data_7WJ7 # _model_server_result.job_id KCzNsjGodLAY-OFJAe0Kvg _model_server_result.datetime_utc '2024-11-07 14:46:24' _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 7wj7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 7WJ7 # _exptl.entry_id 7WJ7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL _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 7WJ7 _cell.length_a 96.228 _cell.length_b 96.228 _cell.length_c 115.482 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7WJ7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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 D N N # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id XYA _chem_comp.mon_nstd_flag . _chem_comp.name 2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 9-BETA-D-XYLOFURANOSYL-ADENINE # 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 O5' C5' XYA sing 376 n n O5' H5' XYA sing 377 n n C5' C4' XYA sing 378 n n C5' "H5'1" XYA sing 379 n n C5' "H5'2" XYA sing 380 n n C4' O4' XYA sing 381 n n C4' C3' XYA sing 382 n n C4' H4' XYA sing 383 n n O4' C1' XYA sing 384 n n C1' N9 XYA sing 385 n n C1' C2' XYA sing 386 n n C1' H1' XYA sing 387 n n N9 C8 XYA sing 388 n y N9 C4 XYA sing 389 n y C8 N7 XYA doub 390 n y C8 H8 XYA sing 391 n n N7 C5 XYA sing 392 n y C5 C6 XYA doub 393 n y C5 C4 XYA sing 394 n y C6 N1 XYA sing 395 n y C6 N6 XYA sing 396 n n N1 C2 XYA doub 397 n y C2 N3 XYA sing 398 n y C2 H2 XYA sing 399 n n N3 C4 XYA doub 400 n y N6 HN61 XYA sing 401 n n N6 HN62 XYA sing 402 n n C2' O2' XYA sing 403 n n C2' C3' XYA sing 404 n n C2' H2' XYA sing 405 n n O2' H1 XYA sing 406 n n C3' O3' XYA sing 407 n n C3' H3' XYA sing 408 n n O3' H3 XYA sing 409 n n # _atom_sites.entry_id 7WJ7 _atom_sites.fract_transf_matrix[1][1] 0.010392 _atom_sites.fract_transf_matrix[1][2] 0.006 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012 _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] 0.008659 _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 XYA A 1 301 301 XYA LIG . D 2 XYA B 1 301 301 XYA LIG . E 3 HOH A 1 401 10 HOH HOH . E 3 HOH A 2 402 6 HOH HOH . E 3 HOH A 3 403 28 HOH HOH . E 3 HOH A 4 404 9 HOH HOH . E 3 HOH A 5 405 4 HOH HOH . E 3 HOH A 6 406 11 HOH HOH . E 3 HOH A 7 407 18 HOH HOH . E 3 HOH A 8 408 23 HOH HOH . E 3 HOH A 9 409 14 HOH HOH . E 3 HOH A 10 410 27 HOH HOH . E 3 HOH A 11 411 31 HOH HOH . E 3 HOH A 12 412 43 HOH HOH . E 3 HOH A 13 413 13 HOH HOH . E 3 HOH A 14 414 24 HOH HOH . E 3 HOH A 15 415 7 HOH HOH . E 3 HOH A 16 416 22 HOH HOH . E 3 HOH A 17 417 17 HOH HOH . E 3 HOH A 18 418 20 HOH HOH . E 3 HOH A 19 419 29 HOH HOH . E 3 HOH A 20 420 19 HOH HOH . E 3 HOH A 21 421 16 HOH HOH . E 3 HOH A 22 422 33 HOH HOH . E 3 HOH A 23 423 39 HOH HOH . E 3 HOH A 24 424 36 HOH HOH . E 3 HOH A 25 425 32 HOH HOH . E 3 HOH A 26 426 25 HOH HOH . F 3 HOH B 1 401 1 HOH HOH . F 3 HOH B 2 402 8 HOH HOH . F 3 HOH B 3 403 37 HOH HOH . F 3 HOH B 4 404 3 HOH HOH . F 3 HOH B 5 405 15 HOH HOH . F 3 HOH B 6 406 2 HOH HOH . F 3 HOH B 7 407 34 HOH HOH . F 3 HOH B 8 408 35 HOH HOH . F 3 HOH B 9 409 5 HOH HOH . F 3 HOH B 10 410 21 HOH HOH . F 3 HOH B 11 411 30 HOH HOH . F 3 HOH B 12 412 38 HOH HOH . F 3 HOH B 13 413 26 HOH HOH . F 3 HOH B 14 414 40 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 O5' XYA . . . D 2 30.458 -20.468 8.919 1 92.96 ? O5' XYA 301 B 1 HETATM 2 C C5' XYA . . . D 2 29.94 -20.21 10.196 1 90.07 ? C5' XYA 301 B 1 HETATM 3 C C4' XYA . . . D 2 28.457 -19.915 10.062 1 94.87 ? C4' XYA 301 B 1 HETATM 4 O O4' XYA . . . D 2 27.894 -20.761 9.269 1 87.89 ? O4' XYA 301 B 1 HETATM 5 C C1' XYA . . . D 2 26.78 -21.394 10.066 1 81.32 ? C1' XYA 301 B 1 HETATM 6 N N9 XYA . . . D 2 26.613 -22.671 9.671 1 76.1 ? N9 XYA 301 B 1 HETATM 7 C C8 XYA . . . D 2 27.09 -23.156 8.532 1 68.84 ? C8 XYA 301 B 1 HETATM 8 N N7 XYA . . . D 2 26.747 -24.437 8.423 1 65.95 ? N7 XYA 301 B 1 HETATM 9 C C5 XYA . . . D 2 26.02 -24.794 9.522 1 73.43 ? C5 XYA 301 B 1 HETATM 10 C C6 XYA . . . D 2 25.388 -25.987 9.981 1 68.6 ? C6 XYA 301 B 1 HETATM 11 N N1 XYA . . . D 2 24.739 -25.987 11.14 1 60.17 ? N1 XYA 301 B 1 HETATM 12 C C2 XYA . . . D 2 24.68 -24.873 11.874 1 64.59 ? C2 XYA 301 B 1 HETATM 13 N N3 XYA . . . D 2 25.249 -23.736 11.496 1 69.09 ? N3 XYA 301 B 1 HETATM 14 C C4 XYA . . . D 2 25.927 -23.674 10.32 1 74.45 ? C4 XYA 301 B 1 HETATM 15 N N6 XYA . . . D 2 25.456 -27.197 9.178 1 56.94 ? N6 XYA 301 B 1 HETATM 16 C C2' XYA . . . D 2 27.275 -21.222 11.549 1 92.93 ? C2' XYA 301 B 1 HETATM 17 O O2' XYA . . . D 2 26.11 -21.26 12.523 1 99.85 ? O2' XYA 301 B 1 HETATM 18 C C3' XYA . . . D 2 27.744 -20.076 11.534 1 94.21 ? C3' XYA 301 B 1 HETATM 19 O O3' XYA . . . D 2 28.747 -19.911 12.62 1 90.05 ? O3' XYA 301 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 19 #