atom_sites.entry_id 7DGC _atom_sites.fract_transf_matrix[1][1] 0.0084 _atom_sites.fract_transf_matrix[1][2] 0.00485 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009699 _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] 0.02512 _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 H5C A 1 201 4 H5C M2X . D 3 ZN A 1 202 2 ZN ZN . E 4 NA A 1 203 1 NA NA . F 2 H5C D 1 201 3 H5C M2X . G 3 ZN D 1 202 1 ZN ZN . H 5 HOH A 1 301 31 HOH HOH . H 5 HOH A 2 302 138 HOH HOH . H 5 HOH A 3 303 37 HOH HOH . H 5 HOH A 4 304 38 HOH HOH . H 5 HOH A 5 305 8 HOH HOH . H 5 HOH A 6 306 49 HOH HOH . H 5 HOH A 7 307 46 HOH HOH . H 5 HOH A 8 308 100 HOH HOH . H 5 HOH A 9 309 4 HOH HOH . H 5 HOH A 10 310 124 HOH HOH . H 5 HOH A 11 311 3 HOH HOH . H 5 HOH A 12 312 119 HOH HOH . H 5 HOH A 13 313 59 HOH HOH . H 5 HOH A 14 314 29 HOH HOH . H 5 HOH A 15 315 71 HOH HOH . H 5 HOH A 16 316 14 HOH HOH . H 5 HOH A 17 317 51 HOH HOH . H 5 HOH A 18 318 18 HOH HOH . H 5 HOH A 19 319 7 HOH HOH . H 5 HOH A 20 320 32 HOH HOH . H 5 HOH A 21 321 128 HOH HOH . H 5 HOH A 22 322 34 HOH HOH . H 5 HOH A 23 323 20 HOH HOH . H 5 HOH A 24 324 97 HOH HOH . H 5 HOH A 25 325 75 HOH HOH . H 5 HOH A 26 326 70 HOH HOH . H 5 HOH A 27 327 6 HOH HOH . H 5 HOH A 28 328 65 HOH HOH . H 5 HOH A 29 329 47 HOH HOH . H 5 HOH A 30 330 99 HOH HOH . H 5 HOH A 31 331 118 HOH HOH . H 5 HOH A 32 332 110 HOH HOH . H 5 HOH A 33 333 88 HOH HOH . H 5 HOH A 34 334 120 HOH HOH . H 5 HOH A 35 335 72 HOH HOH . H 5 HOH A 36 336 62 HOH HOH . H 5 HOH A 37 337 50 HOH HOH . H 5 HOH A 38 338 74 HOH HOH . H 5 HOH A 39 339 15 HOH HOH . H 5 HOH A 40 340 63 HOH HOH . H 5 HOH A 41 341 106 HOH HOH . H 5 HOH A 42 342 102 HOH HOH . H 5 HOH A 43 343 127 HOH HOH . H 5 HOH A 44 344 73 HOH HOH . H 5 HOH A 45 345 27 HOH HOH . H 5 HOH A 46 346 68 HOH HOH . H 5 HOH A 47 347 21 HOH HOH . H 5 HOH A 48 348 41 HOH HOH . H 5 HOH A 49 349 82 HOH HOH . H 5 HOH A 50 350 12 HOH HOH . H 5 HOH A 51 351 115 HOH HOH . H 5 HOH A 52 352 44 HOH HOH . H 5 HOH A 53 353 133 HOH HOH . H 5 HOH A 54 354 60 HOH HOH . H 5 HOH A 55 355 101 HOH HOH . H 5 HOH A 56 356 92 HOH HOH . H 5 HOH A 57 357 77 HOH HOH . H 5 HOH A 58 358 109 HOH HOH . H 5 HOH A 59 359 136 HOH HOH . H 5 HOH A 60 360 45 HOH HOH . H 5 HOH A 61 361 117 HOH HOH . H 5 HOH A 62 362 132 HOH HOH . I 5 HOH D 1 301 13 HOH HOH . I 5 HOH D 2 302 137 HOH HOH . I 5 HOH D 3 303 131 HOH HOH . I 5 HOH D 4 304 130 HOH HOH . I 5 HOH D 5 305 98 HOH HOH . I 5 HOH D 6 306 52 HOH HOH . I 5 HOH D 7 307 104 HOH HOH . I 5 HOH D 8 308 35 HOH HOH . I 5 HOH D 9 309 2 HOH HOH . I 5 HOH D 10 310 56 HOH HOH . I 5 HOH D 11 311 1 HOH HOH . I 5 HOH D 12 312 58 HOH HOH . I 5 HOH D 13 313 22 HOH HOH . I 5 HOH D 14 314 57 HOH HOH . I 5 HOH D 15 315 25 HOH HOH . I 5 HOH D 16 316 114 HOH HOH . I 5 HOH D 17 317 54 HOH HOH . I 5 HOH D 18 318 67 HOH HOH . I 5 HOH D 19 319 24 HOH HOH . I 5 HOH D 20 320 5 HOH HOH . I 5 HOH D 21 321 94 HOH HOH . I 5 HOH D 22 322 11 HOH HOH . I 5 HOH D 23 323 81 HOH HOH . I 5 HOH D 24 324 30 HOH HOH . I 5 HOH D 25 325 93 HOH HOH . I 5 HOH D 26 326 134 HOH HOH . I 5 HOH D 27 327 78 HOH HOH . I 5 HOH D 28 328 42 HOH HOH . I 5 HOH D 29 329 16 HOH HOH . I 5 HOH D 30 330 33 HOH HOH . I 5 HOH D 31 331 28 HOH HOH . I 5 HOH D 32 332 10 HOH HOH . I 5 HOH D 33 333 96 HOH HOH . I 5 HOH D 34 334 26 HOH HOH . I 5 HOH D 35 335 39 HOH HOH . I 5 HOH D 36 336 17 HOH HOH . I 5 HOH D 37 337 105 HOH HOH . I 5 HOH D 38 338 76 HOH HOH . I 5 HOH D 39 339 40 HOH HOH . I 5 HOH D 40 340 9 HOH HOH . I 5 HOH D 41 341 129 HOH HOH . I 5 HOH D 42 342 48 HOH HOH . I 5 HOH D 43 343 107 HOH HOH . I 5 HOH D 44 344 36 HOH HOH . I 5 HOH D 45 345 66 HOH HOH . I 5 HOH D 46 346 55 HOH HOH . I 5 HOH D 47 347 64 HOH HOH . I 5 HOH D 48 348 87 HOH HOH . I 5 HOH D 49 349 84 HOH HOH . I 5 HOH D 50 350 108 HOH HOH . I 5 HOH D 51 351 61 HOH HOH . I 5 HOH D 52 352 95 HOH HOH . I 5 HOH D 53 353 90 HOH HOH . I 5 HOH D 54 354 79 HOH HOH . I 5 HOH D 55 355 69 HOH HOH . I 5 HOH D 56 356 85 HOH HOH . I 5 HOH D 57 357 91 HOH HOH . I 5 HOH D 58 358 89 HOH HOH . I 5 HOH D 59 359 126 HOH HOH . I 5 HOH D 60 360 111 HOH HOH . I 5 HOH D 61 361 86 HOH HOH . I 5 HOH D 62 362 80 HOH HOH . I 5 HOH D 63 363 135 HOH HOH . I 5 HOH D 64 364 123 HOH HOH . I 5 HOH D 65 365 83 HOH HOH . I 5 HOH D 66 366 103 HOH HOH . I 5 HOH D 67 367 53 HOH HOH . I 5 HOH D 68 368 113 HOH HOH . I 5 HOH D 69 369 125 HOH HOH . I 5 HOH D 70 370 121 HOH HOH . I 5 HOH D 71 371 122 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 C02 H5C . . . F 2 -11.381 -51.936 -2.551 1 31.25 ? C02 H5C 201 D 1 HETATM 2 C C03 H5C . . . F 2 -10.547 -51.419 -3.728 1 32.84 ? C03 H5C 201 D 1 HETATM 3 C C05 H5C . . . F 2 -9.56 -50.977 -5.632 1 39.07 ? C05 H5C 201 D 1 HETATM 4 C C07 H5C . . . F 2 -8.045 -49.088 -4.879 1 41.74 ? C07 H5C 201 D 1 HETATM 5 C C08 H5C . . . F 2 -6.84 -49.531 -5.775 1 50.96 ? C08 H5C 201 D 1 HETATM 6 C C10 H5C . . . F 2 -5.679 -50.778 -4.253 1 45.99 ? C10 H5C 201 D 1 HETATM 7 C C11 H5C . . . F 2 -6.668 -48.332 -6.777 1 50.54 ? C11 H5C 201 D 1 HETATM 8 C C13 H5C . . . F 2 -7.868 -47.927 -6.976 1 51 ? C13 H5C 201 D 1 HETATM 9 C C14 H5C . . . F 2 -8.552 -48.797 -7.985 1 48.49 ? C14 H5C 201 D 1 HETATM 10 C C17 H5C . . . F 2 -9.655 -50.403 -3.529 1 38.24 ? C17 H5C 201 D 1 HETATM 11 C C19 H5C . . . F 2 -10.293 -50.275 -1.058 1 32.14 ? C19 H5C 201 D 1 HETATM 12 N N04 H5C . . . F 2 -10.485 -51.769 -5.027 1 32.74 ? N04 H5C 201 D 1 HETATM 13 N N06 H5C . . . F 2 -9.056 -50.141 -4.694 1 38.04 ? N06 H5C 201 D 1 HETATM 14 N N18 H5C . . . F 2 -9.497 -49.787 -2.18 1 35.55 ? N18 H5C 201 D 1 HETATM 15 N N20 H5C . . . F 2 -11.228 -51.351 -1.258 1 35.21 ? N20 H5C 201 D 1 HETATM 16 O O01 H5C . . . F 2 -12.157 -52.815 -2.715 1 29.22 ? O01 H5C 201 D 1 HETATM 17 O O09 H5C . . . F 2 -5.745 -49.625 -5.04 1 49.24 ? O09 H5C 201 D 1 HETATM 18 O O12 H5C . . . F 2 -5.896 -47.265 -6.089 1 52.41 ? O12 H5C 201 D 1 HETATM 19 O O15 H5C . . . F 2 -9.275 -47.986 -8.868 1 53.55 ? O15 H5C 201 D 1 HETATM 20 O O16 H5C . . . F 2 -8.602 -48.076 -5.479 1 45.62 ? O16 H5C 201 D 1 HETATM 21 O O21 H5C . . . F 2 -10.162 -49.783 0.013 1 33.12 ? O21 H5C 201 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #