data_4SKN # _model_server_result.job_id 760hzIpL0m9beLE9pS5OEQ _model_server_result.datetime_utc '2024-10-12 16:30:54' _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 4skn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":305}' # _entry.id 4SKN # _exptl.entry_id 4SKN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 112.087 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URACIL _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 90 _cell.entry_id 4SKN _cell.length_a 48.83 _cell.length_b 65.66 _cell.length_c 97.15 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4SKN _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 4 _struct_asym.id D _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 A O3' DG 4 A DG 4 1_555 A P ORP 5 A ORP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? covale ? covale2 A O3 ORP 5 A ORP 5 1_555 A P DG 6 A DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.615 ? hydrog 'DG-DC PAIR' hydrog1 A N1 DG 4 A DG 4 1_555 B N3 DC 8 B DC 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N1 DG 6 A DG 6 1_555 B N3 DC 6 B DC 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N2 DG 6 A DG 6 1_555 B O2 DC 6 B DC 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A O6 DG 6 A DG 6 1_555 B N4 DC 6 B DC 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N1 DG 7 A DG 7 1_555 B N3 DC 5 B DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N2 DG 7 A DG 7 1_555 B O2 DC 5 B DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O6 DG 7 A DG 7 1_555 B N4 DC 5 B DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 DC 8 A DC 8 1_555 B N1 DG 4 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N4 DC 8 A DC 8 1_555 B O6 DG 4 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A O2 DC 8 A DC 8 1_555 B N2 DG 4 B DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N3 DT 9 A DT 9 1_555 B N1 DA 3 B DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O4 DT 9 A DT 9 1_555 B N6 DA 3 B DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DT 10 A DT 10 1_555 B N1 DA 2 B DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O4 DT 10 A DT 10 1_555 B N6 DA 2 B DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C4 H4 N2 O2' _chem_comp.formula_weight 112.087 _chem_comp.id URA _chem_comp.mon_nstd_flag . _chem_comp.name URACIL _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 URA sing 531 n n N1 C6 URA sing 532 n n N1 HN1 URA sing 533 n n C2 O2 URA doub 534 n n C2 N3 URA sing 535 n n N3 C4 URA sing 536 n n N3 HN3 URA sing 537 n n C4 O4 URA doub 538 n n C4 C5 URA sing 539 n n C5 C6 URA doub 540 n n C5 H5 URA sing 541 n n C6 H6 URA sing 542 n n # _atom_sites.entry_id 4SKN _atom_sites.fract_transf_matrix[1][1] 0.020479 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01523 _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] 0.010293 _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 D 4 URA E 1 305 55 URA URA . E 5 HOH A 1 11 9 HOH HOH . E 5 HOH A 2 12 44 HOH HOH . E 5 HOH A 3 13 45 HOH HOH . E 5 HOH A 4 14 46 HOH HOH . E 5 HOH A 5 15 48 HOH HOH . F 5 HOH B 1 31 26 HOH HOH . F 5 HOH B 2 32 35 HOH HOH . F 5 HOH B 3 33 41 HOH HOH . G 5 HOH E 1 1 1 HOH HOH . G 5 HOH E 2 2 2 HOH HOH . G 5 HOH E 3 3 3 HOH HOH . G 5 HOH E 4 4 4 HOH HOH . G 5 HOH E 5 5 5 HOH HOH . G 5 HOH E 6 6 6 HOH HOH . G 5 HOH E 7 7 7 HOH HOH . G 5 HOH E 8 8 8 HOH HOH . G 5 HOH E 9 10 10 HOH HOH . G 5 HOH E 10 11 11 HOH HOH . G 5 HOH E 11 12 12 HOH HOH . G 5 HOH E 12 13 13 HOH HOH . G 5 HOH E 13 14 14 HOH HOH . G 5 HOH E 14 15 15 HOH HOH . G 5 HOH E 15 16 16 HOH HOH . G 5 HOH E 16 17 17 HOH HOH . G 5 HOH E 17 18 18 HOH HOH . G 5 HOH E 18 19 19 HOH HOH . G 5 HOH E 19 20 20 HOH HOH . G 5 HOH E 20 21 21 HOH HOH . G 5 HOH E 21 22 22 HOH HOH . G 5 HOH E 22 23 23 HOH HOH . G 5 HOH E 23 24 24 HOH HOH . G 5 HOH E 24 25 25 HOH HOH . G 5 HOH E 25 27 27 HOH HOH . G 5 HOH E 26 28 28 HOH HOH . G 5 HOH E 27 29 29 HOH HOH . G 5 HOH E 28 30 30 HOH HOH . G 5 HOH E 29 31 31 HOH HOH . G 5 HOH E 30 32 32 HOH HOH . G 5 HOH E 31 33 33 HOH HOH . G 5 HOH E 32 34 34 HOH HOH . G 5 HOH E 33 36 36 HOH HOH . G 5 HOH E 34 37 37 HOH HOH . G 5 HOH E 35 38 38 HOH HOH . G 5 HOH E 36 39 39 HOH HOH . G 5 HOH E 37 40 40 HOH HOH . G 5 HOH E 38 42 42 HOH HOH . G 5 HOH E 39 43 43 HOH HOH . G 5 HOH E 40 47 47 HOH HOH . G 5 HOH E 41 49 49 HOH HOH . G 5 HOH E 42 50 50 HOH HOH . G 5 HOH E 43 51 51 HOH HOH . G 5 HOH E 44 52 52 HOH HOH . G 5 HOH E 45 53 53 HOH HOH . G 5 HOH E 46 54 54 HOH HOH . G 5 HOH E 47 55 55 HOH HOH . G 5 HOH E 48 56 56 HOH HOH . G 5 HOH E 49 57 57 HOH HOH . G 5 HOH E 50 58 58 HOH HOH . G 5 HOH E 51 59 59 HOH HOH . G 5 HOH E 52 60 60 HOH HOH . G 5 HOH E 53 61 61 HOH HOH . G 5 HOH E 54 62 62 HOH HOH . G 5 HOH E 55 63 63 HOH HOH . G 5 HOH E 56 64 64 HOH HOH . G 5 HOH E 57 65 65 HOH HOH . G 5 HOH E 58 66 66 HOH HOH . G 5 HOH E 59 67 67 HOH HOH . G 5 HOH E 60 68 68 HOH HOH . G 5 HOH E 61 69 69 HOH HOH . G 5 HOH E 62 70 70 HOH HOH . G 5 HOH E 63 71 71 HOH HOH . G 5 HOH E 64 72 72 HOH HOH . G 5 HOH E 65 73 73 HOH HOH . G 5 HOH E 66 74 74 HOH HOH . G 5 HOH E 67 75 75 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 N N1 URA . . . D 4 16.946 2.656 8.286 1 45.76 ? N1 URA 305 E 1 HETATM 2 C C2 URA . . . D 4 16.854 2.759 6.917 1 47.54 ? C2 URA 305 E 1 HETATM 3 O O2 URA . . . D 4 15.792 2.707 6.33 1 47.3 ? O2 URA 305 E 1 HETATM 4 N N3 URA . . . D 4 18.048 2.937 6.264 1 49.39 ? N3 URA 305 E 1 HETATM 5 C C4 URA . . . D 4 19.302 3.062 6.837 1 50.13 ? C4 URA 305 E 1 HETATM 6 O O4 URA . . . D 4 20.281 3.348 6.132 1 49.25 ? O4 URA 305 E 1 HETATM 7 C C5 URA . . . D 4 19.307 2.946 8.266 1 49.41 ? C5 URA 305 E 1 HETATM 8 C C6 URA . . . D 4 18.159 2.747 8.923 1 46.57 ? C6 URA 305 E 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 8 #