data_1XRS # _model_server_result.job_id bGgYglnPa7YA2nntfB5L-g _model_server_result.datetime_utc '2025-04-25 12:11:06' _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 1xrs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":500}' # _entry.id 1XRS # _exptl.entry_id 1XRS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 251.242 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXYADENOSINE" _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 1XRS _cell.length_a 99.7 _cell.length_b 99.7 _cell.length_c 168.8 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XRS _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,PQS _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,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 168.8 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 covale ? covale1 B NZ LYS 144 B LYS 144 1_555 D C4A PLP . B PLP 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? metalc ? metalc1 B NE2 HIS 133 B HIS 133 1_555 C CO B12 . B B12 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc2 E C5' 5AD . B 5AD 500 1_555 C CO B12 . B B12 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? # _chem_comp.formula 'C10 H13 N5 O3' _chem_comp.formula_weight 251.242 _chem_comp.id 5AD _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXYADENOSINE" _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 N1 C2 5AD doub 1 n y N1 C6 5AD sing 2 n y C2 N3 5AD sing 3 n y C2 H2 5AD sing 4 n n N3 C4 5AD doub 5 n y C4 N9 5AD sing 6 n y C4 C5 5AD sing 7 n y N9 C8 5AD sing 8 n y N9 C1' 5AD sing 9 n n C8 N7 5AD doub 10 n y C8 H8 5AD sing 11 n n N7 C5 5AD sing 12 n y C5 C6 5AD doub 13 n y C6 N6 5AD sing 14 n n N6 HN61 5AD sing 15 n n N6 HN62 5AD sing 16 n n C1' C2' 5AD sing 17 n n C1' O4' 5AD sing 18 n n C1' H1' 5AD sing 19 n n C2' C3' 5AD sing 20 n n C2' O2' 5AD sing 21 n n C2' H2' 5AD sing 22 n n C3' C4' 5AD sing 23 n n C3' O3' 5AD sing 24 n n C3' H3' 5AD sing 25 n n C4' C5' 5AD sing 26 n n C4' O4' 5AD sing 27 n n C4' H4' 5AD sing 28 n n C5' "H5'1" 5AD sing 29 n n C5' "H5'2" 5AD sing 30 n n C5' "H5'3" 5AD sing 31 n n O2' HO2' 5AD sing 32 n n O3' HO3' 5AD sing 33 n n # _atom_sites.entry_id 1XRS _atom_sites.fract_transf_matrix[1][1] 0.01003 _atom_sites.fract_transf_matrix[1][2] 0.005791 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011582 _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] 0.005924 _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 3 B12 B 1 800 800 B12 B12 . D 4 PLP B 1 801 801 PLP PLP . E 5 5AD B 1 500 500 5AD 5AD . # 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 N N1 5AD . . . E 5 83.29 43.077 81.194 1 72.49 ? N1 5AD 500 B 1 HETATM 2 C C2 5AD . . . E 5 83.371 44.449 81.144 1 74.51 ? C2 5AD 500 B 1 HETATM 3 N N3 5AD . . . E 5 82.497 45.323 81.676 1 78.05 ? N3 5AD 500 B 1 HETATM 4 C C4 5AD . . . E 5 81.464 44.681 82.31 1 78.77 ? C4 5AD 500 B 1 HETATM 5 N N9 5AD . . . E 5 80.361 45.233 82.975 1 78.94 ? N9 5AD 500 B 1 HETATM 6 C C8 5AD . . . E 5 79.61 44.169 83.439 1 80.32 ? C8 5AD 500 B 1 HETATM 7 N N7 5AD . . . E 5 80.105 42.998 83.144 1 79.07 ? N7 5AD 500 B 1 HETATM 8 C C5 5AD . . . E 5 81.273 43.325 82.429 1 76.81 ? C5 5AD 500 B 1 HETATM 9 C C6 5AD . . . E 5 82.256 42.458 81.828 1 74.6 ? C6 5AD 500 B 1 HETATM 10 N N6 5AD . . . E 5 82.214 41.136 81.851 1 72.45 ? N6 5AD 500 B 1 HETATM 11 C C1' 5AD . . . E 5 80.058 46.64 83.139 1 80.61 ? C1' 5AD 500 B 1 HETATM 12 C C2' 5AD . . . E 5 80.958 47.473 84.036 1 81.01 ? C2' 5AD 500 B 1 HETATM 13 C C3' 5AD . . . E 5 81.706 48.339 83.073 1 80.42 ? C3' 5AD 500 B 1 HETATM 14 C C4' 5AD . . . E 5 80.789 48.48 81.846 1 79.9 ? C4' 5AD 500 B 1 HETATM 15 C C5' 5AD . . . E 5 81.583 48.635 80.561 1 81.43 ? C5' 5AD 500 B 1 HETATM 16 O O4' 5AD . . . E 5 80.012 47.29 81.844 1 83.58 ? O4' 5AD 500 B 1 HETATM 17 O O2' 5AD . . . E 5 80.078 48.135 84.917 1 81.32 ? O2' 5AD 500 B 1 HETATM 18 O O3' 5AD . . . E 5 82.033 49.605 83.512 1 85.97 ? O3' 5AD 500 B 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 18 #